diff --git a/data/STRchive-disease-loci.T2T-chm13.bed b/data/STRchive-disease-loci.T2T-chm13.bed index 58e8e92b..46dcf6ff 100644 --- a/data/STRchive-disease-loci.T2T-chm13.bed +++ b/data/STRchive-disease-loci.T2T-chm13.bed @@ -1,6 +1,6 @@ #chrom start stop id gene reference_motif_reference_orientation pathogenic_motif_reference_orientation pathogenic_min inheritance disease chr1 870158 870178 HMNR7_VWA1 VWA1 GGCGCGGAGC GGCGCGGAGC 1 AR Neuronopathy, distal hereditary motor, autosomal recessive 7 -chr1 57245935 57245973 SCA37_DAB1 DAB1 AAAAT GAAAT 31 AD Spinocerebellar Ataxia Type 37 +chr1 57245935 57245973 SCA37_DAB1 DAB1 AAAAT GAAAT 31 AD Spinocerebellar ataxia type 37 chr1 94266544 94266567 OPDM_ABCD3 ABCD3 GCC GCC 118 AD Oculopharyngodistal myopathy chr1 148519695 148519738 NIID_NOTCH2NLC NOTCH2NLC GGC GGC 66 AD Neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype chr1 154328121 154330802 ADTKD_MUC1 MUC1 GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG GGCTNNGGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG 8 AD Autosomal dominant tubulointerstitial kidney disease @@ -9,8 +9,8 @@ chr2 96703674 96703732 FAME2_STARD7 STARD7 AAAAT AAATG 274 AD Familial adult myo chr2 100563685 100563738 FRA2A_AFF3 AFF3 GCC GCC 300 AD Intellectual disability associated with fragile site FRA2A chr2 176581179 176581224 SD5_HOXD13 HOXD13 GCN GCN 22 AD Syndactyly chr2 191369982 191370024 GDPAG_GLS GLS GCA GCA 680 AR Glutaminase deficiency -chr3 63956302 63956333 SCA7_ATXN7 ATXN7 CAG CAG 37 AD Spinocerebellar Ataxia Type 7 -chr3 131917482 131917557 DM2_CNBP CNBP CAGG CAGG 75 AD Myotonic Dystrophy Type 2 +chr3 63956302 63956333 SCA7_ATXN7 ATXN7 CAG CAG 37 AD Spinocerebellar ataxia type 7 +chr3 131917482 131917557 DM2_CNBP CNBP CAGG CAGG 75 AD Myotonic dystrophy type 2 chr3 141687011 141687054 BPES_FOXL2 FOXL2 NGC NGC 15 AD,AR Blepharophimosis, epicanthus inversus, and ptosis chr3 186521667 186521706 FAME4_YEATS2 YEATS2 TTTTA TTTCA 1000 AD Familial adult myoclonic epilepsy 4 chr4 3073603 3073687 HD_HTT HTT CAG CAG 40 AD Huntington disease @@ -19,7 +19,7 @@ chr4 41719745 41719805 CCHS_PHOX2B PHOX2B GCN GCN 26 AD Congenital central hypov chr4 162693303 162693405 FAME7_RAPGEF2 RAPGEF2 TTTTA TTTCA 60 AD Familial adult myoclonic epilepsy type 7 chr5 10295525 10295593 FAME3_MARCHF6 MARCHF6 TTTTA TTTCA 791 AD Familial adult myoclonic epilepsy type 3 chr5 147414733 147414780 SCA12_PPP2R2B PPP2R2B GCT GCT 51 AD Spinocerebellar ataxia type 12 -chr6 16200188 16200282 SCA1_ATXN1 ATXN1 CTG CTG 39 AD Spinocerebellar Ataxia Type 1 +chr6 16200188 16200282 SCA1_ATXN1 ATXN1 CTG CTG 39 AD Spinocerebellar ataxia type 1 chr6 45257567 45257618 CCD_RUNX2 RUNX2 GCN GCN 20 AD Cleidocranial dysplasia chr6 171935458 171935569 SCA17_TBP TBP GCA GCA 49 AD Spinocerebellar ataxia type 17 chr7 27335684 27335720 HFG_HOXA13-III HOXA13 NGC NGC 22 AD Hand-foot-genital syndrome 3 @@ -35,34 +35,34 @@ chr10 80695718 80695748 OPML1_NUTM2B-AS1 NUTM2B-AS1 GGC GGC 161 AD Oculopharynge chr11 119226662 119226696 JBS_CBL CBL CGG CGG 101 AD Jacobsen syndrome (FRAX11B fragile site) chr12 6947903 6947941 DRPLA_ATN1 ATN1 CAG CAG 48 AD Dentatorubral-Pallidoluysian Atrophy chr12 50468095 50468118 FRA12A_DIP2B DIP2B GGC GGC 273 AD Intellectual developmental disorder, FRA12A type -chr12 111575873 111575940 SCA2_ATXN2 ATXN2 CTG CTG 35 AD,AR Spinocerebellar Ataxia Type 2 +chr12 111575873 111575940 SCA2_ATXN2 ATXN2 CTG CTG 35 AD,AR Spinocerebellar ataxia type 2 chr12 123532573 123532603 OPDM4_RILPL1 RILPL1 GGC GGC 120 AD Oculopharyngodistal myopathy type 4 -chr13 69361243 69361270 SCA8_ATXN8OS ATXN8OS CTG CTG 71 AD Spinocerebellar Ataxia Type 8 +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 GAA 320 AD Spinocerebellar ataxia 27B chr14 17522488 17522519 OPMD_PABPN1 PABPN1 GCN GCN 12 AD,AR Oculopharyngeal muscular dystrophy -chr14 86300519 86300603 SCA3_ATXN3 ATXN3 CTG CTG 60 AD Spinocerebellar Ataxia Type 3/Machado-Joseph Disease +chr14 86300519 86300603 SCA3_ATXN3 ATXN3 CTG CTG 60 AD Spinocerebellar ataxia type 3/Machado-Joseph disease chr15 20458510 20458536 ALS1_NIPA1 NIPA1 GCG GCG 11 AD Amyotrophic lateral sclerosis chr15 86324038 86324057 pre-MIR7-2_CHNG3 pre-MIR7-2 TTTG TTTG 3 AD Nongoitrous congenital hypothyroidism-3 chr15 87088411 87088452 CPEO_POLG POLG GCT GCT None Progressive external ophthalmoplegia, Parkinson's disease chr16 17477909 17478002 DBQD2_XYLT1 XYLT1 GCC GCC 72 AR Baratela-Scott Syndrome/Desbuquois dysplasia 2 chr16 24890366 24890430 FAME6_TNRC6A TNRC6A TTTTA TTTCA 1100 AD Familial adult myoclonic epilepsy type 6 -chr16 72284666 72284761 SCA31_BEAN1 BEAN1 AATAA TGGAA,TAGAA 110 AD Spinocerebellar Ataxia Type 31 +chr16 72284666 72284761 SCA31_BEAN1 BEAN1 AATAA TGGAA,TAGAA 110 AD Spinocerebellar ataxia type 31 chr16 73638636 73638724 SCA_THAP11 THAP11 CAG CAG 45 AD Spinocerebellar ataxia chr16 78605502 78605569 SCA4_ZFHX3 ZFHX3 GCC GCC 46 AD Spinocerebellar ataxia 4 chr16 93675723 93675776 HDL2_JPH3 JPH3 CTG CTG 40 AD Huntington disease-like 2 chr17 17754961 17755053 FAME8_RAI1 RAI1 TTTTA TTTCA 9 AD Familial adult myoclonic epilepsy type 8 chr17 81047404 81047534 RCPS_EIF4A3 EIF4A3 CCTCGCTGTGCCGCTGCCGA CCTCGCTGTGCCGCTGCCGA 14 AR Richieri-Costa-Pereira syndrome chr18 55789233 55789288 FECD3_TCF4 TCF4 CAG CAG 51 AD Fuchs endothelial corneal dystrophy 3 -chr19 13333136 13333176 SCA6_CACNA1A CACNA1A CTG CTG 21 AD Spinocerebellar Ataxia Type 6 +chr19 13333136 13333176 SCA6_CACNA1A CACNA1A CTG CTG 21 AD Spinocerebellar ataxia type 6 chr19 14622655 14622692 OPDM2_GIPC1 GIPC1 CCG CCG 73 AD Oculopharyngodistal myopathy chr19 18921630 18921645 EDM1-PSACH_COMP COMP GTC GTC 6 AD Multiple epiphyseal dysplasia, Pseudoachondroplasia -chr19 48597739 48597756 DM1_DMPK DMPK CAG CAG 50 AD Myotonic Dystrophy Type 1 +chr19 48597739 48597756 DM1_DMPK DMPK CAG CAG 50 AD Myotonic dystrophy type 1 chr20 2683189 2683230 SCA36_NOP56 NOP56 GGCCTG GGCCTG 650 AD Spinocerebellar ataxia type 36 chr20 4738633 4738705 CJD_PRNP PRNP GGTGGTGGCTGGGGGCAGCCTCAT CCTCATGGTGGTGGCTGGGGGCAG 5 AD Creutzfeldt-Jakob disease chr21 42132054 42132091 EPM1_CSTB CSTB CGCGGGGCGGGG CGCGGGGCGGGG 30 AR Progressive Myoclonic Epilepsy Type 1 (EPM1) Unverricht-Lundborg Disease (ULD) chr22 20143615 20143660 TOF_TBX1 TBX1 GCN GCN 25 AD Tetralogy of Fallot -chr22 46280059 46280134 SCA10_ATXN10 ATXN10 ATTCT ATTCT 800 AD Spinocerebellar Ataxia Type 10 +chr22 46280059 46280134 SCA10_ATXN10 ATXN10 ATTCT ATTCT 800 AD Spinocerebellar ataxia type 10 chrX 24597766 24597802 PRTS_ARX ARX NGC NGC 20 XR Partington syndrome chrX 24597886 24597934 EIEE1_ARX ARX NGC NGC 17 XR Early-infantile epileptic encephalopathy chrX 30882677 30882743 DMD_DMD DMD TTC TTC 59 XR Duchenne muscular dystrophy diff --git a/data/STRchive-disease-loci.hg19.bed b/data/STRchive-disease-loci.hg19.bed index 460a2e67..cbcfe6ac 100644 --- a/data/STRchive-disease-loci.hg19.bed +++ b/data/STRchive-disease-loci.hg19.bed @@ -1,6 +1,6 @@ #chrom start stop id gene reference_motif_reference_orientation pathogenic_motif_reference_orientation pathogenic_min inheritance disease chr1 1371178 1371198 HMNR7_VWA1 VWA1 GGCGCGGAGC GGCGCGGAGC 1 AR Neuronopathy, distal hereditary motor, autosomal recessive 7 -chr1 57832715 57832793 SCA37_DAB1 DAB1 AAAAT GAAAT 31 AD Spinocerebellar Ataxia Type 37 +chr1 57832715 57832793 SCA37_DAB1 DAB1 AAAAT GAAAT 31 AD Spinocerebellar ataxia type 37 chr1 94883977 94884000 OPDM_ABCD3 ABCD3 GCC GCC 118 AD Oculopharyngodistal myopathy chr1 145209323 145209354 NIID_NOTCH2NLC NOTCH2NLC GGC GGC 66 AD Neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype chr1 155160981 155162030 ADTKD_MUC1 MUC1 GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG GGCTNNGGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG 8 AD Autosomal dominant tubulointerstitial kidney disease @@ -9,8 +9,8 @@ chr2 96862804 96862862 FAME2_STARD7 STARD7 AAAAT AAATG 274 AD Familial adult myo chr2 100721260 100721286 FRA2A_AFF3 AFF3 GCC GCC 300 AD Intellectual disability associated with fragile site FRA2A chr2 176957786 176957831 SD5_HOXD13 HOXD13 GCN GCN 22 AD Syndactyly chr2 191745598 191745646 GDPAG_GLS GLS GCA GCA 680 AR Glutaminase deficiency -chr3 63898360 63898391 SCA7_ATXN7 ATXN7 CAG CAG 37 AD Spinocerebellar Ataxia Type 7 -chr3 128891419 128891499 DM2_CNBP CNBP CAGG CAGG 75 AD Myotonic Dystrophy Type 2 +chr3 63898360 63898391 SCA7_ATXN7 ATXN7 CAG CAG 37 AD Spinocerebellar ataxia type 7 +chr3 128891419 128891499 DM2_CNBP CNBP CAGG CAGG 75 AD Myotonic dystrophy type 2 chr3 138664861 138664904 BPES_FOXL2 FOXL2 NGC NGC 15 AD,AR Blepharophimosis, epicanthus inversus, and ptosis chr3 183429975 183430014 FAME4_YEATS2 YEATS2 TTTTA TTTCA 1000 AD Familial adult myoclonic epilepsy 4 chr4 3076603 3076660 HD_HTT HTT CAG CAG 40 AD Huntington disease @@ -19,7 +19,7 @@ chr4 41747989 41748049 CCHS_PHOX2B PHOX2B GCN GCN 26 AD Congenital central hypov chr4 160263678 160263770 FAME7_RAPGEF2 RAPGEF2 TTTTA TTTCA 60 AD Familial adult myoclonic epilepsy type 7 chr5 10356455 10356523 FAME3_MARCHF6 MARCHF6 TTTTA TTTCA 791 AD Familial adult myoclonic epilepsy type 3 chr5 146258290 146258322 SCA12_PPP2R2B PPP2R2B GCT GCT 51 AD Spinocerebellar ataxia type 12 -chr6 16327864 16327955 SCA1_ATXN1 ATXN1 CTG CTG 39 AD Spinocerebellar Ataxia Type 1 +chr6 16327864 16327955 SCA1_ATXN1 ATXN1 CTG CTG 39 AD Spinocerebellar ataxia type 1 chr6 45390487 45390538 CCD_RUNX2 RUNX2 GCN GCN 20 AD Cleidocranial dysplasia chr6 170870994 170871105 SCA17_TBP TBP GCA GCA 49 AD Spinocerebellar ataxia type 17 chr7 27239297 27239351 HFG_HOXA13-III HOXA13 NGC NGC 22 AD Hand-foot-genital syndrome 3 @@ -35,34 +35,34 @@ chr10 81586139 81586160 OPML1_NUTM2B-AS1 NUTM2B-AS1 GGC GGC 161 AD Oculopharynge chr11 119076999 119077033 JBS_CBL CBL CGG CGG 101 AD Jacobsen syndrome (FRAX11B fragile site) chr12 7045879 7045938 DRPLA_ATN1 ATN1 CAG CAG 48 AD Dentatorubral-Pallidoluysian Atrophy chr12 50898784 50898807 FRA12A_DIP2B DIP2B GGC GGC 273 AD Intellectual developmental disorder, FRA12A type -chr12 112036753 112036823 SCA2_ATXN2 ATXN2 CTG CTG 35 AD,AR Spinocerebellar Ataxia Type 2 +chr12 112036753 112036823 SCA2_ATXN2 ATXN2 CTG CTG 35 AD,AR Spinocerebellar ataxia type 2 chr12 124018267 124018297 OPDM4_RILPL1 RILPL1 GGC GGC 120 AD Oculopharyngodistal myopathy type 4 -chr13 70713515 70713561 SCA8_ATXN8OS ATXN8OS CTG CTG 71 AD Spinocerebellar Ataxia Type 8 +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 GAA 320 AD Spinocerebellar ataxia 27B chr14 23790681 23790712 OPMD_PABPN1 PABPN1 GCN GCN 12 AD,AR Oculopharyngeal muscular dystrophy -chr14 92537354 92537396 SCA3_ATXN3 ATXN3 CTG CTG 60 AD Spinocerebellar Ataxia Type 3/Machado-Joseph Disease +chr14 92537354 92537396 SCA3_ATXN3 ATXN3 CTG CTG 60 AD Spinocerebellar ataxia type 3/Machado-Joseph disease chr15 23086363 23086389 ALS1_NIPA1 NIPA1 GCG GCG 11 AD Amyotrophic lateral sclerosis chr15 89112664 89112683 pre-MIR7-2_CHNG3 pre-MIR7-2 TTTG TTTG 3 AD Nongoitrous congenital hypothyroidism-3 chr15 89876819 89876860 CPEO_POLG POLG GCT GCT None Progressive external ophthalmoplegia, Parkinson's disease chr16 17564764 17564779 DBQD2_XYLT1 XYLT1 GCC GCC 72 AR Baratela-Scott Syndrome/Desbuquois dysplasia 2 chr16 24624759 24624853 FAME6_TNRC6A TNRC6A TTTTA TTTCA 1100 AD Familial adult myoclonic epilepsy type 6 -chr16 66524299 66524369 SCA31_BEAN1 BEAN1 AATAA TGGAA,TAGAA 110 AD Spinocerebellar Ataxia Type 31 +chr16 66524299 66524369 SCA31_BEAN1 BEAN1 AATAA TGGAA,TAGAA 110 AD Spinocerebellar ataxia type 31 chr16 67876765 67876853 SCA_THAP11 THAP11 CAG CAG 45 AD Spinocerebellar ataxia chr16 72821593 72821657 SCA4_ZFHX3 ZFHX3 GCC GCC 46 AD Spinocerebellar ataxia 4 chr16 87637888 87637935 HDL2_JPH3 JPH3 CTG CTG 40 AD Huntington disease-like 2 chr17 17711672 17711774 FAME8_RAI1 RAI1 TTTTA TTTCA 9 AD Familial adult myoclonic epilepsy type 8 chr17 78120808 78120938 RCPS_EIF4A3 EIF4A3 CCTCGCTGTGCCGCTGCCGA CCTCGCTGTGCCGCTGCCGA 14 AR Richieri-Costa-Pereira syndrome chr18 53253384 53253460 FECD3_TCF4 TCF4 CAG CAG 51 AD Fuchs endothelial corneal dystrophy 3 -chr19 13318672 13318712 SCA6_CACNA1A CACNA1A CTG CTG 21 AD Spinocerebellar Ataxia Type 6 +chr19 13318672 13318712 SCA6_CACNA1A CACNA1A CTG CTG 21 AD Spinocerebellar ataxia type 6 chr19 14606853 14606887 OPDM2_GIPC1 GIPC1 CCG CCG 73 AD Oculopharyngodistal myopathy chr19 18896844 18896860 EDM1-PSACH_COMP COMP GTC GTC 6 AD Multiple epiphyseal dysplasia, Pseudoachondroplasia -chr19 46273462 46273524 DM1_DMPK DMPK CAG CAG 50 AD Myotonic Dystrophy Type 1 +chr19 46273462 46273524 DM1_DMPK DMPK CAG CAG 50 AD Myotonic dystrophy type 1 chr20 2633378 2633403 SCA36_NOP56 NOP56 GGCCTG GGCCTG 650 AD Spinocerebellar ataxia type 36 chr20 4680043 4680139 CJD_PRNP PRNP GGTGGTGGCTGGGGGCAGCCTCAT CCTCATGGTGGTGGCTGGGGGCAG 5 AD Creutzfeldt-Jakob disease chr21 45196323 45196360 EPM1_CSTB CSTB CGCGGGGCGGGG CGCGGGGCGGGG 30 AR Progressive Myoclonic Epilepsy Type 1 (EPM1) Unverricht-Lundborg Disease (ULD) chr22 19754285 19754330 TOF_TBX1 TBX1 GCN GCN 25 AD Tetralogy of Fallot -chr22 46191234 46191304 SCA10_ATXN10 ATXN10 ATTCT ATTCT 800 AD Spinocerebellar Ataxia Type 10 +chr22 46191234 46191304 SCA10_ATXN10 ATXN10 ATTCT ATTCT 800 AD Spinocerebellar ataxia type 10 chrX 25031646 25031682 PRTS_ARX ARX NGC NGC 20 XR Partington syndrome chrX 25031766 25031814 EIEE1_ARX ARX NGC NGC 17 XR Early-infantile epileptic encephalopathy chrX 31302674 31302722 DMD_DMD DMD TTC TTC 59 XR Duchenne muscular dystrophy diff --git a/data/STRchive-disease-loci.hg38.bed b/data/STRchive-disease-loci.hg38.bed index 3b13d5eb..24483d10 100644 --- a/data/STRchive-disease-loci.hg38.bed +++ b/data/STRchive-disease-loci.hg38.bed @@ -1,6 +1,6 @@ #chrom start stop id gene reference_motif_reference_orientation pathogenic_motif_reference_orientation pathogenic_min inheritance disease chr1 1435798 1435818 HMNR7_VWA1 VWA1 GGCGCGGAGC GGCGCGGAGC 1 AR Neuronopathy, distal hereditary motor, autosomal recessive 7 -chr1 57367043 57367121 SCA37_DAB1 DAB1 AAAAT GAAAT 31 AD Spinocerebellar Ataxia Type 37 +chr1 57367043 57367121 SCA37_DAB1 DAB1 AAAAT GAAAT 31 AD Spinocerebellar ataxia type 37 chr1 94418421 94418444 OPDM_ABCD3 ABCD3 GCC GCC 118 AD Oculopharyngodistal myopathy chr1 149390802 149390842 NIID_NOTCH2NLC NOTCH2NLC GGC GGC 66 AD Neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype chr1 155188505 155192239 ADTKD_MUC1 MUC1 GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG GGCTNNGGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG 8 AD Autosomal dominant tubulointerstitial kidney disease @@ -9,8 +9,8 @@ chr2 96197066 96197124 FAME2_STARD7 STARD7 AAAAT AAATG 274 AD Familial adult myo chr2 100104798 100104824 FRA2A_AFF3 AFF3 GCC GCC 300 AD Intellectual disability associated with fragile site FRA2A chr2 176093058 176093103 SD5_HOXD13 HOXD13 GCN GCN 22 AD Syndactyly chr2 190880872 190880920 GDPAG_GLS GLS GCA GCA 680 AR Glutaminase deficiency -chr3 63912684 63912715 SCA7_ATXN7 ATXN7 CAG CAG 37 AD Spinocerebellar Ataxia Type 7 -chr3 129172576 129172656 DM2_CNBP CNBP CAGG CAGG 75 AD Myotonic Dystrophy Type 2 +chr3 63912684 63912715 SCA7_ATXN7 ATXN7 CAG CAG 37 AD Spinocerebellar ataxia type 7 +chr3 129172576 129172656 DM2_CNBP CNBP CAGG CAGG 75 AD Myotonic dystrophy type 2 chr3 138946019 138946062 BPES_FOXL2 FOXL2 NGC NGC 15 AD,AR Blepharophimosis, epicanthus inversus, and ptosis chr3 183712187 183712226 FAME4_YEATS2 YEATS2 TTTTA TTTCA 1000 AD Familial adult myoclonic epilepsy 4 chr4 3074876 3074933 HD_HTT HTT CAG CAG 40 AD Huntington disease @@ -19,7 +19,7 @@ chr4 41745972 41746032 CCHS_PHOX2B PHOX2B GCN GCN 26 AD Congenital central hypov chr4 159342526 159342618 FAME7_RAPGEF2 RAPGEF2 TTTTA TTTCA 60 AD Familial adult myoclonic epilepsy type 7 chr5 10356343 10356411 FAME3_MARCHF6 MARCHF6 TTTTA TTTCA 791 AD Familial adult myoclonic epilepsy type 3 chr5 146878727 146878759 SCA12_PPP2R2B PPP2R2B GCT GCT 51 AD Spinocerebellar ataxia type 12 -chr6 16327633 16327724 SCA1_ATXN1 ATXN1 CTG CTG 39 AD Spinocerebellar Ataxia Type 1 +chr6 16327633 16327724 SCA1_ATXN1 ATXN1 CTG CTG 39 AD Spinocerebellar ataxia type 1 chr6 45422750 45422801 CCD_RUNX2 RUNX2 GCN GCN 20 AD Cleidocranial dysplasia chr6 170561906 170562017 SCA17_TBP TBP GCA GCA 49 AD Spinocerebellar ataxia type 17 chr7 27199678 27199732 HFG_HOXA13-III HOXA13 NGC NGC 22 AD Hand-foot-genital syndrome 3 @@ -35,34 +35,34 @@ chr10 79826383 79826404 OPML1_NUTM2B-AS1 NUTM2B-AS1 GGC GGC 161 AD Oculopharynge chr11 119206289 119206323 JBS_CBL CBL CGG CGG 101 AD Jacobsen syndrome (FRAX11B fragile site) chr12 6936716 6936775 DRPLA_ATN1 ATN1 CAG CAG 48 AD Dentatorubral-Pallidoluysian Atrophy chr12 50505001 50505024 FRA12A_DIP2B DIP2B GGC GGC 273 AD Intellectual developmental disorder, FRA12A type -chr12 111598949 111599019 SCA2_ATXN2 ATXN2 CTG CTG 35 AD,AR Spinocerebellar Ataxia Type 2 +chr12 111598949 111599019 SCA2_ATXN2 ATXN2 CTG CTG 35 AD,AR Spinocerebellar ataxia type 2 chr12 123533720 123533750 OPDM4_RILPL1 RILPL1 GGC GGC 120 AD Oculopharyngodistal myopathy type 4 -chr13 70139383 70139429 SCA8_ATXN8OS ATXN8OS CTG CTG 71 AD Spinocerebellar Ataxia Type 8 +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 GAA 320 AD Spinocerebellar ataxia 27B chr14 23321472 23321503 OPMD_PABPN1 PABPN1 GCN GCN 12 AD,AR Oculopharyngeal muscular dystrophy -chr14 92071010 92071052 SCA3_ATXN3 ATXN3 CTG CTG 60 AD Spinocerebellar Ataxia Type 3/Machado-Joseph Disease +chr14 92071010 92071052 SCA3_ATXN3 ATXN3 CTG CTG 60 AD Spinocerebellar ataxia type 3/Machado-Joseph disease chr15 22786677 22786703 ALS1_NIPA1 NIPA1 GCG GCG 11 AD Amyotrophic lateral sclerosis chr15 88569433 88569452 pre-MIR7-2_CHNG3 pre-MIR7-2 TTTG TTTG 3 AD Nongoitrous congenital hypothyroidism-3 chr15 89333588 89333629 CPEO_POLG POLG GCT GCT None Progressive external ophthalmoplegia, Parkinson's disease chr16 17470907 17470922 DBQD2_XYLT1 XYLT1 GCC GCC 72 AR Baratela-Scott Syndrome/Desbuquois dysplasia 2 chr16 24613438 24613532 FAME6_TNRC6A TNRC6A TTTTA TTTCA 1100 AD Familial adult myoclonic epilepsy type 6 -chr16 66490396 66490466 SCA31_BEAN1 BEAN1 AATAA TGGAA,TAGAA 110 AD Spinocerebellar Ataxia Type 31 +chr16 66490396 66490466 SCA31_BEAN1 BEAN1 AATAA TGGAA,TAGAA 110 AD Spinocerebellar ataxia type 31 chr16 67842862 67842950 SCA_THAP11 THAP11 CAG CAG 45 AD Spinocerebellar ataxia chr16 72787694 72787758 SCA4_ZFHX3 ZFHX3 GCC GCC 46 AD Spinocerebellar ataxia 4 chr16 87604282 87604329 HDL2_JPH3 JPH3 CTG CTG 40 AD Huntington disease-like 2 chr17 17808358 17808460 FAME8_RAI1 RAI1 TTTTA TTTCA 9 AD Familial adult myoclonic epilepsy type 8 chr17 80147009 80147139 RCPS_EIF4A3 EIF4A3 CCTCGCTGTGCCGCTGCCGA CCTCGCTGTGCCGCTGCCGA 14 AR Richieri-Costa-Pereira syndrome chr18 55586153 55586229 FECD3_TCF4 TCF4 CAG CAG 51 AD Fuchs endothelial corneal dystrophy 3 -chr19 13207858 13207898 SCA6_CACNA1A CACNA1A CTG CTG 21 AD Spinocerebellar Ataxia Type 6 +chr19 13207858 13207898 SCA6_CACNA1A CACNA1A CTG CTG 21 AD Spinocerebellar ataxia type 6 chr19 14496041 14496075 OPDM2_GIPC1 GIPC1 CCG CCG 73 AD Oculopharyngodistal myopathy chr19 18786034 18786050 EDM1-PSACH_COMP COMP GTC GTC 6 AD Multiple epiphyseal dysplasia, Pseudoachondroplasia -chr19 45770204 45770266 DM1_DMPK DMPK CAG CAG 50 AD Myotonic Dystrophy Type 1 +chr19 45770204 45770266 DM1_DMPK DMPK CAG CAG 50 AD Myotonic dystrophy type 1 chr20 2652732 2652757 SCA36_NOP56 NOP56 GGCCTG GGCCTG 650 AD Spinocerebellar ataxia type 36 chr20 4699397 4699493 CJD_PRNP PRNP GGTGGTGGCTGGGGGCAGCCTCAT CCTCATGGTGGTGGCTGGGGGCAG 5 AD Creutzfeldt-Jakob disease chr21 43776442 43776479 EPM1_CSTB CSTB CGCGGGGCGGGG CGCGGGGCGGGG 30 AR Progressive Myoclonic Epilepsy Type 1 (EPM1) Unverricht-Lundborg Disease (ULD) chr22 19766762 19766807 TOF_TBX1 TBX1 GCN GCN 25 AD Tetralogy of Fallot -chr22 45795354 45795424 SCA10_ATXN10 ATXN10 ATTCT ATTCT 800 AD Spinocerebellar Ataxia Type 10 +chr22 45795354 45795424 SCA10_ATXN10 ATXN10 ATTCT ATTCT 800 AD Spinocerebellar ataxia type 10 chrX 25013529 25013565 PRTS_ARX ARX NGC NGC 20 XR Partington syndrome chrX 25013649 25013697 EIEE1_ARX ARX NGC NGC 17 XR Early-infantile epileptic encephalopathy chrX 31284557 31284605 DMD_DMD DMD TTC TTC 59 XR Duchenne muscular dystrophy diff --git a/data/STRchive-loci.json b/data/STRchive-loci.json index eae6abf4..cafaa5b3 100644 --- a/data/STRchive-loci.json +++ b/data/STRchive-loci.json @@ -465,7 +465,7 @@ "benign_motif_gene_orientation": [], "unknown_motif_reference_orientation": [], "unknown_motif_gene_orientation": [], - "disease": "Spinocerebellar Ataxia Type 1", + "disease": "Spinocerebellar ataxia type 1", "gene": "ATXN1", "flank_motif": null, "locus_structure": "(CTG)*", @@ -529,7 +529,7 @@ "benign_motif_gene_orientation": [], "unknown_motif_reference_orientation": [], "unknown_motif_gene_orientation": [], - "disease": "Spinocerebellar Ataxia Type 10", + "disease": "Spinocerebellar ataxia type 10", "gene": "ATXN10", "flank_motif": null, "locus_structure": "(ATTCT)*", @@ -593,7 +593,7 @@ "benign_motif_gene_orientation": [], "unknown_motif_reference_orientation": [], "unknown_motif_gene_orientation": [], - "disease": "Spinocerebellar Ataxia Type 2", + "disease": "Spinocerebellar ataxia type 2", "gene": "ATXN2", "flank_motif": null, "locus_structure": "(CTG)*", @@ -657,7 +657,7 @@ "benign_motif_gene_orientation": [], "unknown_motif_reference_orientation": [], "unknown_motif_gene_orientation": [], - "disease": "Spinocerebellar Ataxia Type 3/Machado-Joseph Disease", + "disease": "Spinocerebellar ataxia type 3/Machado-Joseph disease", "gene": "ATXN3", "flank_motif": null, "locus_structure": "(CTG)*", @@ -721,7 +721,7 @@ "benign_motif_gene_orientation": [], "unknown_motif_reference_orientation": [], "unknown_motif_gene_orientation": [], - "disease": "Spinocerebellar Ataxia Type 7", + "disease": "Spinocerebellar ataxia type 7", "gene": "ATXN7", "flank_motif": "(CAG)n(CCG)4", "locus_structure": "(CAG)*(CCG)+", @@ -785,7 +785,7 @@ "benign_motif_gene_orientation": [], "unknown_motif_reference_orientation": [], "unknown_motif_gene_orientation": [], - "disease": "Spinocerebellar Ataxia Type 8", + "disease": "Spinocerebellar ataxia type 8", "gene": "ATXN8OS", "flank_motif": "(CTA)10(CTG)n", "locus_structure": "(CTA)*(CTG)*", @@ -849,7 +849,7 @@ "benign_motif_gene_orientation": [], "unknown_motif_reference_orientation": ["AAAAA", "AAAAC", "AAATG", "AGAAA", "ATAAG", "TAAAC", "TAACA", "TACAA", "TCAAA", "TGCAA"], "unknown_motif_gene_orientation": ["AAAAA", "AAAAC", "AAATG", "AAAAG", "AAGAT", "AAACT", "AACAT", "AATAC", "AAATC", "AATGC"], - "disease": "Spinocerebellar Ataxia Type 31", + "disease": "Spinocerebellar ataxia type 31", "gene": "BEAN1", "flank_motif": null, "locus_structure": "(TGGAA)*(TAGAA)*", @@ -977,7 +977,7 @@ "benign_motif_gene_orientation": [], "unknown_motif_reference_orientation": [], "unknown_motif_gene_orientation": [], - "disease": "Spinocerebellar Ataxia Type 6", + "disease": "Spinocerebellar ataxia type 6", "gene": "CACNA1A", "flank_motif": null, "locus_structure": "(CTG)*", @@ -1105,7 +1105,7 @@ "benign_motif_gene_orientation": [], "unknown_motif_reference_orientation": ["CAGA"], "unknown_motif_gene_orientation": ["CTGT"], - "disease": "Myotonic Dystrophy Type 2", + "disease": "Myotonic dystrophy type 2", "gene": "CNBP", "flank_motif": "(CAGG)n(CAGA)10(CA)19", "locus_structure": "(CAGG)*(CAGA)*(CA)*", @@ -1297,7 +1297,7 @@ "benign_motif_gene_orientation": [], "unknown_motif_reference_orientation": ["AAAAA"], "unknown_motif_gene_orientation": ["TTTTT"], - "disease": "Spinocerebellar Ataxia Type 37", + "disease": "Spinocerebellar ataxia type 37", "gene": "DAB1", "flank_motif": null, "locus_structure": "(AAAAT)*(GAAAT)*(AAAAT)*", @@ -1489,7 +1489,7 @@ "benign_motif_gene_orientation": [], "unknown_motif_reference_orientation": [], "unknown_motif_gene_orientation": [], - "disease": "Myotonic Dystrophy Type 1", + "disease": "Myotonic dystrophy type 1", "gene": "DMPK", "flank_motif": null, "locus_structure": "(CAG)*",