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Merged
hdashnow merged 7 commits into from
Aug 14, 2026
Merged

Add ep400 #508

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edb06f1
ep400 addition
gaberbz Jul 30, 2026
4eb17f2
Update data
hdashnow Aug 14, 2026
4d20f2f
suggested EP400 details rewording
hdashnow Aug 14, 2026
4957644
explain the pure vs interruptions even more and adjust the benign ran…
hdashnow Aug 14, 2026
b3656d6
Update data
hdashnow Aug 14, 2026
4c069ec
remove mech detail
gaberbz Aug 14, 2026
e26f78d
version
hdashnow Aug 14, 2026
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4 changes: 2 additions & 2 deletions CITATION.cff
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Original file line number Diff line number Diff line change
@@ -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
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330 changes: 318 additions & 12 deletions data/STRchive-citations.json
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69 changes: 68 additions & 1 deletion data/STRchive-loci.json
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Expand Up @@ -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": "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].",

@hdashnow hdashnow Aug 14, 2026

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Didn't they use ExpansionHunter on short reads as well? For controls? This was the stated reason for using the narrow locus definition I think.

@gaberbz gaberbz Aug 14, 2026

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They did in the controls. We do not know if short read is able to actually detect this expansion (from this paper at least) since the affected individuals were flagged from long read. I could put info that it is useful for controls, though the convention for other detection fields has been about detecting the expansion. What do you think?

@hdashnow hdashnow Aug 14, 2026

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If it's not in the other loci, I think it's probably fine to skip it.

"mechanism": "Unknown",
"mechanism_detail": null,
"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": 19,
"benign_max": 39,
"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",
Expand Down Expand Up @@ -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,
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed
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Expand Up @@ -39,6 +39,7 @@ chr12 6947903 6947941 ID=DRPLA_ATN1;MOTIFS=CAG;STRUC=<TR>
chr12 50468095 50468118 ID=FRA12A_DIP2B;MOTIFS=CGG;STRUC=<TR>
chr12 111575873 111575940 ID=SCA2_ATXN2;MOTIFS=CTG;STRUC=<TR>
chr12 123532573 123532603 ID=OPDM4_RILPL1;MOTIFS=CGG;STRUC=<TR>
chr12 132111361 132111451 ID=SCA_EP400;MOTIFS=CAG;STRUC=<TR>
chr13 69361213 69361270 ID=SCA8_ATXN8OS;MOTIFS=CTA,CTG;STRUC=<TR>
chr13 99196358 99196404 ID=HPE5_ZIC2;MOTIFS=GCN;STRUC=<TR>
chr13 101377549 101377792 ID=SCA27B_FGF14;MOTIFS=AAG,GAA,AGG,CAG;STRUC=<TR>
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.T2T-chm13.general.bed
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Expand Up @@ -40,6 +40,7 @@ chr12 6947903 6947941 DRPLA_ATN1 ATN1 CAG CAG 48 AD Dentatorubral-Pallidoluysian
chr12 50468095 50468118 FRA12A_DIP2B DIP2B CGG CGG 273 AD Intellectual developmental disorder, FRA12A type
chr12 111575873 111575940 SCA2_ATXN2 ATXN2 CTG CTG 35 AD,AR Spinocerebellar ataxia type 2
chr12 123532573 123532603 OPDM4_RILPL1 RILPL1 CGG CGG 120 AD Oculopharyngodistal myopathy type 4
chr12 132111361 132111451 SCA_EP400 EP400 CAG CAG 71 AD Spinocerebellar ataxia
chr13 69361243 69361270 SCA8_ATXN8OS ATXN8OS CTG CTG 71 AD Spinocerebellar ataxia type 8
chr13 99196358 99196404 HPE5_ZIC2 ZIC2 GCN GCN 25 AD Holoprosencephaly-5
chr13 101377549 101377792 SCA27B_FGF14 FGF14 GAA AAG 320 AD Spinocerebellar ataxia 27B
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.T2T-chm13.longTR.bed
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Expand Up @@ -39,6 +39,7 @@ chr12 6947904 6947941 CAG DRPLA_ATN1
chr12 50468096 50468118 CGG FRA12A_DIP2B
chr12 111575874 111575940 CTG SCA2_ATXN2
chr12 123532574 123532603 CGG OPDM4_RILPL1
chr12 132111362 132111451 CAG SCA_EP400
chr13 69361244 69361270 CTG SCA8_ATXN8OS
chr13 99196359 99196404 GCN HPE5_ZIC2
chr13 101377550 101377792 AAG,AGG,CAG,GAA SCA27B_FGF14
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.T2T-chm13.straglr.bed
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Expand Up @@ -43,6 +43,7 @@ chr12 6947903 6947941 CAG DRPLA_ATN1 DRPLA_ATN1
chr12 50468095 50468118 CGG FRA12A_DIP2B FRA12A_DIP2B
chr12 111575873 111575940 CTG SCA2_ATXN2 SCA2_ATXN2
chr12 123532573 123532603 CGG OPDM4_RILPL1 OPDM4_RILPL1
chr12 132111361 132111451 CAG SCA_EP400 SCA_EP400
chr13 69361213 69361243 CTA SCA8_ATXN8OS SCA8_ATXN8OS_CTA
chr13 69361243 69361270 CTG SCA8_ATXN8OS SCA8_ATXN8OS
chr13 99196358 99196404 GCN HPE5_ZIC2 HPE5_ZIC2
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13 changes: 13 additions & 0 deletions data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json
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Expand Up @@ -530,6 +530,19 @@
"PathologicMin": 120,
"Gene": "RILPL1"
},
{
"LocusId": "SCA_EP400",
"ReferenceRegion": "chr12:132111361-132111451",
"LocusStructure": "(CAG)*",
"VariantType": "Repeat",
"HGNCId": null,
"InheritanceMode": ["AD"],
"DisplayRU": "CAG",
"Disease": "SCA",
"NormalMax": 39,
"PathologicMin": 71,
"Gene": "EP400"
},
{
"LocusId": "SCA8_ATXN8OS",
"ReferenceRegion": ["chr13:69361213-69361243", "chr13:69361243-69361270"],
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.hg19.TRGT.bed
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Expand Up @@ -39,6 +39,7 @@ chr12 7045879 7045938 ID=DRPLA_ATN1;MOTIFS=CAG;STRUC=<TR>
chr12 50898784 50898807 ID=FRA12A_DIP2B;MOTIFS=CGG;STRUC=<TR>
chr12 112036753 112036823 ID=SCA2_ATXN2;MOTIFS=CTG;STRUC=<TR>
chr12 124018267 124018297 ID=OPDM4_RILPL1;MOTIFS=CGG;STRUC=<TR>
chr12 132547069 132547156 ID=SCA_EP400;MOTIFS=CAG;STRUC=<TR>
chr13 70713485 70713561 ID=SCA8_ATXN8OS;MOTIFS=CTA,CTG;STRUC=<TR>
chr13 100637702 100637748 ID=HPE5_ZIC2;MOTIFS=GCN;STRUC=<TR>
chr13 102813924 102814076 ID=SCA27B_FGF14;MOTIFS=AAG,GAA,AGG,CAG;STRUC=<TR>
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.hg19.atarva.bed
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Expand Up @@ -46,6 +46,7 @@ chr12 7045879 7045938 CAG 3 DRPLA_ATN1
chr12 50898784 50898807 CGG 3 FRA12A_DIP2B
chr12 112036753 112036823 CTG 3 SCA2_ATXN2
chr12 124018267 124018297 CGG 3 OPDM4_RILPL1
chr12 132547069 132547156 CAG 3 SCA_EP400
chr13 70713485 70713515 CTA 3 SCA8_ATXN8OS_flank
chr13 70713515 70713561 CTG 3 SCA8_ATXN8OS
chr13 100637702 100637748 GCN 3 HPE5_ZIC2
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.hg19.general.bed
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Expand Up @@ -40,6 +40,7 @@ chr12 7045879 7045938 DRPLA_ATN1 ATN1 CAG CAG 48 AD Dentatorubral-Pallidoluysian
chr12 50898784 50898807 FRA12A_DIP2B DIP2B CGG CGG 273 AD Intellectual developmental disorder, FRA12A type
chr12 112036753 112036823 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
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.hg19.longTR.bed
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.hg19.straglr.bed
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Expand Up @@ -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
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13 changes: 13 additions & 0 deletions data/catalogs/STRchive-disease-loci.hg19.stranger.json
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Expand Up @@ -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": 39,
"PathologicMin": 71,
"Gene": "EP400"
},
{
"LocusId": "SCA8_ATXN8OS",
"ReferenceRegion": ["chr13:70713485-70713515", "chr13:70713515-70713561"],
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.hg38.TRGT.bed
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Expand Up @@ -39,6 +39,7 @@ chr12 6936716 6936775 ID=DRPLA_ATN1;MOTIFS=CAG;STRUC=<TR>
chr12 50505001 50505024 ID=FRA12A_DIP2B;MOTIFS=CGG;STRUC=<TR>
chr12 111598949 111599019 ID=SCA2_ATXN2;MOTIFS=CTG;STRUC=<TR>
chr12 123533720 123533750 ID=OPDM4_RILPL1;MOTIFS=CGG;STRUC=<TR>
chr12 132062524 132062611 ID=SCA_EP400;MOTIFS=CAG;STRUC=<TR>
chr13 70139353 70139429 ID=SCA8_ATXN8OS;MOTIFS=CTA,CTG;STRUC=<TR>
chr13 99985448 99985494 ID=HPE5_ZIC2;MOTIFS=GCN;STRUC=<TR>
chr13 102161574 102161726 ID=SCA27B_FGF14;MOTIFS=AAG,GAA,AGG,CAG;STRUC=<TR>
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.hg38.atarva.bed
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Expand Up @@ -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
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Binary file modified data/catalogs/STRchive-disease-loci.hg38.atarva.bed.gz
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.hg38.general.bed
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.hg38.longTR.bed
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions data/catalogs/STRchive-disease-loci.hg38.straglr.bed
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Expand Up @@ -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
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13 changes: 13 additions & 0 deletions data/catalogs/STRchive-disease-loci.hg38.stranger.json
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Expand Up @@ -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": 39,
"PathologicMin": 71,
"Gene": "EP400"
},
{
"LocusId": "SCA8_ATXN8OS",
"ReferenceRegion": ["chr13:70139353-70139383", "chr13:70139383-70139429"],
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