Skip to content

Commit 1848be9

Browse files
Macayla-weinerhdashnow
Macayla-weiner
authored and
hdashnow
committed
MODY8_CEL added
adjust MODY CEL coordinates more MODY CEL updates including pathogenic motif
1 parent f61e589 commit 1848be9

15 files changed

+3055
-38
lines changed

‎CITATION.cff‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
title: STRchive
2-
version: 2.9.0
2+
version: 2.10.0
33
date-released: "2025-08-12"
44
url: https://github.com/dashnowlab/STRchive
55
authors:

‎data/STRchive-citations.json‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -152610,6 +152610,12 @@
152610152610
"link": "https://omim.org/entry/147791",
152611152611
"note": "WARNING: Manubot does not support url:https://omim.org/entry/147791. Skipping"
152612152612
},
152613+
{
152614+
"id": "omim:609812",
152615+
"manubot_success": false,
152616+
"link": "https://omim.org/entry/609812",
152617+
"note": "WARNING: Manubot does not support url:https://omim.org/entry/609812. Skipping"
152618+
},
152613152619
{
152614152620
"id": "omim:615945",
152615152621
"manubot_success": false,

‎data/STRchive-disease-loci.T2T-chm13.TRGT.bed‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -30,6 +30,7 @@ chr8 119495247 119495353 ID=FAME1_SAMD12;MOTIFS=TAAAA,TGAAA;STRUC=<TR>
3030
chr9 27584063 27584155 ID=FTDALS1_C9orf72;MOTIFS=GGCCCC;STRUC=<TR>
3131
chr9 81210818 81210861 ID=FRDA_FXN;MOTIFS=A,GAA;STRUC=<TR>
3232
chr9 142886568 142886595 ID=HSAN-VIII_PRDM12;MOTIFS=GCC;STRUC=<TR>
33+
chr9 145285396 145285622 ID=MODY8_CEL;MOTIFS=GGCCCCCCCCGTGCCGCCCACGGGTGACTCCGG,GGCCCCCCCGTGCCGCCCACGGGTGACTCCGG;STRUC=<TR>
3334
chr10 80695718 80695748 ID=OPML1_NUTM2B-AS1;MOTIFS=GGC;STRUC=<TR>
3435
chr11 119226662 119226696 ID=JBS_CBL;MOTIFS=CGG;STRUC=<TR>
3536
chr12 6947903 6947941 ID=DRPLA_ATN1;MOTIFS=CAG;STRUC=<TR>

‎data/STRchive-disease-loci.T2T-chm13.bed‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -31,6 +31,7 @@ chr8 119495247 119495353 FAME1_SAMD12 SAMD12 TAAAA TGAAA 105 AD Familial adult m
3131
chr9 27584063 27584155 FTDALS1_C9orf72 C9orf72 GGCCCC GGCCCC 251 AD Frontotemporal dementia (FTD) and/or amyotrophic lateral sclerosis (ALS)
3232
chr9 81210834 81210861 FRDA_FXN FXN GAA GAA 56 AR Friedreich ataxia
3333
chr9 142886568 142886595 HSAN-VIII_PRDM12 PRDM12 GCC GCC 18 AR Hereditary sensory and autonomic neuropathy type VIII
34+
chr9 145285396 145285622 MODY8_CEL CEL GGCCCCCCCCGTGCCGCCCACGGGTGACTCCGG GGCCCCCCCGTGCCGCCCACGGGTGACTCCGG 3 AD Maturity-Onset Diabetes of the Young Type 8
3435
chr10 80695718 80695748 OPML1_NUTM2B-AS1 NUTM2B-AS1 GGC GGC 161 AD Oculopharyngeal myopathy with leukoencephalopathy 1
3536
chr11 119226662 119226696 JBS_CBL CBL CGG CGG 101 AD Jacobsen syndrome (FRAX11B fragile site)
3637
chr12 6947903 6947941 DRPLA_ATN1 ATN1 CAG CAG 48 AD Dentatorubral-Pallidoluysian Atrophy

‎data/STRchive-disease-loci.hg19.TRGT.bed‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -30,6 +30,7 @@ chr8 119379051 119379157 ID=FAME1_SAMD12;MOTIFS=TAAAA,TGAAA;STRUC=<TR>
3030
chr9 27573482 27573544 ID=FTDALS1_C9orf72;MOTIFS=GGCCCC;STRUC=<TR>
3131
chr9 71652186 71652220 ID=FRDA_FXN;MOTIFS=A,GAA;STRUC=<TR>
3232
chr9 133556992 133557028 ID=HSAN-VIII_PRDM12;MOTIFS=GCC;STRUC=<TR>
33+
chr9 135946627 135946886 ID=MODY8_CEL;MOTIFS=GGCCCCCCCCGTGCCGCCCACGGGTGACTCCGG,GGCCCCCCCGTGCCGCCCACGGGTGACTCCGG;STRUC=<TR>
3334
chr10 81586139 81586160 ID=OPML1_NUTM2B-AS1;MOTIFS=GGC;STRUC=<TR>
3435
chr11 119076999 119077033 ID=JBS_CBL;MOTIFS=CGG;STRUC=<TR>
3536
chr12 7045879 7045938 ID=DRPLA_ATN1;MOTIFS=CAG;STRUC=<TR>

‎data/STRchive-disease-loci.hg19.bed‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -31,6 +31,7 @@ chr8 119379051 119379157 FAME1_SAMD12 SAMD12 TAAAA TGAAA 105 AD Familial adult m
3131
chr9 27573482 27573544 FTDALS1_C9orf72 C9orf72 GGCCCC GGCCCC 251 AD Frontotemporal dementia (FTD) and/or amyotrophic lateral sclerosis (ALS)
3232
chr9 71652202 71652220 FRDA_FXN FXN GAA GAA 56 AR Friedreich ataxia
3333
chr9 133556992 133557028 HSAN-VIII_PRDM12 PRDM12 GCC GCC 18 AR Hereditary sensory and autonomic neuropathy type VIII
34+
chr9 135946627 135946886 MODY8_CEL CEL GGCCCCCCCCGTGCCGCCCACGGGTGACTCCGG GGCCCCCCCGTGCCGCCCACGGGTGACTCCGG 3 AD Maturity-Onset Diabetes of the Young Type 8
3435
chr10 81586139 81586160 OPML1_NUTM2B-AS1 NUTM2B-AS1 GGC GGC 161 AD Oculopharyngeal myopathy with leukoencephalopathy 1
3536
chr11 119076999 119077033 JBS_CBL CBL CGG CGG 101 AD Jacobsen syndrome (FRAX11B fragile site)
3637
chr12 7045879 7045938 DRPLA_ATN1 ATN1 CAG CAG 48 AD Dentatorubral-Pallidoluysian Atrophy

‎data/STRchive-disease-loci.hg38.TRGT.bed‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -30,6 +30,7 @@ chr8 118366812 118366918 ID=FAME1_SAMD12;MOTIFS=TAAAA,TGAAA;STRUC=<TR>
3030
chr9 27573484 27573546 ID=FTDALS1_C9orf72;MOTIFS=GGCCCC;STRUC=<TR>
3131
chr9 69037270 69037304 ID=FRDA_FXN;MOTIFS=A,GAA;STRUC=<TR>
3232
chr9 130681605 130681641 ID=HSAN-VIII_PRDM12;MOTIFS=GCC;STRUC=<TR>
33+
chr9 133071240 133071499 ID=MODY8_CEL;MOTIFS=GGCCCCCCCCGTGCCGCCCACGGGTGACTCCGG,GGCCCCCCCGTGCCGCCCACGGGTGACTCCGG;STRUC=<TR>
3334
chr10 79826383 79826404 ID=OPML1_NUTM2B-AS1;MOTIFS=GGC;STRUC=<TR>
3435
chr11 119206289 119206323 ID=JBS_CBL;MOTIFS=CGG;STRUC=<TR>
3536
chr12 6936716 6936775 ID=DRPLA_ATN1;MOTIFS=CAG;STRUC=<TR>

‎data/STRchive-disease-loci.hg38.bed‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -31,6 +31,7 @@ chr8 118366812 118366918 FAME1_SAMD12 SAMD12 TAAAA TGAAA 105 AD Familial adult m
3131
chr9 27573484 27573546 FTDALS1_C9orf72 C9orf72 GGCCCC GGCCCC 251 AD Frontotemporal dementia (FTD) and/or amyotrophic lateral sclerosis (ALS)
3232
chr9 69037286 69037304 FRDA_FXN FXN GAA GAA 56 AR Friedreich ataxia
3333
chr9 130681605 130681641 HSAN-VIII_PRDM12 PRDM12 GCC GCC 18 AR Hereditary sensory and autonomic neuropathy type VIII
34+
chr9 133071240 133071499 MODY8_CEL CEL GGCCCCCCCCGTGCCGCCCACGGGTGACTCCGG GGCCCCCCCGTGCCGCCCACGGGTGACTCCGG 3 AD Maturity-Onset Diabetes of the Young Type 8
3435
chr10 79826383 79826404 OPML1_NUTM2B-AS1 NUTM2B-AS1 GGC GGC 161 AD Oculopharyngeal myopathy with leukoencephalopathy 1
3536
chr11 119206289 119206323 JBS_CBL CBL CGG CGG 101 AD Jacobsen syndrome (FRAX11B fragile site)
3637
chr12 6936716 6936775 DRPLA_ATN1 ATN1 CAG CAG 48 AD Dentatorubral-Pallidoluysian Atrophy

‎data/STRchive-loci.json‎

Lines changed: 64 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1087,6 +1087,70 @@
10871087
"references": ["pmid:38467784", "pmid:7603564", "pmid:10767345", "pmid:19267933", "omim:147791", "mondo:0007838"],
10881088
"additional_literature": ["pmid:37422244", "pmid:22131879", "pmid:22084433", "pmid:16474167"]
10891089
},
1090+
{
1091+
"chrom": "chr9",
1092+
"start_hg38": 133071240,
1093+
"stop_hg38": 133071499,
1094+
"start_hg19": 135946627,
1095+
"stop_hg19": 135946886,
1096+
"start_t2t": 145285396,
1097+
"stop_t2t": 145285622,
1098+
"id": "MODY8_CEL",
1099+
"disease_id": "MODY8",
1100+
"gene_strand": "+",
1101+
"reference_motif_reference_orientation": ["GGCCCCCCCCGTGCCGCCCACGGGTGACTCCGG"],
1102+
"pathogenic_motif_reference_orientation": ["GGCCCCCCCGTGCCGCCCACGGGTGACTCCGG"],
1103+
"pathogenic_motif_gene_orientation": ["ACGGGTGACTCCGGGGCCCCCCCGTGCCGCCC"],
1104+
"benign_motif_reference_orientation": [],
1105+
"benign_motif_gene_orientation": [],
1106+
"unknown_motif_reference_orientation": [],
1107+
"unknown_motif_gene_orientation": [],
1108+
"disease": "Maturity-Onset Diabetes of the Young Type 8",
1109+
"gene": "CEL",
1110+
"flank_motif": null,
1111+
"locus_structure": "(GGCCCCCCCCGTGCCGCCCACGGGTGACTCCGG)*",
1112+
"inheritance": ["AD"],
1113+
"type": "Exonic",
1114+
"location_in_gene": "Exon 11",
1115+
"benign_min": 7,
1116+
"benign_max": 23,
1117+
"intermediate_min": null,
1118+
"intermediate_max": null,
1119+
"pathogenic_min": 3,
1120+
"pathogenic_max": 3,
1121+
"ref_copies": 7.8,
1122+
"motif_len": 33,
1123+
"age_onset": "11-17 [@pmid:19760265]",
1124+
"age_onset_min": 11,
1125+
"age_onset_max": 17,
1126+
"typ_age_onset_min": null,
1127+
"typ_age_onset_max": null,
1128+
"novel": "novel",
1129+
"mechanism": "LoF?",
1130+
"mechanism_detail": "Loss of function at the protein level is possibly a part of the molecular mechanism. Research suggests that the mutations disrupt the C-terminal protein, leading to reduced stability of the mutant lipase in vitro [@pmid:16369531].",
1131+
"source": [],
1132+
"details": "There are two types of mutations proposed, a single basepair deletion causing a frameshift mutation [@pmid:16369531; @pmid:19760265]. One of these is a (C)8 to (C)7 within the VNTR causing a motif change (this is the pathogenic motif represented here). Also, a possible contraction from 4 to 3 VNTR repeats may be pathogenic with reduced penetrance, although evidence for this is sparse [@pmid:19760265].",
1133+
"omim": ["609812"],
1134+
"prevalence": null,
1135+
"prevalence_details": "Found in individuals of Danish and Norwegian ancestry [@pmid:16369531; @pmid:19760265].",
1136+
"stripy": [],
1137+
"gnomad": [],
1138+
"genereviews": [],
1139+
"mondo": ["0012348"],
1140+
"year": "2005",
1141+
"medgen": ["342845"],
1142+
"orphanet": ["552"],
1143+
"gard": [],
1144+
"malacard": ["MTR082"],
1145+
"webstr_hg38": [],
1146+
"webstr_hg19": [],
1147+
"tr_atlas": [],
1148+
"disease_description": "Maturity-onset diabetes of the young type 8 (MODY8) is characterized by onset of diabetes before age 25 years, with slowly progressive pancreatic exocrine dysfunction, fatty replacement of pancreatic parenchyma (lipomatosis), and development of pancreatic cysts [@omim:609812]. Other types of this disease have been associated with various genes and variant types. Comorbidity has been proposed between MODY and fecal elastase deficiency (FED).",
1149+
"locus_tags": ["unknown_evidence", "contraction"],
1150+
"disease_tags": [],
1151+
"references": ["pmid:19760265", "pmid:16369531", "omim:609812"],
1152+
"additional_literature": ["pmid:40641008", "pmid:39710966", "pmid:38483348", "pmid:38473919", "pmid:38458477", "pmid:36379850", "pmid:35583610", "pmid:35215948", "pmid:35156195", "pmid:35082198", "pmid:34850019", "pmid:34507899", "pmid:34100900", "pmid:33862081", "pmid:27802312", "pmid:27650499", "pmid:27773618", "pmid:23395566", "pmid:21784842", "pmid:15841033"]
1153+
},
10901154
{
10911155
"chrom": "chr3",
10921156
"start_hg38": 129172576,

0 commit comments

Comments
 (0)