From edb06f16d6b9f760a783599afa1e2bd25eeb7d2f Mon Sep 17 00:00:00 2001 From: Gabriel Zinser Date: Thu, 30 Jul 2026 14:00:42 -0600 Subject: [PATCH 1/7] ep400 addition Update evidence and genomic coordinates for SCA_EP400 ep400 provisional liftover adding family 2 Update data add family 2 info Update data fix nomad Update data add description Update data ep400 nuance Update data add exon fix actually fix this time clarify broad range why is year a string and not an int? Update data show alternate locus definition --- data/STRchive-citations.json | 318 +++++++++++++++++- data/STRchive-loci.json | 69 +++- .../STRchive-disease-loci.T2T-chm13.TRGT.bed | 1 + ...STRchive-disease-loci.T2T-chm13.atarva.bed | 1 + ...chive-disease-loci.T2T-chm13.atarva.bed.gz | Bin 1864 -> 1878 bytes ...e-disease-loci.T2T-chm13.atarva.bed.gz.tbi | Bin 4468 -> 4491 bytes ...TRchive-disease-loci.T2T-chm13.general.bed | 1 + ...STRchive-disease-loci.T2T-chm13.longTR.bed | 1 + ...TRchive-disease-loci.T2T-chm13.straglr.bed | 1 + ...chive-disease-loci.T2T-chm13.stranger.json | 13 + .../STRchive-disease-loci.hg19.TRGT.bed | 1 + .../STRchive-disease-loci.hg19.atarva.bed | 1 + .../STRchive-disease-loci.hg19.atarva.bed.gz | Bin 1881 -> 1898 bytes ...Rchive-disease-loci.hg19.atarva.bed.gz.tbi | Bin 4468 -> 4470 bytes .../STRchive-disease-loci.hg19.general.bed | 1 + .../STRchive-disease-loci.hg19.longTR.bed | 1 + .../STRchive-disease-loci.hg19.straglr.bed | 1 + .../STRchive-disease-loci.hg19.stranger.json | 13 + .../STRchive-disease-loci.hg38.TRGT.bed | 1 + .../STRchive-disease-loci.hg38.atarva.bed | 1 + .../STRchive-disease-loci.hg38.atarva.bed.gz | Bin 1866 -> 1882 bytes ...Rchive-disease-loci.hg38.atarva.bed.gz.tbi | Bin 4433 -> 4459 bytes .../STRchive-disease-loci.hg38.general.bed | 1 + .../STRchive-disease-loci.hg38.longTR.bed | 1 + .../STRchive-disease-loci.hg38.straglr.bed | 1 + .../STRchive-disease-loci.hg38.stranger.json | 13 + data/plots/age-onset.json | 50 +-- data/plots/path-size.json | 33 +- data/ref-alleles/ref-alleles.T2T-chm13.txt | 6 + data/ref-alleles/ref-alleles.hg19.txt | 6 + data/ref-alleles/ref-alleles.hg38.txt | 6 + 31 files changed, 500 insertions(+), 42 deletions(-) diff --git a/data/STRchive-citations.json b/data/STRchive-citations.json index ca4126a5..cc0edfce 100644 --- a/data/STRchive-citations.json +++ b/data/STRchive-citations.json @@ -166376,6 +166376,285 @@ "language": "eng", "note": "PMID: 20301363\nThis CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: url:https://www.ncbi.nlm.nih.gov/books/NBK1184" }, +{ + "id": "pmid:28600779", + "manubot_success": true, + "link": "https://www.ncbi.nlm.nih.gov/pubmed/28600779", + "title": "The landscape of genetic diseases in Saudi Arabia based on the first 1000 diagnostic panels and exomes.", + "type": "article-journal", + "doi": "10.1007/s00439-017-1821-8", + "authors": [ + ["Dorota", "Monies"], + ["Mohamed", "Abouelhoda"], + ["Moeenaldeen", "AlSayed"], + ["Zuhair", "Alhassnan"], + ["Maha", "Alotaibi"], + ["Husam", "Kayyali"], + ["Mohammed", "Al-Owain"], + ["Ayaz", "Shah"], + ["Zuhair", "Rahbeeni"], + ["Mohammad A", "Al-Muhaizea"], + ["Hamad I", "Alzaidan"], + ["Edward", "Cupler"], + ["Saeed", "Bohlega"], + ["Eissa", "Faqeih"], + ["Maha", "Faden"], + ["Banan", "Alyounes"], + ["Dyala", "Jaroudi"], + ["Ewa", "Goljan"], + ["Hadeel", "Elbardisy"], + ["Asma", "Akilan"], + ["Renad", "Albar"], + ["Hesham", "Aldhalaan"], + ["Shamshad", "Gulab"], + ["Aziza", "Chedrawi"], + ["Bandar K", "Al Saud"], + ["Wesam", "Kurdi"], + ["Nawal", "Makhseed"], + ["Tahani", "Alqasim"], + ["Heba Y", "El Khashab"], + ["Hamoud", "Al-Mousa"], + ["Amal", "Alhashem"], + ["Imaduddin", "Kanaan"], + ["Talal", "Algoufi"], + ["Khalid", "Alsaleem"], + ["Talal A", "Basha"], + ["Fathiya", "Al-Murshedi"], + ["Sameena", "Khan"], + ["Adila", "Al-Kindy"], + ["Maha", "Alnemer"], + ["Sami", "Al-Hajjar"], + ["Suad", "Alyamani"], + ["Hasan", "Aldhekri"], + ["Ali", "Al-Mehaidib"], + ["Rand", "Arnaout"], + ["Omar", "Dabbagh"], + ["Mohammad", "Shagrani"], + ["Dieter", "Broering"], + ["Maha", "Tulbah"], + ["Amal", "Alqassmi"], + ["Maisoon", "Almugbel"], + ["Mohammed", "AlQuaiz"], + ["Abdulaziz", "Alsaman"], + ["Khalid", "Al-Thihli"], + ["Raashda A", "Sulaiman"], + ["Wajeeh", "Al-Dekhail"], + ["Abeer", "Alsaegh"], + ["Fahad A", "Bashiri"], + ["Alya", "Qari"], + ["Suzan", "Alhomadi"], + ["Hisham", "Alkuraya"], + ["Mohammed", "Alsebayel"], + ["Muddathir H", "Hamad"], + ["Laszlo", "Szonyi"], + ["Faisal", "Abaalkhail"], + ["Sulaiman M", "Al-Mayouf"], + ["Hamad", "Almojalli"], + ["Khalid S", "Alqadi"], + ["Hussien", "Elsiesy"], + ["Taghreed M", "Shuaib"], + ["Mohammed Zain", "Seidahmed"], + ["Ibraheem", "Abosoudah"], + ["Hana", "Akleh"], + ["Abdulaziz", "AlGhonaium"], + ["Turki M", "Alkharfy"], + ["Fuad", "Al Mutairi"], + ["Wafa", "Eyaid"], + ["Abdullah", "Alshanbary"], + ["Farrukh R", "Sheikh"], + ["Fahad I", "Alsohaibani"], + ["Abdullah", "Alsonbul"], + ["Saeed", "Al Tala"], + ["Soher", "Balkhy"], + ["Randa", "Bassiouni"], + ["Ahmed S", "Alenizi"], + ["Maged H", "Hussein"], + ["Saeed", "Hassan"], + ["Mohamed", "Khalil"], + ["Brahim", "Tabarki"], + ["Saad", "Alshahwan"], + ["Amira", "Oshi"], + ["Yasser", "Sabr"], + ["Saad", "Alsaadoun"], + ["Mustafa A", "Salih"], + ["Sarar", "Mohamed"], + ["Habiba", "Sultana"], + ["Abdullah", "Tamim"], + ["Moayad", "El-Haj"], + ["Saif", "Alshahrani"], + ["Dalal K", "Bubshait"], + ["Majid", "Alfadhel"], + ["Tariq", "Faquih"], + ["Mohamed", "El-Kalioby"], + ["Shazia", "Subhani"], + ["Zeeshan", "Shah"], + ["Nabil", "Moghrabi"], + ["Brian F", "Meyer"], + ["Fowzan S", "Alkuraya"] + ], + "publisher": "Human genetics", + "issn": "1432-1203", + "date": "2017-06-09", + "abstract": "In this study, we report the experience of the only reference clinical next-generation sequencing lab in Saudi Arabia with the first 1000 families who span a wide-range of suspected Mendelian phenotypes. A total of 1019 tests were performed in the period of March 2016-December 2016 comprising 972 solo (index only), 14 duo (parents or affected siblings only), and 33 trio (index and parents). Multigene panels accounted for 672 tests, while whole exome sequencing (WES) represented the remaining 347 tests. Pathogenic or likely pathogenic variants that explain the clinical indications were identified in 34% (27% in panels and 43% in exomes), spanning 279 genes and including 165 novel variants. While recessive mutations dominated the landscape of solved cases (71% of mutations, and 97% of which are homozygous), a substantial minority (27%) were solved on the basis of dominant mutations. The highly consanguineous nature of the study population also facilitated homozygosity for many private mutations (only 32.5% of the recessive mutations are founder), as well as the first instances of recessive inheritance of previously assumed strictly dominant disorders (involving ITPR1, VAMP1, MCTP2, and TBP). Surprisingly, however, dual molecular diagnosis was only observed in 1.5% of cases. Finally, we have encountered candidate variants in 75 genes (ABHD6, ACY3, ADGRB2, ADGRG7, AGTPBP1, AHNAK2, AKAP6, ASB3, ATXN1L, C17orf62, CABP1, CCDC186, CCP110, CLSTN2, CNTN3, CNTN5, CTNNA2, CWC22, DMAP1, DMKN, DMXL1, DSCAM, DVL2, ECI1, EP400, EPB41L5, FBXL22, GAP43, GEMIN7, GIT1, GRIK4, GRSF1, GTRP1, HID1, IFNL1, KCNC4, LRRC52, MAP7D3, MCTP2, MED26, MPP7, MRPS35, MTDH, MTMR9, NECAP2, NPAT, NRAP, PAX7, PCNX, PLCH2, PLEKHF1, PTPN12, QKI, RILPL2, RIMKLA, RIMS2, RNF213, ROBO1, SEC16A, SIAH1, SIRT2, SLAIN2, SLC22A20, SMDT1, SRRT, SSTR1, ST20, SYT9, TSPAN6, UBR4, VAMP4, VPS36, WDR59, WDYHV1, and WHSC1) not previously linked to human phenotypes and these are presented to accelerate post-publication matchmaking. Two of these genes were independently mutated in more than one family with similar phenotypes, which substantiates their link to human disease (AKAP6 in intellectual disability and UBR4 in early dementia). If the novel candidate disease genes in this cohort are independently confirmed, the yield of WES will have increased to 83%, which suggests that most \"negative\" clinical exome tests are unsolved due to interpretation rather than technical limitations.", + "language": "en", + "note": "This CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: pubmed:28600779" +}, +{ + "id": "pmid:39708813", + "manubot_success": true, + "link": "https://www.ncbi.nlm.nih.gov/pubmed/39708813", + "title": "Variants in EP400, encoding a chromatin remodeler, cause epilepsy with neurodevelopmental disorders.", + "type": "article-journal", + "doi": "10.1016/j.ajhg.2024.11.010", + "authors": [ + ["Sheng", "Luo"], + ["Peng-Yu", "Wang"], + ["Peng", "Zhou"], + ["Wen-Jun", "Zhang"], + ["Yu-Jie", "Gu"], + ["Xiao-Yu", "Liang"], + ["Jing-Wen", "Zhang"], + ["Jun-Xia", "Luo"], + ["Hong-Wei", "Zhang"], + ["Song", "Lan"], + ["Ting-Ting", "Zhang"], + ["Jie-Hua", "Yang"], + ["Su-Zhen", "Sun"], + ["Xiang-Yang", "Guo"], + ["Ju-Li", "Wang"], + ["Lin-Fan", "Deng"], + ["Ze-Hai", "Xu"], + ["Liang", "Jin"], + ["Yun-Yan", "He"], + ["Zi-Long", "Ye"], + ["Wei-Yue", "Gu"], + ["Bing-Mei", "Li"], + ["Yi-Wu", "Shi"], + ["Xiao-Rong", "Liu"], + ["Hong-Jun", "Yan"], + ["Yong-Hong", "Yi"], + ["Yu-Wu", "Jiang"], + ["Xiao", "Mao"], + ["Wen-Ling", "Li"], + ["Heng", "Meng"], + ["Wei-Ping", "Liao"] + ], + "publisher": "American journal of human genetics", + "issn": "1537-6605", + "date": "2024-12-20", + "abstract": "EP400 encodes a core catalytic ATPase subunit of ATP-dependent chromatin remodeling complexes. The gene-disease association of EP400 is undetermined. In this study, we performed trio-based whole-exome sequencing in a cohort of 402 families with epilepsy and neurodevelopmental disorders (NDDs) and identified compound heterozygous EP400 variants in six unrelated individuals. Six additional EP400 individuals were recruited via the match platform of China, including two de novo heterozygous and four compound heterozygous variants. The individual with a heterozygous de novo frameshift variant presented with NDDs, while the others exhibited epilepsy and NDDs, explained by the damaged genetic dependence quantity. EP400 presented significantly higher excesses of variants in the individuals. Clustering analysis revealed that the majority paralogs of EP400 were associated with NDDs/epilepsy and co-expressed highly with EP400. Analysis of the spatiotemporal expression indicated that EP400 is highly expressed in the developing brain and cells during differentiation, indicating its vital role in neurodevelopment; EP400 is predominantly expressed in inhibitory neurons in the early stage but in excitatory neurons in the mature stage. The development-dependent expression pattern of neuron specificity explained the favorable outcome of epilepsy. Knockdown of EP400 ortholog in Drosophila caused significantly increased susceptibility to seizures and abnormal neuronal firing. The ep400 crispant zebrafish exhibited brain developmental abnormalities, poorer adaptability, lower response to stimulation, epileptic discharges, abnormal cellular apoptosis, and increased susceptibility to seizures. Transcriptome analysis showed that ep400 deficiency caused expressional dysregulation of 84 epilepsy/NDD-associated genes, including 11 highly dose-sensitive genes. This study identified EP400 as a causative gene of epilepsy/NDDs.", + "language": "en", + "note": "This CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: pubmed:39708813" +}, +{ + "id": "pmid:31081019", + "manubot_success": true, + "link": "https://www.ncbi.nlm.nih.gov/pubmed/31081019", + "title": "Chromatin remodeler Ep400 ensures oligodendrocyte survival and is required for myelination in the vertebrate central nervous system.", + "type": "article-journal", + "doi": "10.1093/nar/gkz376", + "authors": [ + ["Olga", "Elsesser"], + ["Franziska", "Fr\u00f6b"], + ["Melanie", "K\u00fcspert"], + ["Ernst R", "Tamm"], + ["Toshihiro", "Fujii"], + ["Rikiro", "Fukunaga"], + ["Michael", "Wegner"] + ], + "publisher": "Nucleic acids research", + "issn": "1362-4962", + "date": "2019-07-09", + "abstract": "Differentiating oligodendrocytes generate myelin to ensure rapid saltatory conduction in the vertebrate central nervous system. Although oligodendroglial differentiation and myelination are accompanied by dramatic chromatin reorganizations, previously studied chromatin remodelers had only limited direct effects on the process. To study the functional significance of chromatin changes for myelination and identify relevant remodelers, we deleted Ep400, the central ATP-hydrolyzing subunit of the TIP60/EP400 complex, at defined times of mouse oligodendrocyte development. Whereas Ep400-deficient oligodendrocyte precursors develop normally, terminal differentiation and myelination are dramatically impaired. Mechanistically, Ep400 interacts with transcription factor Sox10, binds to regulatory regions of the Myrf gene and is required to induce this central transcriptional regulator of the myelination program. In addition to reduced and aberrant myelin formation, oligodendrocytes exhibit increased DNA damage and apoptosis so that numbers never reach wildtype levels during the short lifespan of Ep400-deficient mice. Ep400 deletion in already mature oligodendrocytes remains phenotypically inapparent arguing that Ep400 is dispensable for myelin maintenance. Given its essential function in myelin formation, modulation of Ep400 activity may be beneficial in conditions such as multiple sclerosis where this process is compromised.", + "language": "en", + "note": "This CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: pubmed:31081019" +}, +{ + "id": "pmid:33602898", + "manubot_success": true, + "link": "https://www.ncbi.nlm.nih.gov/pubmed/33602898", + "title": "A unique missense variant in the E1A-binding protein P400 gene is implicated in schizophrenia by whole-exome sequencing and mutant mouse models.", + "type": "article-journal", + "doi": "10.1038/s41398-021-01258-1", + "authors": [ + ["Yoshiro", "Morimoto"], + ["Shinji", "Ono"], + ["Shintaro", "Yoshida"], + ["Hiroyuki", "Mishima"], + ["Akira", "Kinoshita"], + ["Takeshi", "Tanaka"], + ["Yoshihiro", "Komohara"], + ["Naohiro", "Kurotaki"], + ["Tatsuya", "Kishino"], + ["Yuji", "Okazaki"], + ["Hiroki", "Ozawa"], + ["Koh-Ichiro", "Yoshiura"], + ["Akira", "Imamura"] + ], + "publisher": "Translational psychiatry", + "issn": "2158-3188", + "date": "2021-02-18", + "abstract": "Genetic and epidemiological evidence has suggested that genetic factors are important in schizophrenia, although its pathophysiology is poorly understood. This study used whole-exome sequencing to investigate potential novel schizophrenia-causing genes in a Japanese family containing several members affected by severe or treatment-resistant schizophrenia. A missense variant, chr12:132064747C>T (rs200626129, P2805L), in the E1A-binding protein P400 (EP400) gene completely segregated with schizophrenia in this family. Furthermore, numerous other EP400 mutations were identified in the targeted sequencing of a schizophrenia patient cohort. We also created two lines of Ep400 gene-edited mice, which had anxiety-like behaviours and reduced axon diameters. Our findings suggest that rs200626129 in EP400 is likely to cause schizophrenia in this Japanese family, and may lead to a better understanding and treatment of schizophrenia.", + "language": "en", + "note": "This CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: pubmed:33602898" +}, +{ + "id": "doi:10.1101/2025.01.06.631535", + "manubot_success": true, + "title": "Population-scale variability at short tandem repeat loci reveals pathogenicity signature", + "type": "manuscript", + "doi": "10.1101/2025.01.06.631535", + "authors": [ + ["Matt C.", "Danzi"], + ["Isaac R. L.", "Xu"], + ["Sarah", "Fazal"], + ["Egor", "Dolzhenko"], + ["David", "Pellerin"], + ["Ben", "Weisburd"], + ["Liedewei", "Van de Vondel"], + ["Chloe", "Reuter"], + ["Jacinda B.", "Sampson"], + ["Chiara", "Folland"], + ["Carolin K.", "Scriba"], + ["Gavin", "Monahan"], + ["Phillipa J.", "Lamont"], + ["Julie", "Wertz"], + ["Adriana", "Rebelo"], + ["Sophia B.", "Gibson"], + ["Daniel G.", "Calame"], + ["Haloom", "Rafehi"], + ["Penny", "Snell"], + ["Kate", "Kotschet"], + ["Kayli C.", "Davies"], + ["Igor", "Stevanovski"], + ["Ira W.", "Deveson"], + ["Danny E.", "Miller"], + ["Chia-Lin", "Wei"], + ["Jane", "Grimwood"], + ["Donna M.", "Muzny"], + ["Niall", "Lennon"], + ["Melanie", "Bahlo"], + ["Paul J.", "Lockhart"], + ["Matthew", "Wheeler"], + ["Anne", "O\u2019Donnell-Luria"], + ["Stefan", "Wuchty"], + ["Gianina", "Ravenscroft"], + ["Michael A.", "Eberle"], + ["Kiran V.", "Garimella"], + ["Fritz J.", "Sedlazeck"], + ["Michael E.", "Talkowski"], + ["Michael C.", "Schatz"], + ["Evan E.", "Eichler"], + ["Stephan", "Zuchner"] + ], + "publisher": "openRxiv", + "issn": "", + "date": "2025-01-07", + "link": "https://doi.org/hcc9nc", + "abstract": "Summary\n \n Short tandem repeat (STR) instability is a major cause of disease association, yet their full length-distributions and sequence content have been difficult to resolve with short-read sequencing. By analyzing long-read sequencing genomes from 2,645 participants of the\n All of Us\n Research Program, we establish a comprehensive STR resource of 23 billion alleles covering a catalog of 4.4 million loci. We find that known disease-associated STR loci exhibit markedly elevated allelic variability relative to genome-wide distributions, which is most pronounced when based on the length of uninterrupted, pure repeat motifs (Odds Ratio: 244, p=1.62e-29). We establish the Pure Length Variability Index (PLVI) as a measure of this instability, which is robust across ancestries and replicated in 500 samples from the 1000 Genomes Project (Odds Ratio: 84, p=2.72e-28). To illustrate, we identify 55 unstable coding CAG and 5\u2019-UTR CGG STR loci with this metric, 60% of which have not been associated with disease. From this set, we document potential pathogenic repeat expansions for\n FAM193B\n and\n EP400\n by integrating PLVI with single-genome length outlier analysis. These data establish a population-scale framework for STR discovery in rare and common diseases using long-read sequencing cohorts.\n ", + "language": "en", + "note": "This CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: doi:10.1101/2025.01.06.631535" +}, { "id": "omim:309548", "manubot_success": false, @@ -166630,9 +166909,22 @@ }, { "id": "genereviews:NBK1119", - "manubot_success": false, - "link": "https://www.ncbi.nlm.nih.gov/books/NBK1119", - "note": "WARNING: Manubot could not generate citation: Command '['manubot', 'cite', 'url:https://www.ncbi.nlm.nih.gov/books/NBK1119']' timed out after 3 seconds" + "manubot_success": true, + "link": "http://www.ncbi.nlm.nih.gov/books/NBK1119/", + "title": "Dystrophinopathies", + "type": "chapter", + "doi": "", + "authors": [ + ["Basil T.", "Darras"], + ["David K.", "Urion"], + ["Partha S.", "Ghosh"] + ], + "publisher": "GeneReviews\u00ae", + "issn": "", + "date": "1993-01-01", + "abstract": "The dystrophinopathies cover a spectrum of X-linked muscle disease ranging from mild to severe that includes Duchenne muscular dystrophy, Becker muscular dystrophy, and DMD-associated dilated cardiomyopathy (DCM). The mild end of the spectrum includes the phenotypes of asymptomatic increase in serum concentration of creatine phosphokinase (CK) and muscle cramps with myoglobinuria. The severe end of the spectrum includes progressive muscle diseases that are classified as Duchenne/Becker muscular dystrophy when skeletal muscle is primarily affected and as DMD-associated DCM when the heart is primarily affected. Duchenne muscular dystrophy (DMD) usually presents in early childhood with delayed motor milestones including delays in walking independently and standing up from a supine position. Proximal weakness causes a waddling gait and difficulty climbing stairs, running, jumping, and standing up from a squatting position. DMD is rapidly progressive, with affected children being wheelchair dependent by age 12 years. Cardiomyopathy occurs in almost all individuals with DMD after age 18 years. Few survive beyond the third decade, with respiratory complications and progressive cardiomyopathy being common causes of death. Becker muscular dystrophy (BMD) is characterized by later-onset skeletal muscle weakness. With improved diagnostic techniques, it has been recognized that the mild end of the spectrum includes men with onset of symptoms after age 30 years who remain ambulatory even into their 60s. Despite the milder skeletal muscle involvement, heart failure from DCM is a common cause of morbidity and the most common cause of death in BMD. Mean age of death is in the mid-40s. DMD-associated DCM is characterized by left ventricular dilatation and congestive heart failure. Females heterozygous for a DMD pathogenic variant are at increased risk for DCM., The diagnosis of a dystrophinopathy is established in a proband with the characteristic clinical findings and elevated CK concentration and/or by identification of a hemizygous pathogenic variant in DMD on molecular genetic testing in a male and of a heterozygous pathogenic variant in DMD on molecular genetic testing in a female. Females may present with a classic dystrophinopathy or may be asymptomatic carriers., Treatment of manifestations: ACE inhibitors are used with or without beta blockers for cardiomyopathy in both DMD and BMD phenotypes. Congestive heart failure is treated with diuretics and oxygen as needed; cardiac transplantation is offered to persons with severe dilated cardiomyopathy and BMD with limited or no clinical evidence of skeletal muscle disease. Scoliosis is treated with bracing and surgery. Corticosteroid therapy improves muscle strength and function for individuals with DMD between ages five and 15 years; the same treatment is used in BMD, although the efficacy is less clear. Dystrophin restoration therapies have been developed by using synthetic antisense oligonucleotides to restore the reading frame by exon skipping for individuals with specific pathogenic variants in DMD. Prevention of secondary complications: Evaluation by a pulmonologist and cardiologist before surgeries; pneumococcal and influenza immunizations annually; nutrition assessment; physical therapy to promote mobility and prevent contractures; sunshine and a balanced diet rich in vitamin D and calcium to improve bone density and reduce the risk of fractures; weight control to avoid obesity. Surveillance: For males with DMD or BMD: annual or biannual evaluation by a cardiologist beginning at the time of diagnosis; monitoring for scoliosis; baseline pulmonary function testing before wheelchair dependence; frequent evaluations by a pediatric pulmonologist. For heterozygous females: cardiac evaluation at least once after the teenage years. Agents/circumstances to avoid: Botulinum toxin injections; succinylcholine and inhalational anesthetics because of susceptibility to malignant hyperthermia or malignant hyperthermia-like reactions. Evaluation of relatives at risk: Early identification of heterozygous females who are at increased risk for cardiomyopathy and, thus, need routine cardiac surveillance and prompt treatment., The dystrophinopathies are inherited in an X-linked manner. The risk to the sibs of a proband depends on the genetic status of the mother. Heterozygous females have a 50% chance of transmitting the DMD pathogenic variant in each pregnancy. Sons who inherit the pathogenic variant will be affected; daughters who inherit the pathogenic variant are heterozygous and may have a range of clinical manifestations. Males with DMD usually do not reproduce. Males with BMD or DMD-associated DCM may reproduce: all of their daughters are heterozygotes; none of their sons inherit their father's DMD pathogenic variant. Carrier testing for at-risk females, prenatal testing, and preimplantation genetic testing are possible if the DMD pathogenic variant in the family is known.", + "language": "eng", + "note": "PMID: 20301298\nThis CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: url:https://www.ncbi.nlm.nih.gov/books/NBK1119" }, { "id": "genereviews:NBK1384", @@ -166642,9 +166934,23 @@ }, { "id": "genereviews:NBK1281", - "manubot_success": false, - "link": "https://www.ncbi.nlm.nih.gov/books/NBK1281", - "note": "WARNING: Manubot could not generate citation: Command '['manubot', 'cite', 'url:https://www.ncbi.nlm.nih.gov/books/NBK1281']' timed out after 3 seconds" + "manubot_success": true, + "link": "http://www.ncbi.nlm.nih.gov/books/NBK1281/", + "title": "Friedreich Ataxia", + "type": "chapter", + "doi": "", + "authors": [ + ["Sanjay I.", "Bidichandani"], + ["Martin B.", "Delatycki"], + ["Marek", "Napierala"], + ["Antoine", "Duquette"] + ], + "publisher": "GeneReviews\u00ae", + "issn": "", + "date": "1993-01-01", + "abstract": "Typical Friedreich ataxia (FRDA) is characterized by progressive ataxia with onset from early childhood to early adulthood with mean age at onset from 10 to 15 years (range: age two years to the eighth decade). Ataxia, manifesting initially as poor balance when walking, is typically followed by upper-limb ataxia, dysarthria, dysphagia, peripheral motor and sensory neuropathy, spasticity, autonomic disturbance, and often abnormal eye movements and optic atrophy. Hypertrophic cardiomyopathy is present in about two thirds of individuals; occasionally it is diagnosed prior to the onset of ataxia. Diabetes mellitus and impaired glucose tolerance can also occur. Among individuals with FRDA, about 75% have \"typical Friedreich ataxia\" and about 25% of individuals with biallelic FXN full-penetrance GAA repeat expansions have \"atypical Friedreich ataxia\" that includes late-onset FRDA (LOFA) (i.e., onset after age 25 years), very late-onset FRDA (VLOFA) (i.e., onset after age 40 years), and FRDA with retained reflexes (FARR)., The diagnosis of Friedreich ataxia is established in a proband with suggestive findings and biallelic pathogenic variants in FXN identified by molecular genetic testing. The two classes of FXN pathogenic variants are (1) GAA repeat expansions and (2) FXN pathogenic sequence variants, including base substitutions and small indels or large deletions. Approximately 96% of individuals with FRDA have biallelic FXN GAA repeat expansions in intron 1; approximately 4% are compound heterozygotes for an FXN GAA repeat expansion and either an intragenic FXN pathogenic variant or a large deletion., Targeted therapy: Omaveloxolone, an Nrf2 activator, has been shown to slow the progression of FRDA; it is approved in the United States and Europe for individuals age 16 years and older. Supportive care: Multidisciplinary care by specialists in relevant fields, such as neurologists, ophthalmologists, orthoptists, physical therapists, occupational therapists, cardiologists, endocrinologists, speech and language therapists, and psychologists. Surveillance: Routinely scheduled evaluations by the treating multidisciplinary specialists. Agents/circumstances to avoid: Use and misuse of illegal and controlled drugs, as they may affect neuronal well-being and, thus, exacerbate disease manifestations; medications that are toxic or potentially toxic to people with neuropathy; circumstances that increase the risk of falling (e.g., rough surfaces). Evaluation of relatives at risk: If at-risk minor and adult sibs of an individual with FRDA have not had testing for the FXN pathogenic variant(s) in their family, they should be offered echocardiography surveillance to determine if treatable cardiac manifestations of presymptomatic disease are present. Pregnancy management: Worsening, improving, or unchanged manifestations during pregnancy were each reported with equal frequency by women with FRDA. Close cardiac monitoring and regular testing for diabetes mellitus during pregnancy is recommended in any woman with FRDA. If cesarean section is required, epidural or spinal anesthesia is recommended rather than general anesthesia if possible., FRDA is inherited in an autosomal recessive manner. If both parents are heterozygous for a pathogenic variant in FXN, each sib of an affected individual has at conception a 25% chance of inheriting biallelic FRDA-related genetic alterations, a 50% chance of inheriting one FRDA-related genetic alteration, and a 25% chance of inheriting neither of the familial FRDA-related genetic alterations. Sibs who inherit biallelic FXN pathogenic variants will be affected. Once the FRDA-related genetic alterations have been identified in an affected family member, carrier testing for at-risk relatives and prenatal/preimplantation genetic testing are possible.", + "language": "eng", + "note": "PMID: 20301458\nThis CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: url:https://www.ncbi.nlm.nih.gov/books/NBK1281" }, { "id": "genereviews:NBK1305", diff --git a/data/STRchive-loci.json b/data/STRchive-loci.json index a5baa95d..8bdcbb9b 100644 --- a/data/STRchive-loci.json +++ b/data/STRchive-loci.json @@ -1940,6 +1940,73 @@ "references": ["pmid:24360810", "genereviews:NBK535148", "gnomad:EIF4A3", "pmid:29112243", "doi:10.1016/j.omsc.2023.100340", "mondo:0009998", "pmid:1632438"], "additional_literature": [] }, +{ + "id": "SCA_EP400", + "disease_id": "SCA", + "gene": "EP400", + "evidence": ["Provisional"], + "chrom": "chr12", + "start_hg38": 132062524, + "stop_hg38": 132062611, + "start_hg19": 132547069, + "stop_hg19": 132547156, + "start_t2t": 132111361, + "stop_t2t": 132111451, + "disease": "Spinocerebellar ataxia", + "inheritance": ["AD"], + "association_type": ["Mendelian"], + "disease_description": "A provisional form of spinocerebellar ataxia. Progressive gait ataxia is present in all reported cases, ranging from juvenile-onset (age 15, rapidly progressive with bulbar and respiratory involvement) to adult-onset (40s, slowly progressive over decades). Other features vary by family and include cerebellar dysarthria, abnormal eye movements, dysphagia, and limb incoordination [@doi:10.1101/2025.01.06.631535]. This locus has not yet been assigned an SCA number and is not yet listed in OMIM, GeneReviews, MONDO, or other clinical genetics databases.", + "hpo_terms": null, + "prevalence": null, + "prevalence_details": null, + "age_onset": null, + "age_onset_min": 15.0, + "age_onset_max": 43.0, + "typ_age_onset_min": null, + "typ_age_onset_max": null, + "details": "Disease link reported in Danzi et al. Family 1 (father and daughter) had a longest pure tract of 56-58 repeats, while Family 2 (mother-son, mother ungenotyped) had 75 pure CAG repeats. STRchive is using the broad locus definition of chr12:132062524-132062611, where the reference locus structure is (CAG)6-(CAA)2-(CAG)14-(CAA)1-(CAG)4-(CAA)1-(CAG)1. A narrower locus definition of chr12:132062548-132062611 has also been used to describe this locus and results in a differently described pathogenic range [@doi:10.1101/2025.01.06.631535].", + "detection": "Long-read sequencing with targeted sanger confirmation has detected expansions in this locus [@doi:10.1101/2025.01.06.631535].", + "mechanism": "Unknown", + "mechanism_detail": "Polyglutamine expansion", + "year": "2026", + "location_in_gene": "Exon 47", + "gene_strand": "+", + "reference_motif_reference_orientation": ["CAG"], + "pathogenic_motif_reference_orientation": ["CAG"], + "benign_motif_reference_orientation": [], + "unknown_motif_reference_orientation": [], + "interruption_reference_orientation": ["CAA"], + "pathogenic_motif_gene_orientation": ["CAG"], + "benign_motif_gene_orientation": [], + "unknown_motif_gene_orientation": [], + "interruption_gene_orientation": ["CAA"], + "locus_structure": [], + "benign_min": 0, + "benign_max": 24, + "intermediate_min": null, + "intermediate_max": null, + "pathogenic_min": 71, + "pathogenic_max": 77, + "motif_len": 3, + "ref_copies": 29.0, + "novel": null, + "gard": [], + "genereviews": [], + "malacard": [], + "medgen": [], + "mondo": [], + "omim": [], + "orphanet": [], + "gnomad": ["EP400"], + "stripy": [], + "tr_atlas": [], + "webstr_hg38": [], + "webstr_hg19": [], + "locus_tags": [], + "disease_tags": ["spinocerebellar_ataxia"], + "references": ["doi:10.1101/2025.01.06.631535"], + "additional_literature": ["pmid:38871700", "pmid:28600779", "pmid:39708813", "pmid:31081019", "pmid:33602898"] +}, { "id": "OPDM_FAM193B", "disease_id": "OPDM", @@ -2445,7 +2512,7 @@ "typ_age_onset_max": 55.0, "details": "Variation in repeat length, motif length, and motif sequence, with long CT-dimer expansions strongly associated with aFTLD-U risk. CCTT and CCCTCT motif expansions have been observed in unaffected individuals. CCCCT repeats were present in one aFTLD-U case. Proposed risk-associated expansions are typically >450 bp with >80% CT content and/or contain >190 CT dimers, though unaffected carriers have also been observed. Although the functional consequence of this repeat remains unknown, its presence in nearly 60% of aFTLD-U cases points to a major role in disease pathogenesis [@pmid:41820575].", "detection": null, - "mechanism": "Unknown [@pmid:41820575].", + "mechanism": "Unknown", "mechanism_detail": null, "year": "2026 [@pmid:41820575]", "location_in_gene": null, diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed b/data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed index 1c4b36c1..41da6bed 100644 --- a/data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed +++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed @@ -39,6 +39,7 @@ chr12 6947903 6947941 ID=DRPLA_ATN1;MOTIFS=CAG;STRUC= chr12 50468095 50468118 ID=FRA12A_DIP2B;MOTIFS=CGG;STRUC= chr12 111575873 111575940 ID=SCA2_ATXN2;MOTIFS=CTG;STRUC= chr12 123532573 123532603 ID=OPDM4_RILPL1;MOTIFS=CGG;STRUC= +chr12 132111361 132111451 ID=SCA_EP400;MOTIFS=CAG;STRUC= chr13 69361213 69361270 ID=SCA8_ATXN8OS;MOTIFS=CTA,CTG;STRUC= chr13 99196358 99196404 ID=HPE5_ZIC2;MOTIFS=GCN;STRUC= chr13 101377549 101377792 ID=SCA27B_FGF14;MOTIFS=AAG,GAA,AGG,CAG;STRUC= diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed b/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed index 94bc7152..cc032aa0 100644 --- a/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed +++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed @@ -46,6 +46,7 @@ chr12 6947903 6947941 CAG 3 DRPLA_ATN1 chr12 50468095 50468118 CGG 3 FRA12A_DIP2B chr12 111575873 111575940 CTG 3 SCA2_ATXN2 chr12 123532573 123532603 CGG 3 OPDM4_RILPL1 +chr12 132111361 132111451 CAG 3 SCA_EP400 chr13 69361213 69361243 CTA 3 SCA8_ATXN8OS_flank chr13 69361243 69361270 CTG 3 SCA8_ATXN8OS chr13 99196358 99196404 GCN 3 HPE5_ZIC2 diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz b/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz index 7cac8294b74009190bb3e50c60e85956df75e1ec..09a8c70d91f6a167fd1ad06346c05dc131f7ca6e 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SCA2_ATXN2 ATXN2 CTG CTG 35 AD,AR Spinocerebellar ataxia type 2 chr12 124018267 124018297 OPDM4_RILPL1 RILPL1 CGG CGG 120 AD Oculopharyngodistal myopathy type 4 +chr12 132547069 132547156 SCA_EP400 EP400 CAG CAG 71 AD Spinocerebellar ataxia chr13 70713515 70713561 SCA8_ATXN8OS ATXN8OS CTG CTG 71 AD Spinocerebellar ataxia type 8 chr13 100637702 100637748 HPE5_ZIC2 ZIC2 GCN GCN 25 AD Holoprosencephaly-5 chr13 102813924 102814076 SCA27B_FGF14 FGF14 GAA AAG 320 AD Spinocerebellar ataxia 27B diff --git a/data/catalogs/STRchive-disease-loci.hg19.longTR.bed b/data/catalogs/STRchive-disease-loci.hg19.longTR.bed index 036835f7..e5064baa 100644 --- a/data/catalogs/STRchive-disease-loci.hg19.longTR.bed +++ b/data/catalogs/STRchive-disease-loci.hg19.longTR.bed @@ -39,6 +39,7 @@ chr12 7045880 7045938 CAG DRPLA_ATN1 chr12 50898785 50898807 CGG FRA12A_DIP2B chr12 112036754 112036823 CTG SCA2_ATXN2 chr12 124018268 124018297 CGG OPDM4_RILPL1 +chr12 132547070 132547156 CAG SCA_EP400 chr13 70713516 70713561 CTG SCA8_ATXN8OS chr13 100637703 100637748 GCN HPE5_ZIC2 chr13 102813925 102814076 AAG,AGG,CAG,GAA SCA27B_FGF14 diff --git a/data/catalogs/STRchive-disease-loci.hg19.straglr.bed b/data/catalogs/STRchive-disease-loci.hg19.straglr.bed index 573e87ae..baa94354 100644 --- a/data/catalogs/STRchive-disease-loci.hg19.straglr.bed +++ b/data/catalogs/STRchive-disease-loci.hg19.straglr.bed @@ -43,6 +43,7 @@ chr12 7045879 7045938 CAG DRPLA_ATN1 DRPLA_ATN1 chr12 50898784 50898807 CGG FRA12A_DIP2B FRA12A_DIP2B chr12 112036753 112036823 CTG SCA2_ATXN2 SCA2_ATXN2 chr12 124018267 124018297 CGG OPDM4_RILPL1 OPDM4_RILPL1 +chr12 132547069 132547156 CAG SCA_EP400 SCA_EP400 chr13 70713485 70713515 CTA SCA8_ATXN8OS SCA8_ATXN8OS_CTA chr13 70713515 70713561 CTG SCA8_ATXN8OS SCA8_ATXN8OS chr13 100637702 100637748 GCN HPE5_ZIC2 HPE5_ZIC2 diff --git a/data/catalogs/STRchive-disease-loci.hg19.stranger.json b/data/catalogs/STRchive-disease-loci.hg19.stranger.json index e5ca1eda..e1162019 100644 --- a/data/catalogs/STRchive-disease-loci.hg19.stranger.json +++ b/data/catalogs/STRchive-disease-loci.hg19.stranger.json @@ -530,6 +530,19 @@ "PathologicMin": 120, "Gene": "RILPL1" }, +{ + "LocusId": "SCA_EP400", + "ReferenceRegion": "chr12:132547069-132547156", + "LocusStructure": "(CAG)*", + "VariantType": "Repeat", + "HGNCId": null, + "InheritanceMode": ["AD"], + "DisplayRU": "CAG", + "Disease": "SCA", + "NormalMax": 24, + "PathologicMin": 71, + "Gene": "EP400" +}, { "LocusId": "SCA8_ATXN8OS", "ReferenceRegion": ["chr13:70713485-70713515", "chr13:70713515-70713561"], diff --git a/data/catalogs/STRchive-disease-loci.hg38.TRGT.bed b/data/catalogs/STRchive-disease-loci.hg38.TRGT.bed index b30d49e7..738c4b8c 100644 --- a/data/catalogs/STRchive-disease-loci.hg38.TRGT.bed +++ b/data/catalogs/STRchive-disease-loci.hg38.TRGT.bed @@ -39,6 +39,7 @@ chr12 6936716 6936775 ID=DRPLA_ATN1;MOTIFS=CAG;STRUC= chr12 50505001 50505024 ID=FRA12A_DIP2B;MOTIFS=CGG;STRUC= chr12 111598949 111599019 ID=SCA2_ATXN2;MOTIFS=CTG;STRUC= chr12 123533720 123533750 ID=OPDM4_RILPL1;MOTIFS=CGG;STRUC= +chr12 132062524 132062611 ID=SCA_EP400;MOTIFS=CAG;STRUC= chr13 70139353 70139429 ID=SCA8_ATXN8OS;MOTIFS=CTA,CTG;STRUC= chr13 99985448 99985494 ID=HPE5_ZIC2;MOTIFS=GCN;STRUC= chr13 102161574 102161726 ID=SCA27B_FGF14;MOTIFS=AAG,GAA,AGG,CAG;STRUC= diff --git a/data/catalogs/STRchive-disease-loci.hg38.atarva.bed b/data/catalogs/STRchive-disease-loci.hg38.atarva.bed index 081f2d2e..aed15453 100644 --- a/data/catalogs/STRchive-disease-loci.hg38.atarva.bed +++ b/data/catalogs/STRchive-disease-loci.hg38.atarva.bed @@ -46,6 +46,7 @@ chr12 6936716 6936775 CAG 3 DRPLA_ATN1 chr12 50505001 50505024 CGG 3 FRA12A_DIP2B chr12 111598949 111599019 CTG 3 SCA2_ATXN2 chr12 123533720 123533750 CGG 3 OPDM4_RILPL1 +chr12 132062524 132062611 CAG 3 SCA_EP400 chr13 70139353 70139383 CTA 3 SCA8_ATXN8OS_flank chr13 70139383 70139429 CTG 3 SCA8_ATXN8OS chr13 99985448 99985494 GCN 3 HPE5_ZIC2 diff --git 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za0M0?>edXTK}rYb&B!;fU;>TVTSn2Nv`U;dT{98YT;cuPkcd^7KSUYd_X6z!xf5bF eTk}jcttWHn-KX}_DK3GH1Do@3!7M1mWZB;!R{n+n diff --git a/data/catalogs/STRchive-disease-loci.hg38.general.bed b/data/catalogs/STRchive-disease-loci.hg38.general.bed index 404bcdc9..09c9cb52 100644 --- a/data/catalogs/STRchive-disease-loci.hg38.general.bed +++ b/data/catalogs/STRchive-disease-loci.hg38.general.bed @@ -40,6 +40,7 @@ chr12 6936716 6936775 DRPLA_ATN1 ATN1 CAG CAG 48 AD Dentatorubral-Pallidoluysian chr12 50505001 50505024 FRA12A_DIP2B DIP2B CGG CGG 273 AD Intellectual developmental disorder, FRA12A type chr12 111598949 111599019 SCA2_ATXN2 ATXN2 CTG CTG 35 AD,AR Spinocerebellar ataxia type 2 chr12 123533720 123533750 OPDM4_RILPL1 RILPL1 CGG CGG 120 AD Oculopharyngodistal myopathy type 4 +chr12 132062524 132062611 SCA_EP400 EP400 CAG CAG 71 AD Spinocerebellar ataxia chr13 70139383 70139429 SCA8_ATXN8OS ATXN8OS CTG CTG 71 AD Spinocerebellar ataxia type 8 chr13 99985448 99985494 HPE5_ZIC2 ZIC2 GCN GCN 25 AD Holoprosencephaly-5 chr13 102161574 102161726 SCA27B_FGF14 FGF14 GAA AAG 320 AD Spinocerebellar ataxia 27B diff --git a/data/catalogs/STRchive-disease-loci.hg38.longTR.bed b/data/catalogs/STRchive-disease-loci.hg38.longTR.bed index 00f62070..ed179b6d 100644 --- a/data/catalogs/STRchive-disease-loci.hg38.longTR.bed +++ b/data/catalogs/STRchive-disease-loci.hg38.longTR.bed @@ -39,6 +39,7 @@ chr12 6936717 6936775 CAG DRPLA_ATN1 chr12 50505002 50505024 CGG FRA12A_DIP2B chr12 111598950 111599019 CTG SCA2_ATXN2 chr12 123533721 123533750 CGG OPDM4_RILPL1 +chr12 132062525 132062611 CAG SCA_EP400 chr13 70139384 70139429 CTG SCA8_ATXN8OS chr13 99985449 99985494 GCN HPE5_ZIC2 chr13 102161575 102161726 AAG,AGG,CAG,GAA SCA27B_FGF14 diff --git a/data/catalogs/STRchive-disease-loci.hg38.straglr.bed b/data/catalogs/STRchive-disease-loci.hg38.straglr.bed index 85ee6834..7be6c47c 100644 --- a/data/catalogs/STRchive-disease-loci.hg38.straglr.bed +++ b/data/catalogs/STRchive-disease-loci.hg38.straglr.bed @@ -43,6 +43,7 @@ chr12 6936716 6936775 CAG DRPLA_ATN1 DRPLA_ATN1 chr12 50505001 50505024 CGG FRA12A_DIP2B FRA12A_DIP2B chr12 111598949 111599019 CTG SCA2_ATXN2 SCA2_ATXN2 chr12 123533720 123533750 CGG OPDM4_RILPL1 OPDM4_RILPL1 +chr12 132062524 132062611 CAG SCA_EP400 SCA_EP400 chr13 70139353 70139383 CTA SCA8_ATXN8OS SCA8_ATXN8OS_CTA chr13 70139383 70139429 CTG SCA8_ATXN8OS SCA8_ATXN8OS chr13 99985448 99985494 GCN HPE5_ZIC2 HPE5_ZIC2 diff --git a/data/catalogs/STRchive-disease-loci.hg38.stranger.json b/data/catalogs/STRchive-disease-loci.hg38.stranger.json index b54442ee..6229a9d1 100644 --- a/data/catalogs/STRchive-disease-loci.hg38.stranger.json +++ b/data/catalogs/STRchive-disease-loci.hg38.stranger.json @@ -530,6 +530,19 @@ "PathologicMin": 120, "Gene": "RILPL1" }, +{ + "LocusId": "SCA_EP400", + "ReferenceRegion": "chr12:132062524-132062611", + "LocusStructure": "(CAG)*", + "VariantType": "Repeat", + "HGNCId": null, + "InheritanceMode": ["AD"], + "DisplayRU": "CAG", + "Disease": "SCA", + "NormalMax": 24, + "PathologicMin": 71, + "Gene": "EP400" +}, { "LocusId": "SCA8_ATXN8OS", "ReferenceRegion": ["chr13:70139353-70139383", "chr13:70139383-70139429"], diff --git a/data/plots/age-onset.json b/data/plots/age-onset.json index 6d3e1831..c224c179 100644 --- a/data/plots/age-onset.json +++ b/data/plots/age-onset.json @@ -1,7 +1,7 @@ { "data": [ { - "base": [49.0, 32.0, 31.0, 28.0, 25.0, 23.0, 22.0, 21.0, 20.0, 20.0, 0, 18.0, 18.0, 18.0, 16.0, 16.0, 15.0, 0, 12.0, 12.0, 11.0, 11.0, 10.0, 10.0, 10.0, 10.0, 10.0, 8.0, 8.0, 8.0, 0, 7.0, 7.0, 6.0, 0, 0, 4.0, 4.0, 3.0, 3.0, 3.0, 2.0, 2.0, 0, 0, 0, 2.0, 1.0, 1.0, 0, 0, 0.0, 0.0, 0.0, 0.0, 0.0, 0, 0.0, 0, 0, 0.0, 0.0, 0, 0], + "base": [49.0, 32.0, 31.0, 28.0, 25.0, 23.0, 22.0, 21.0, 20.0, 20.0, 0, 18.0, 18.0, 18.0, 16.0, 16.0, 15.0, 15.0, 0, 12.0, 12.0, 11.0, 11.0, 10.0, 10.0, 10.0, 10.0, 10.0, 8.0, 8.0, 8.0, 0, 7.0, 7.0, 6.0, 0, 0, 4.0, 4.0, 3.0, 3.0, 3.0, 2.0, 2.0, 0, 0, 0, 2.0, 1.0, 1.0, 0, 0, 0.0, 0.0, 0.0, 0.0, 0.0, 0, 0.0, 0, 0, 0.0, 0.0, 0, 0], "hovertemplate": "Disease: %{y} \u003cbr\u003e Range onset: %{base} - %{x} years", "legendgroup": "AD", "marker": @@ -12,12 +12,12 @@ "offset": -0.1, "orientation": "h", "width": 0.2, - "x": [2.0, 47.0, 32.0, 39.0, 52.0, 51.0, 44.0, 66.0, 71.0, 59.0, 0, 41.0, 19.0, 46.0, 54.0, 57.0, 25.0, 0, 53.0, 54.0, 6.0, 72.0, 40.0, 23.0, 68.0, 40.0, 20.0, 75.0, 54.0, 60.0, 0, 61.0, 59.0, 57.0, 0, 0, 47.0, 56.0, 59.0, 10.0, 70.0, 84.0, 68.0, 0, 0, 0, 1.0, 84.0, 6.0, 0, 0, 73.0, 76.0, 72.0, 74.0, 10.0, 0, 92.0, 0, 0, 3.0, 36.0, 0, 0], - "y": ["OPDM", "FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "OPDM", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "XDP", "SCA4", "HDL2", "MODY8", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "OPDM2", "FRDA", "FRAXG", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "EPM, DEE", "XLID, PHPX", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"], + "x": [2.0, 47.0, 32.0, 39.0, 52.0, 51.0, 44.0, 66.0, 71.0, 59.0, 0, 41.0, 19.0, 46.0, 54.0, 57.0, 28.0, 25.0, 0, 53.0, 54.0, 6.0, 72.0, 40.0, 23.0, 68.0, 40.0, 20.0, 75.0, 54.0, 60.0, 0, 61.0, 59.0, 57.0, 0, 0, 47.0, 56.0, 59.0, 10.0, 70.0, 84.0, 68.0, 0, 0, 0, 1.0, 84.0, 6.0, 0, 0, 73.0, 76.0, 72.0, 74.0, 10.0, 0, 92.0, 0, 0, 3.0, 36.0, 0, 0], + "y": ["OPDM", "FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "OPDM", "FAME7", "SCA37", "ADTKD", "SCA6", "SCA", "OPML1", "XDP", "SCA4", "HDL2", "MODY8", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "OPDM2", "FRDA", "FRAXG", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "EPM, 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"EPM, DEE", "XLID, PHPX", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"], + "x": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 64.0, 0], + "y": ["OPDM", "FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "OPDM", "FAME7", "SCA37", "ADTKD", "SCA6", "SCA", "OPML1", "XDP", "SCA4", "HDL2", "MODY8", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "OPDM2", "FRDA", "FRAXG", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "EPM, DEE", "XLID, PHPX", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"], "type": "bar" }, { - "base": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 39.7, 0, 0, 0, 0, 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300, 280, 255, 249, 219, 216, 213, 213, 210, 198, 186, 180, 177, 168, 155, 153, 153, 150, 147, 144, 138, 135, 120, 120, 117, 114, 111, 108, 105, 78, 75, 75, 66, 66, 66, 66, 63, 60, 60, 54, 54, 51, 45, 45, 36, 36, 33, 18, 12, 10, 0], "hovertemplate": "Disease: %{y} \u003cbr\u003e Range: %{base} - %{x} bp", "legendgroup": "Pathogenic", "marker": @@ -44,8 +44,8 @@ "offset": -0.3, "orientation": "h", "width": 0.6, - "x": [0, 0, 18500, 11100, 1287, 1925, 705, 2460, 11750, 2268, 1420, 0, 294, 0, 1851, 0, 99, 5397, 5397, 12, 3250, 17875, 1617, 820, 1140, 231, 1728, 597, 43700, 10700, 40, 612, 195, 273, 114, 3687, 102, 1353, 24342, 81, 69, 4932, 220, 81, 7647, 11850, 51, 135, 84, 165, 60, 264, 156, 90, 1269, 642, 1395, 21, 0, 0, 0, 30, 3, 12, 36, 0, 21, 0, 3, 30, 27, 1625, 18, 0, 135, 3, 0, 20, 0], - "y": ["FAME6", "FAME4", "SCA10", "SCA36", "MRUPAV", "FAME3", "EPM, DEE", "GDPAG", "CANVAS", "FRAXG", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "OPDM", "SCA31", "FAME1", "OPML1", "aFTLD-U", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM", "OPDM2", "DBQD2, BSS", "SCA8", "XDP", "NIID", "FTDALS1", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA51", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLID, PHPX", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"], + "x": [0, 0, 18500, 11100, 1287, 1925, 705, 2460, 11750, 2268, 1420, 0, 294, 0, 1851, 0, 99, 5397, 5397, 12, 3250, 17875, 1617, 820, 1140, 231, 1728, 597, 43700, 10700, 40, 612, 195, 273, 114, 3687, 18, 102, 1353, 24342, 81, 69, 4932, 220, 81, 7647, 11850, 51, 135, 84, 165, 60, 264, 156, 90, 1269, 642, 1395, 21, 0, 0, 0, 30, 3, 12, 36, 0, 21, 0, 3, 30, 27, 1625, 18, 0, 135, 3, 0, 20, 0], + "y": ["FAME6", "FAME4", "SCA10", "SCA36", "MRUPAV", "FAME3", "EPM, DEE", "GDPAG", "CANVAS", "FRAXG", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "OPDM", "SCA31", "FAME1", "OPML1", "aFTLD-U", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM", "OPDM2", "DBQD2, BSS", "SCA8", "SCA", "XDP", "NIID", "FTDALS1", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA51", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLID, PHPX", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"], "type": "bar" }, { @@ -555,6 +555,19 @@ "y": ["SCA8", "SCA8"], "type": "scatter" }, + { + "hoverinfo": "skip", + "line": + { + "color": "#aeaeae", + "dash": "dot" + }, + "mode": "lines", + "showlegend": false, + "x": [72, 213], + "y": ["SCA", "SCA"], + "type": "scatter" + }, { "hoverinfo": "skip", "line": @@ -1947,7 +1960,7 @@ "yaxis": { "tickmode": "array", - "tickvals": ["FAME6", "FAME4", "SCA10", "SCA36", "MRUPAV", "FAME3", "EPM, DEE", "GDPAG", "CANVAS", "FRAXG", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "OPDM", "SCA31", "FAME1", "OPML1", "aFTLD-U", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM", "OPDM2", "DBQD2, BSS", "SCA8", "XDP", "NIID", "FTDALS1", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA51", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLID, PHPX", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"], + "tickvals": ["FAME6", "FAME4", "SCA10", "SCA36", "MRUPAV", "FAME3", "EPM, DEE", "GDPAG", "CANVAS", "FRAXG", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "OPDM", "SCA31", "FAME1", "OPML1", "aFTLD-U", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM", "OPDM2", "DBQD2, BSS", "SCA8", "SCA", "XDP", "NIID", "FTDALS1", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA51", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLID, PHPX", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"], "title": { "text": "Disease" diff --git a/data/ref-alleles/ref-alleles.T2T-chm13.txt b/data/ref-alleles/ref-alleles.T2T-chm13.txt index 821fcd1d..28427db9 100644 --- a/data/ref-alleles/ref-alleles.T2T-chm13.txt +++ b/data/ref-alleles/ref-alleles.T2T-chm13.txt @@ -244,6 +244,12 @@ chr12 123532573 123532603 CGG TRGT CTCCCGAGTG GG CGG CGG CGG CGG CGG CGG CGG CGG CGG C AGCGGGGAGG CTCCCGAGTG GG CGG CGG CGG CGG CGG CGG CGG CGG CGG C AGCGGGGAGG +SCA_EP400 +chr12 132111361 132111451 CAG STRchive +chr12 132111361 132111451 CAG TRGT +GCTTCTCAGG CAG CAG CAG CAG CAG CAG CAACAA CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CAG CAG CAG CAA CAG ACGACGACGA +GCTTCTCAGG CAG CAG CAG CAG CAG CAG CAACAA CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CAG CAG CAG CAA CAG ACGACGACGA + SCA8_ATXN8OS chr13 69361243 69361270 CTG STRchive chr13 69361213 69361270 CTA,CTG TRGT diff --git a/data/ref-alleles/ref-alleles.hg19.txt b/data/ref-alleles/ref-alleles.hg19.txt index c889b455..860195f4 100644 --- a/data/ref-alleles/ref-alleles.hg19.txt +++ b/data/ref-alleles/ref-alleles.hg19.txt @@ -244,6 +244,12 @@ chr12 124018267 124018297 CGG TRGT CTCCCGAGTG GG CGG CGG CGG CGG CGG CGG CGG CGG CGG C AGCGGGGAGG CTCCCGAGTG GG CGG CGG CGG CGG CGG CGG CGG CGG CGG C AGCGGGGAGG +SCA_EP400 +chr12 132547069 132547156 CAG STRchive +chr12 132547069 132547156 CAG TRGT +GCTTCTCAGG CAG CAG CAG CAG CAG CAG CAACAA CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CAG CAG CAG CAA CAG ACGACGACGA +GCTTCTCAGG CAG CAG CAG CAG CAG CAG CAACAA CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CAG CAG CAG CAA CAG ACGACGACGA + SCA8_ATXN8OS chr13 70713515 70713561 CTG STRchive chr13 70713485 70713561 CTA,CTG TRGT diff --git a/data/ref-alleles/ref-alleles.hg38.txt b/data/ref-alleles/ref-alleles.hg38.txt index 2f91909b..e4f89b83 100644 --- a/data/ref-alleles/ref-alleles.hg38.txt +++ b/data/ref-alleles/ref-alleles.hg38.txt @@ -244,6 +244,12 @@ chr12 123533720 123533750 CGG TRGT CTCCCGAGTG GG CGG CGG CGG CGG CGG CGG CGG CGG CGG C AGCGGGGAGG CTCCCGAGTG GG CGG CGG CGG CGG CGG CGG CGG CGG CGG C AGCGGGGAGG +SCA_EP400 +chr12 132062524 132062611 CAG STRchive +chr12 132062524 132062611 CAG TRGT +GCTTCTCAGG CAG CAG CAG CAG CAG CAG CAACAA CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CAG CAG CAG CAA CAG ACGACGACGA +GCTTCTCAGG CAG CAG CAG CAG CAG CAG CAACAA CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CAG CAG CAG CAA CAG ACGACGACGA + SCA8_ATXN8OS chr13 70139383 70139429 CTG STRchive chr13 70139353 70139429 CTA,CTG TRGT From 4eb17f28acf97650664d67bb53637e0ef9cdbcab Mon Sep 17 00:00:00 2001 From: hdashnow <3794821+hdashnow@users.noreply.github.com> Date: Fri, 14 Aug 2026 21:20:25 +0000 Subject: [PATCH 2/7] Update data --- data/STRchive-citations.json | 78 ++++++++++++++++++------------------ 1 file changed, 39 insertions(+), 39 deletions(-) diff --git a/data/STRchive-citations.json b/data/STRchive-citations.json index cc0edfce..e5895d3e 100644 --- a/data/STRchive-citations.json +++ b/data/STRchive-citations.json @@ -166655,6 +166655,45 @@ "language": "en", "note": "This CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: doi:10.1101/2025.01.06.631535" }, +{ + "id": "genereviews:NBK1119", + "manubot_success": true, + "link": "http://www.ncbi.nlm.nih.gov/books/NBK1119/", + "title": "Dystrophinopathies", + "type": "chapter", + "doi": "", + "authors": [ + ["Basil T.", "Darras"], + ["David K.", "Urion"], + ["Partha S.", "Ghosh"] + ], + "publisher": "GeneReviews\u00ae", + "issn": "", + "date": "1993-01-01", + "abstract": "The dystrophinopathies cover a spectrum of X-linked muscle disease ranging from mild to severe that includes Duchenne muscular dystrophy, Becker muscular dystrophy, and DMD-associated dilated cardiomyopathy (DCM). The mild end of the spectrum includes the phenotypes of asymptomatic increase in serum concentration of creatine phosphokinase (CK) and muscle cramps with myoglobinuria. The severe end of the spectrum includes progressive muscle diseases that are classified as Duchenne/Becker muscular dystrophy when skeletal muscle is primarily affected and as DMD-associated DCM when the heart is primarily affected. Duchenne muscular dystrophy (DMD) usually presents in early childhood with delayed motor milestones including delays in walking independently and standing up from a supine position. Proximal weakness causes a waddling gait and difficulty climbing stairs, running, jumping, and standing up from a squatting position. DMD is rapidly progressive, with affected children being wheelchair dependent by age 12 years. Cardiomyopathy occurs in almost all individuals with DMD after age 18 years. Few survive beyond the third decade, with respiratory complications and progressive cardiomyopathy being common causes of death. Becker muscular dystrophy (BMD) is characterized by later-onset skeletal muscle weakness. With improved diagnostic techniques, it has been recognized that the mild end of the spectrum includes men with onset of symptoms after age 30 years who remain ambulatory even into their 60s. Despite the milder skeletal muscle involvement, heart failure from DCM is a common cause of morbidity and the most common cause of death in BMD. Mean age of death is in the mid-40s. DMD-associated DCM is characterized by left ventricular dilatation and congestive heart failure. Females heterozygous for a DMD pathogenic variant are at increased risk for DCM., The diagnosis of a dystrophinopathy is established in a proband with the characteristic clinical findings and elevated CK concentration and/or by identification of a hemizygous pathogenic variant in DMD on molecular genetic testing in a male and of a heterozygous pathogenic variant in DMD on molecular genetic testing in a female. Females may present with a classic dystrophinopathy or may be asymptomatic carriers., Treatment of manifestations: ACE inhibitors are used with or without beta blockers for cardiomyopathy in both DMD and BMD phenotypes. Congestive heart failure is treated with diuretics and oxygen as needed; cardiac transplantation is offered to persons with severe dilated cardiomyopathy and BMD with limited or no clinical evidence of skeletal muscle disease. Scoliosis is treated with bracing and surgery. Corticosteroid therapy improves muscle strength and function for individuals with DMD between ages five and 15 years; the same treatment is used in BMD, although the efficacy is less clear. Dystrophin restoration therapies have been developed by using synthetic antisense oligonucleotides to restore the reading frame by exon skipping for individuals with specific pathogenic variants in DMD. Prevention of secondary complications: Evaluation by a pulmonologist and cardiologist before surgeries; pneumococcal and influenza immunizations annually; nutrition assessment; physical therapy to promote mobility and prevent contractures; sunshine and a balanced diet rich in vitamin D and calcium to improve bone density and reduce the risk of fractures; weight control to avoid obesity. Surveillance: For males with DMD or BMD: annual or biannual evaluation by a cardiologist beginning at the time of diagnosis; monitoring for scoliosis; baseline pulmonary function testing before wheelchair dependence; frequent evaluations by a pediatric pulmonologist. For heterozygous females: cardiac evaluation at least once after the teenage years. Agents/circumstances to avoid: Botulinum toxin injections; succinylcholine and inhalational anesthetics because of susceptibility to malignant hyperthermia or malignant hyperthermia-like reactions. Evaluation of relatives at risk: Early identification of heterozygous females who are at increased risk for cardiomyopathy and, thus, need routine cardiac surveillance and prompt treatment., The dystrophinopathies are inherited in an X-linked manner. The risk to the sibs of a proband depends on the genetic status of the mother. Heterozygous females have a 50% chance of transmitting the DMD pathogenic variant in each pregnancy. Sons who inherit the pathogenic variant will be affected; daughters who inherit the pathogenic variant are heterozygous and may have a range of clinical manifestations. Males with DMD usually do not reproduce. Males with BMD or DMD-associated DCM may reproduce: all of their daughters are heterozygotes; none of their sons inherit their father's DMD pathogenic variant. Carrier testing for at-risk females, prenatal testing, and preimplantation genetic testing are possible if the DMD pathogenic variant in the family is known.", + "language": "eng", + "note": "PMID: 20301298\nThis CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: url:https://www.ncbi.nlm.nih.gov/books/NBK1119" +}, +{ + "id": "genereviews:NBK1281", + "manubot_success": true, + "link": "http://www.ncbi.nlm.nih.gov/books/NBK1281/", + "title": "Friedreich Ataxia", + "type": "chapter", + "doi": "", + "authors": [ + ["Sanjay I.", "Bidichandani"], + ["Martin B.", "Delatycki"], + ["Marek", "Napierala"], + ["Antoine", "Duquette"] + ], + "publisher": "GeneReviews\u00ae", + "issn": "", + "date": "1993-01-01", + "abstract": "Typical Friedreich ataxia (FRDA) is characterized by progressive ataxia with onset from early childhood to early adulthood with mean age at onset from 10 to 15 years (range: age two years to the eighth decade). Ataxia, manifesting initially as poor balance when walking, is typically followed by upper-limb ataxia, dysarthria, dysphagia, peripheral motor and sensory neuropathy, spasticity, autonomic disturbance, and often abnormal eye movements and optic atrophy. Hypertrophic cardiomyopathy is present in about two thirds of individuals; occasionally it is diagnosed prior to the onset of ataxia. Diabetes mellitus and impaired glucose tolerance can also occur. Among individuals with FRDA, about 75% have \"typical Friedreich ataxia\" and about 25% of individuals with biallelic FXN full-penetrance GAA repeat expansions have \"atypical Friedreich ataxia\" that includes late-onset FRDA (LOFA) (i.e., onset after age 25 years), very late-onset FRDA (VLOFA) (i.e., onset after age 40 years), and FRDA with retained reflexes (FARR)., The diagnosis of Friedreich ataxia is established in a proband with suggestive findings and biallelic pathogenic variants in FXN identified by molecular genetic testing. The two classes of FXN pathogenic variants are (1) GAA repeat expansions and (2) FXN pathogenic sequence variants, including base substitutions and small indels or large deletions. Approximately 96% of individuals with FRDA have biallelic FXN GAA repeat expansions in intron 1; approximately 4% are compound heterozygotes for an FXN GAA repeat expansion and either an intragenic FXN pathogenic variant or a large deletion., Targeted therapy: Omaveloxolone, an Nrf2 activator, has been shown to slow the progression of FRDA; it is approved in the United States and Europe for individuals age 16 years and older. Supportive care: Multidisciplinary care by specialists in relevant fields, such as neurologists, ophthalmologists, orthoptists, physical therapists, occupational therapists, cardiologists, endocrinologists, speech and language therapists, and psychologists. Surveillance: Routinely scheduled evaluations by the treating multidisciplinary specialists. Agents/circumstances to avoid: Use and misuse of illegal and controlled drugs, as they may affect neuronal well-being and, thus, exacerbate disease manifestations; medications that are toxic or potentially toxic to people with neuropathy; circumstances that increase the risk of falling (e.g., rough surfaces). Evaluation of relatives at risk: If at-risk minor and adult sibs of an individual with FRDA have not had testing for the FXN pathogenic variant(s) in their family, they should be offered echocardiography surveillance to determine if treatable cardiac manifestations of presymptomatic disease are present. Pregnancy management: Worsening, improving, or unchanged manifestations during pregnancy were each reported with equal frequency by women with FRDA. Close cardiac monitoring and regular testing for diabetes mellitus during pregnancy is recommended in any woman with FRDA. If cesarean section is required, epidural or spinal anesthesia is recommended rather than general anesthesia if possible., FRDA is inherited in an autosomal recessive manner. If both parents are heterozygous for a pathogenic variant in FXN, each sib of an affected individual has at conception a 25% chance of inheriting biallelic FRDA-related genetic alterations, a 50% chance of inheriting one FRDA-related genetic alteration, and a 25% chance of inheriting neither of the familial FRDA-related genetic alterations. Sibs who inherit biallelic FXN pathogenic variants will be affected. Once the FRDA-related genetic alterations have been identified in an affected family member, carrier testing for at-risk relatives and prenatal/preimplantation genetic testing are possible.", + "language": "eng", + "note": "PMID: 20301458\nThis CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: url:https://www.ncbi.nlm.nih.gov/books/NBK1281" +}, { "id": "omim:309548", "manubot_success": false, @@ -166907,51 +166946,12 @@ "link": "https://www.ncbi.nlm.nih.gov/books/NBK1491", "note": "WARNING: Manubot could not generate citation: Command '['manubot', 'cite', 'url:https://www.ncbi.nlm.nih.gov/books/NBK1491']' timed out after 3 seconds" }, -{ - "id": "genereviews:NBK1119", - "manubot_success": true, - "link": "http://www.ncbi.nlm.nih.gov/books/NBK1119/", - "title": "Dystrophinopathies", - "type": "chapter", - "doi": "", - "authors": [ - ["Basil T.", "Darras"], - ["David K.", "Urion"], - ["Partha S.", "Ghosh"] - ], - "publisher": "GeneReviews\u00ae", - "issn": "", - "date": "1993-01-01", - "abstract": "The dystrophinopathies cover a spectrum of X-linked muscle disease ranging from mild to severe that includes Duchenne muscular dystrophy, Becker muscular dystrophy, and DMD-associated dilated cardiomyopathy (DCM). The mild end of the spectrum includes the phenotypes of asymptomatic increase in serum concentration of creatine phosphokinase (CK) and muscle cramps with myoglobinuria. The severe end of the spectrum includes progressive muscle diseases that are classified as Duchenne/Becker muscular dystrophy when skeletal muscle is primarily affected and as DMD-associated DCM when the heart is primarily affected. Duchenne muscular dystrophy (DMD) usually presents in early childhood with delayed motor milestones including delays in walking independently and standing up from a supine position. Proximal weakness causes a waddling gait and difficulty climbing stairs, running, jumping, and standing up from a squatting position. DMD is rapidly progressive, with affected children being wheelchair dependent by age 12 years. Cardiomyopathy occurs in almost all individuals with DMD after age 18 years. Few survive beyond the third decade, with respiratory complications and progressive cardiomyopathy being common causes of death. Becker muscular dystrophy (BMD) is characterized by later-onset skeletal muscle weakness. With improved diagnostic techniques, it has been recognized that the mild end of the spectrum includes men with onset of symptoms after age 30 years who remain ambulatory even into their 60s. Despite the milder skeletal muscle involvement, heart failure from DCM is a common cause of morbidity and the most common cause of death in BMD. Mean age of death is in the mid-40s. DMD-associated DCM is characterized by left ventricular dilatation and congestive heart failure. Females heterozygous for a DMD pathogenic variant are at increased risk for DCM., The diagnosis of a dystrophinopathy is established in a proband with the characteristic clinical findings and elevated CK concentration and/or by identification of a hemizygous pathogenic variant in DMD on molecular genetic testing in a male and of a heterozygous pathogenic variant in DMD on molecular genetic testing in a female. Females may present with a classic dystrophinopathy or may be asymptomatic carriers., Treatment of manifestations: ACE inhibitors are used with or without beta blockers for cardiomyopathy in both DMD and BMD phenotypes. Congestive heart failure is treated with diuretics and oxygen as needed; cardiac transplantation is offered to persons with severe dilated cardiomyopathy and BMD with limited or no clinical evidence of skeletal muscle disease. Scoliosis is treated with bracing and surgery. Corticosteroid therapy improves muscle strength and function for individuals with DMD between ages five and 15 years; the same treatment is used in BMD, although the efficacy is less clear. Dystrophin restoration therapies have been developed by using synthetic antisense oligonucleotides to restore the reading frame by exon skipping for individuals with specific pathogenic variants in DMD. Prevention of secondary complications: Evaluation by a pulmonologist and cardiologist before surgeries; pneumococcal and influenza immunizations annually; nutrition assessment; physical therapy to promote mobility and prevent contractures; sunshine and a balanced diet rich in vitamin D and calcium to improve bone density and reduce the risk of fractures; weight control to avoid obesity. Surveillance: For males with DMD or BMD: annual or biannual evaluation by a cardiologist beginning at the time of diagnosis; monitoring for scoliosis; baseline pulmonary function testing before wheelchair dependence; frequent evaluations by a pediatric pulmonologist. For heterozygous females: cardiac evaluation at least once after the teenage years. Agents/circumstances to avoid: Botulinum toxin injections; succinylcholine and inhalational anesthetics because of susceptibility to malignant hyperthermia or malignant hyperthermia-like reactions. Evaluation of relatives at risk: Early identification of heterozygous females who are at increased risk for cardiomyopathy and, thus, need routine cardiac surveillance and prompt treatment., The dystrophinopathies are inherited in an X-linked manner. The risk to the sibs of a proband depends on the genetic status of the mother. Heterozygous females have a 50% chance of transmitting the DMD pathogenic variant in each pregnancy. Sons who inherit the pathogenic variant will be affected; daughters who inherit the pathogenic variant are heterozygous and may have a range of clinical manifestations. Males with DMD usually do not reproduce. Males with BMD or DMD-associated DCM may reproduce: all of their daughters are heterozygotes; none of their sons inherit their father's DMD pathogenic variant. Carrier testing for at-risk females, prenatal testing, and preimplantation genetic testing are possible if the DMD pathogenic variant in the family is known.", - "language": "eng", - "note": "PMID: 20301298\nThis CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: url:https://www.ncbi.nlm.nih.gov/books/NBK1119" -}, { "id": "genereviews:NBK1384", "manubot_success": false, "link": "https://www.ncbi.nlm.nih.gov/books/NBK1384", "note": "WARNING: Manubot could not generate citation: Command '['manubot', 'cite', 'url:https://www.ncbi.nlm.nih.gov/books/NBK1384']' timed out after 3 seconds" }, -{ - "id": "genereviews:NBK1281", - "manubot_success": true, - "link": "http://www.ncbi.nlm.nih.gov/books/NBK1281/", - "title": "Friedreich Ataxia", - "type": "chapter", - "doi": "", - "authors": [ - ["Sanjay I.", "Bidichandani"], - ["Martin B.", "Delatycki"], - ["Marek", "Napierala"], - ["Antoine", "Duquette"] - ], - "publisher": "GeneReviews\u00ae", - "issn": "", - "date": "1993-01-01", - "abstract": "Typical Friedreich ataxia (FRDA) is characterized by progressive ataxia with onset from early childhood to early adulthood with mean age at onset from 10 to 15 years (range: age two years to the eighth decade). Ataxia, manifesting initially as poor balance when walking, is typically followed by upper-limb ataxia, dysarthria, dysphagia, peripheral motor and sensory neuropathy, spasticity, autonomic disturbance, and often abnormal eye movements and optic atrophy. Hypertrophic cardiomyopathy is present in about two thirds of individuals; occasionally it is diagnosed prior to the onset of ataxia. Diabetes mellitus and impaired glucose tolerance can also occur. Among individuals with FRDA, about 75% have \"typical Friedreich ataxia\" and about 25% of individuals with biallelic FXN full-penetrance GAA repeat expansions have \"atypical Friedreich ataxia\" that includes late-onset FRDA (LOFA) (i.e., onset after age 25 years), very late-onset FRDA (VLOFA) (i.e., onset after age 40 years), and FRDA with retained reflexes (FARR)., The diagnosis of Friedreich ataxia is established in a proband with suggestive findings and biallelic pathogenic variants in FXN identified by molecular genetic testing. The two classes of FXN pathogenic variants are (1) GAA repeat expansions and (2) FXN pathogenic sequence variants, including base substitutions and small indels or large deletions. Approximately 96% of individuals with FRDA have biallelic FXN GAA repeat expansions in intron 1; approximately 4% are compound heterozygotes for an FXN GAA repeat expansion and either an intragenic FXN pathogenic variant or a large deletion., Targeted therapy: Omaveloxolone, an Nrf2 activator, has been shown to slow the progression of FRDA; it is approved in the United States and Europe for individuals age 16 years and older. Supportive care: Multidisciplinary care by specialists in relevant fields, such as neurologists, ophthalmologists, orthoptists, physical therapists, occupational therapists, cardiologists, endocrinologists, speech and language therapists, and psychologists. Surveillance: Routinely scheduled evaluations by the treating multidisciplinary specialists. Agents/circumstances to avoid: Use and misuse of illegal and controlled drugs, as they may affect neuronal well-being and, thus, exacerbate disease manifestations; medications that are toxic or potentially toxic to people with neuropathy; circumstances that increase the risk of falling (e.g., rough surfaces). Evaluation of relatives at risk: If at-risk minor and adult sibs of an individual with FRDA have not had testing for the FXN pathogenic variant(s) in their family, they should be offered echocardiography surveillance to determine if treatable cardiac manifestations of presymptomatic disease are present. Pregnancy management: Worsening, improving, or unchanged manifestations during pregnancy were each reported with equal frequency by women with FRDA. Close cardiac monitoring and regular testing for diabetes mellitus during pregnancy is recommended in any woman with FRDA. If cesarean section is required, epidural or spinal anesthesia is recommended rather than general anesthesia if possible., FRDA is inherited in an autosomal recessive manner. If both parents are heterozygous for a pathogenic variant in FXN, each sib of an affected individual has at conception a 25% chance of inheriting biallelic FRDA-related genetic alterations, a 50% chance of inheriting one FRDA-related genetic alteration, and a 25% chance of inheriting neither of the familial FRDA-related genetic alterations. Sibs who inherit biallelic FXN pathogenic variants will be affected. Once the FRDA-related genetic alterations have been identified in an affected family member, carrier testing for at-risk relatives and prenatal/preimplantation genetic testing are possible.", - "language": "eng", - "note": "PMID: 20301458\nThis CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: url:https://www.ncbi.nlm.nih.gov/books/NBK1281" -}, { "id": "genereviews:NBK1305", "manubot_success": false, From 4d20f2fd816355d5b80307eb820298c9fd1dd3d4 Mon Sep 17 00:00:00 2001 From: Harriet Dashnow Date: Fri, 14 Aug 2026 15:48:09 -0600 Subject: [PATCH 3/7] suggested EP400 details rewording --- data/STRchive-loci.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/STRchive-loci.json b/data/STRchive-loci.json index 8bdcbb9b..f8f1db41 100644 --- a/data/STRchive-loci.json +++ b/data/STRchive-loci.json @@ -1964,7 +1964,7 @@ "age_onset_max": 43.0, "typ_age_onset_min": null, "typ_age_onset_max": null, - "details": "Disease link reported in Danzi et al. Family 1 (father and daughter) had a longest pure tract of 56-58 repeats, while Family 2 (mother-son, mother ungenotyped) had 75 pure CAG repeats. STRchive is using the broad locus definition of chr12:132062524-132062611, where the reference locus structure is (CAG)6-(CAA)2-(CAG)14-(CAA)1-(CAG)4-(CAA)1-(CAG)1. A narrower locus definition of chr12:132062548-132062611 has also been used to describe this locus and results in a differently described pathogenic range [@doi:10.1101/2025.01.06.631535].", + "details": "STRchive is using the broad locus definition of hg38 chr12:132062524-132062611, where the reference locus structure is (CAG)6(CAA)2(CAG)14(CAA)1(CAG)4(CAA)(CAG). A narrower locus definition of hg38 chr12:132062548-132062611 has also been used to describe this locus and results in a differently described pathogenic range [@doi:10.1101/2025.01.06.631535]. Disease link was proposed by Danzi et al [@doi:10.1101/2025.01.06.631535]. Family 1 (father and daughter) had a longest pure tract of 56-58 repeats with the structure (CAG)6(CAA)2(CAG)46-58(CAA)1(CAG)4(CAA)(CAG), while the son in Family 2 (mother ungenotyped) had 75 pure CAG repeats with the structure (CAG)75(CAA)(CAG), i.e. loss of several CAA interruptions.", "detection": "Long-read sequencing with targeted sanger confirmation has detected expansions in this locus [@doi:10.1101/2025.01.06.631535].", "mechanism": "Unknown", "mechanism_detail": "Polyglutamine expansion", From 49576443356cc950bbd1d56af3832bcd2aecad2a Mon Sep 17 00:00:00 2001 From: Harriet Dashnow Date: Fri, 14 Aug 2026 16:22:55 -0600 Subject: [PATCH 4/7] explain the pure vs interruptions even more and adjust the benign range to include the length with interruptions. --- data/STRchive-loci.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/data/STRchive-loci.json b/data/STRchive-loci.json index f8f1db41..84a466e2 100644 --- a/data/STRchive-loci.json +++ b/data/STRchive-loci.json @@ -1964,7 +1964,7 @@ "age_onset_max": 43.0, "typ_age_onset_min": null, "typ_age_onset_max": null, - "details": "STRchive is using the broad locus definition of hg38 chr12:132062524-132062611, where the reference locus structure is (CAG)6(CAA)2(CAG)14(CAA)1(CAG)4(CAA)(CAG). A narrower locus definition of hg38 chr12:132062548-132062611 has also been used to describe this locus and results in a differently described pathogenic range [@doi:10.1101/2025.01.06.631535]. Disease link was proposed by Danzi et al [@doi:10.1101/2025.01.06.631535]. Family 1 (father and daughter) had a longest pure tract of 56-58 repeats with the structure (CAG)6(CAA)2(CAG)46-58(CAA)1(CAG)4(CAA)(CAG), while the son in Family 2 (mother ungenotyped) had 75 pure CAG repeats with the structure (CAG)75(CAA)(CAG), i.e. loss of several CAA interruptions.", + "details": "56 to 75 pure CAGs have been observed in affected individuals [@doi:10.1101/2025.01.06.631535], however differences in locus definitions make defining the pathogenic range challenging. STRchive is using the broad locus definition of hg38 chr12:132062524-132062611, where the reference locus structure is (CAG)6(CAA)2(CAG)14(CAA)1(CAG)4(CAA)(CAG). All allele size ranges in STRchive are based on this definition and report the total length of the allele including CAA interruptions. A narrower locus definition of hg38 chr12:132062548-132062611 has also been used to describe this locus and results in a differently described pathogenic range [@doi:10.1101/2025.01.06.631535]. Disease link was proposed by Danzi et al [@doi:10.1101/2025.01.06.631535]. Family 1 (father and daughter) had a longest pure tract of 56-58 repeats with the structure (CAG)6(CAA)2(CAG)46-58(CAA)1(CAG)4(CAA)(CAG), while the son in Family 2 (mother ungenotyped) had 75 pure CAG repeats with the structure (CAG)75(CAA)(CAG), i.e. loss of several CAA interruptions.", "detection": "Long-read sequencing with targeted sanger confirmation has detected expansions in this locus [@doi:10.1101/2025.01.06.631535].", "mechanism": "Unknown", "mechanism_detail": "Polyglutamine expansion", @@ -1981,8 +1981,8 @@ "unknown_motif_gene_orientation": [], "interruption_gene_orientation": ["CAA"], "locus_structure": [], - "benign_min": 0, - "benign_max": 24, + "benign_min": 19, + "benign_max": 39, "intermediate_min": null, "intermediate_max": null, "pathogenic_min": 71, From b3656d6504a3fb7caa91ff6be0f78e5704738a77 Mon Sep 17 00:00:00 2001 From: hdashnow <3794821+hdashnow@users.noreply.github.com> Date: Fri, 14 Aug 2026 22:31:06 +0000 Subject: [PATCH 5/7] Update data --- data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json | 2 +- data/catalogs/STRchive-disease-loci.hg19.stranger.json | 2 +- data/catalogs/STRchive-disease-loci.hg38.stranger.json | 2 +- data/plots/path-size.json | 6 +++--- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json b/data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json index d955692c..0ee3db50 100644 --- a/data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json +++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json @@ -539,7 +539,7 @@ "InheritanceMode": ["AD"], "DisplayRU": "CAG", "Disease": "SCA", - "NormalMax": 24, + "NormalMax": 39, "PathologicMin": 71, "Gene": "EP400" }, diff --git a/data/catalogs/STRchive-disease-loci.hg19.stranger.json b/data/catalogs/STRchive-disease-loci.hg19.stranger.json index e1162019..0e163e0f 100644 --- a/data/catalogs/STRchive-disease-loci.hg19.stranger.json +++ b/data/catalogs/STRchive-disease-loci.hg19.stranger.json @@ -539,7 +539,7 @@ "InheritanceMode": ["AD"], "DisplayRU": "CAG", "Disease": "SCA", - "NormalMax": 24, + "NormalMax": 39, "PathologicMin": 71, "Gene": "EP400" }, diff --git a/data/catalogs/STRchive-disease-loci.hg38.stranger.json b/data/catalogs/STRchive-disease-loci.hg38.stranger.json index 6229a9d1..4a6f8b02 100644 --- a/data/catalogs/STRchive-disease-loci.hg38.stranger.json +++ b/data/catalogs/STRchive-disease-loci.hg38.stranger.json @@ -539,7 +539,7 @@ "InheritanceMode": ["AD"], "DisplayRU": "CAG", "Disease": "SCA", - "NormalMax": 24, + "NormalMax": 39, "PathologicMin": 71, "Gene": "EP400" }, diff --git a/data/plots/path-size.json b/data/plots/path-size.json index 06af35e2..9a60941d 100644 --- a/data/plots/path-size.json +++ b/data/plots/path-size.json @@ -1,7 +1,7 @@ { "data": [ { - "base": [0, 0, 50, 18, 2871, 0, 1, 15, 1, 15, 0, 15, 252, 10, 24, 9, 18, 12, 15, 1, 0, 0, 9, 0, 24, 18, 9, 15, 44, 0, 20, 39, 1, 1, 1, 45, 1, 0, 21, 12, 33, 48, 15, 1, 18, 30, 15, 75, 18, 42, 60, 18, 96, 18, 27, 12, 18, 42, 27, 45, 45, 42, 24, 45, 45, 12, 36, 12, 36, 21, 30, 42, 0, 30, 30, 18, 15, 16, 20, 30], + "base": [0, 0, 50, 18, 2871, 0, 1, 15, 1, 15, 0, 15, 252, 10, 24, 9, 18, 12, 15, 1, 0, 0, 9, 0, 24, 18, 9, 15, 44, 0, 20, 39, 1, 1, 1, 45, 57, 0, 21, 12, 33, 48, 15, 1, 18, 30, 15, 75, 18, 42, 60, 18, 96, 18, 27, 12, 18, 42, 27, 45, 45, 42, 24, 45, 45, 12, 36, 12, 36, 21, 30, 42, 0, 30, 30, 18, 15, 16, 20, 30], "hovertemplate": "Disease: %{y} \u003cbr\u003e Range: %{base} - %{x} bp", "legendgroup": "Benign", "marker": @@ -12,7 +12,7 @@ "offset": -0.3, "orientation": "h", "width": 0.6, - "x": [0, 0, 110, 66, 198, 0, 143, 99, 54, 54, 0, 51, 780, 25, 513, 51, 51, 105, 117, 149, 0, 0, 39, 0, 12, 30, 123, 222, 60, 0, 220, 96, 179, 95, 59, 105, 71, 0, 90, 126, 99, 51, 84, 149, 78, 87, 87, 45, 87, 36, 54, 66, 0, 87, 75, 69, 60, 42, 33, 0, 0, 0, 30, 0, 0, 42, 0, 39, 0, 21, 18, 0, 0, 0, 0, 12, 0, 0, 0, 0], + "x": [0, 0, 110, 66, 198, 0, 143, 99, 54, 54, 0, 51, 780, 25, 513, 51, 51, 105, 117, 149, 0, 0, 39, 0, 12, 30, 123, 222, 60, 0, 220, 96, 179, 95, 59, 105, 60, 0, 90, 126, 99, 51, 84, 149, 78, 87, 87, 45, 87, 36, 54, 66, 0, 87, 75, 69, 60, 42, 33, 0, 0, 0, 30, 0, 0, 42, 0, 39, 0, 21, 18, 0, 0, 0, 0, 12, 0, 0, 0, 0], "y": ["FAME6", "FAME4", "SCA10", "SCA36", "MRUPAV", "FAME3", "EPM, DEE", "GDPAG", "CANVAS", "FRAXG", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "OPDM", "SCA31", "FAME1", "OPML1", "aFTLD-U", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM", "OPDM2", "DBQD2, BSS", "SCA8", "SCA", "XDP", "NIID", "FTDALS1", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA51", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLID, PHPX", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"], "type": "bar" }, @@ -564,7 +564,7 @@ }, "mode": "lines", "showlegend": false, - "x": [72, 213], + "x": [117, 213], "y": ["SCA", "SCA"], "type": "scatter" }, From 4c069ec9cb2b04cb75fee435b1534aad5d2914c1 Mon Sep 17 00:00:00 2001 From: Gabriel Zinser Date: Fri, 14 Aug 2026 16:34:13 -0600 Subject: [PATCH 6/7] remove mech detail --- data/STRchive-loci.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/STRchive-loci.json b/data/STRchive-loci.json index 84a466e2..19b36f9b 100644 --- a/data/STRchive-loci.json +++ b/data/STRchive-loci.json @@ -1967,7 +1967,7 @@ "details": "56 to 75 pure CAGs have been observed in affected individuals [@doi:10.1101/2025.01.06.631535], however differences in locus definitions make defining the pathogenic range challenging. STRchive is using the broad locus definition of hg38 chr12:132062524-132062611, where the reference locus structure is (CAG)6(CAA)2(CAG)14(CAA)1(CAG)4(CAA)(CAG). All allele size ranges in STRchive are based on this definition and report the total length of the allele including CAA interruptions. A narrower locus definition of hg38 chr12:132062548-132062611 has also been used to describe this locus and results in a differently described pathogenic range [@doi:10.1101/2025.01.06.631535]. Disease link was proposed by Danzi et al [@doi:10.1101/2025.01.06.631535]. Family 1 (father and daughter) had a longest pure tract of 56-58 repeats with the structure (CAG)6(CAA)2(CAG)46-58(CAA)1(CAG)4(CAA)(CAG), while the son in Family 2 (mother ungenotyped) had 75 pure CAG repeats with the structure (CAG)75(CAA)(CAG), i.e. loss of several CAA interruptions.", "detection": "Long-read sequencing with targeted sanger confirmation has detected expansions in this locus [@doi:10.1101/2025.01.06.631535].", "mechanism": "Unknown", - "mechanism_detail": "Polyglutamine expansion", + "mechanism_detail": null, "year": "2026", "location_in_gene": "Exon 47", "gene_strand": "+", From e26f78d6c8081bcf37a3f000481a82e23597e2fe Mon Sep 17 00:00:00 2001 From: Harriet Dashnow Date: Fri, 14 Aug 2026 16:46:09 -0600 Subject: [PATCH 7/7] version --- CITATION.cff | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 108aa3a2..e16fd836 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,6 +1,6 @@ title: STRchive -version: 2.24.2 -date-released: "2026-07-23" +version: 2.25.0 +date-released: "2026-08-14" url: https://github.com/dashnowlab/STRchive authors: - family-names: Dashnow