Useful Resources

STR disease loci resource

Maintainers: Harriet Dashnow, Laurel Hiatt

Contributions welcome here.

chrom start_hg38 stop_hg38 start_hg19 stop_hg19 start_t2t-chm13-v1.0 stop_t2t-chm13-v1.0 notes_t2t-chm13-v1.0 id disease_id repeatunit_pathogenic_geneorientation repeatunit_path_plusstrand disease gene repeatunit_ref locus_structure Inheritance type location_in_gene normal normal_min normal_max intermediate intermediate_min intermediate_max pathogenic pathogenic_min pathogenic_max ref_copies repeat_unit_lenth age_onset age_onset_min age_onset_max novel Mechanism Mechanism_detail Mechanism source source notes width repeatunit_path_norm repeatunit OMIM ID Incidence Prevalence
chrX 148500605 148500753 147582125 147582273 146765191 146765342 (GCC)51.3 FRAXE_AFF2 FRAXE CGG GCC Fragile X syndrome, FRAXE type AFF2/FMR2 CGG "(GCC)*" XR 5' UTR 5’ Region 4-39 4 39 200-2000 200 2000 50.3 3 2-10 2 10 ref LOF, reduced gene expression Loss of function via transcriptional silencing (doi.org/10.1038/nrg1691) (doi.org/10.1007/s11604-022-01343-5) Mirkin 2007, OMIM, "SourceId": "NBK535148" 148 CCG CGG OMIM:309548 Unknown
chr2 100104799 100104824 100721261 100721286 100563686 100563738 (GCC)17.7 FRA2A_AFF3 FRA2A CGG CGG Intellectual disability associated with fragile site FRA2A AFF3 GCC AD 5' UTR 3-20 3 20 300+ 300 300 8.7 3 ref Decreased gene expression, methylation "silencing of the FMR2 gene as a consequence of a CCG expansion located upstream of this gene" malacard https://doi.org/10.1038/s41580-021-00382-6, PMC3998887 Path threshold may actually be higher than 300, assay was not sensitive enough 25 CCG N/A
chrX 67545317 67545419 66765159 66765261 65975148 65975250 (GCA)33.3 SBMA_AR SBMA CAG GCA Spinal and bulbar muscular atrophy, Kennedy Disease AR CAG "(GCA)*" XR Coding Exon 1 9–34 9 34 36-37 36 37 38–68 38 68 34 3 20-49 20 49 ref Polyglutamine Polyglutamine (doi.org/10.1038/nrg.2017.115) (doi.org/10.1007/s11604-022-01343-5) Hannan 2018, Mirkin 2007, GeneReviews, "SourceId": "NBK535148", s40478-021-01201-x 102 AGC CAG OMIM:313200 1:300,000 males (SBMA); 1/40,000 (Kennedy Disease)
chrX 25013654 25013697 25031779 25031808 24597891 24597934 (GCC)14.7 EIEE1_ARX EIEE1 GCG NGC Early-infantile epileptic encephalopathy ARX NGC "(NGC)*" XR Coding Exon 2 10-16 10 16 17-27 17 27 14.7 3 0 0 0 ref Polyalanine Polyalanine (doi.org/10.1038/nature05977) (doi.org/10.1007/s11604-022-01343-5) GeneReviews, OMIM, "SourceId": "NBK535148" Exon 2 aa 110-115 43 CCG GCG OMIM:308350; OMIM:300419; OMIM:300215 1-2/100,000 ~<1/35,000
chrX 25013530 25013565 25031647 25031682 24597767 24597799 (GGCCGCGGCGGCCGC)2.2 PRTS_ARX PRTS GCG NGC Partington syndrome ARX NGC "(NGC)*" XR Coding Exon 2 12 12 12 20 20 20 12 3 1-3 1 3 ref Polyalanine Polyalanine (OMIM) (doi.org/10.1007/s11604-022-01343-5) GeneReviews, OMIM, "SourceId": "NBK535148" Novel, Exon 2 aa 144-155 35 CCG GCG OMIM:309510 Unknown
chr12 6936717 6936775 7045880 7045938 6947904 6947941 (CAG)12.7 DRPLA_ATN1 DRPLA CAG CAG Dentatorubral-Pallidoluysian Atrophy ATN1 CAG "(CAG)*" AD Coding Exon 5 3–35 3 35 48-93 48 93 19 3 1-72 1 72 ref Polyglutamine Polyglutamine (doi.org/10.1038/nrg.2017.115) (doi.org/10.1007/s11604-022-01343-5) Hannan 2018, Mirkin 2007, GeneReviews, "SourceId": "NBK535148". s40478-021-01201-x 58 AGC CAG OMIM:125370 2-7/1,000,000
chr6 16327634 16327724 16327865 16327955 16200189 16200282 (TGC)31.1 SCA1_ATXN1 SCA1 CTG TGC Spinocerebellar Ataxia Type 1 ATXN1 CTG "(TGC)*" AD Coding Exon 8 6–35 6 35 36-38 36 38 39–91 39 91 30.3 3 20-40 typical 13 60 ref Polyglutamine Polyglutamine (doi.org/10.1038/nrg.2017.115) (doi.org/10.1007/s11604-022-01343-5) Hannan 2018, Mirkin 2007, GeneReviews, "SourceId": "NBK1184", s40478-021-01201-x Interruptions: CAT 90 AGC CTG OMIM:164400 1-2/100,000
chr22 45795355 45795424 46191235 46191304 46280060 46280129 (ATTCT)15.0 SCA10_ATXN10 SCA10 ATTCT ATTCT Spinocerebellar Ataxia Type 10 ATXN10 ATTCT "(ATTCT)*" AD Intronic Intron 9/11 10–32 10 32 280-850 280 850 800-4500 800 4500 14 5 12-48 12 48 ref Unknown Transdominant mechanism theorized (malacard) Hannan 2018, Mirkin 2007, GeneReviews, "SourceId": "NBK535148", s40478-021-01201-x Interruptions: ATCCT 69 AATAG ATTCT OMIM:603516 Unknown
chr12 111598950 111599019 112036754 112036823 111575873 111575940 (GCT)22.3 SCA2_ATXN2 SCA2 CAG GCT Spinocerebellar Ataxia Type 2 ATXN2 CTG "(GCT)*" AD/AR Coding Exon 1 14–31 14 31 32-34 32 34 33–200 33 200 23.3 3 30-40 typical 25 50 ref Polyglutamine Polyglutamine (doi.org/10.1038/nrg.2017.115) (doi.org/10.1007/s11604-022-01343-5) Hannan 2018, GeneReviews, "SourceId": "NBK1275", s40478-021-01201-x 29–32 repeats: increased ALS risk, Interruptions: CAA, CGG, CGC. Parkinson disease, late-onset, susceptibility. 69 AGC CAG OMIM:183090 1-2/100,000 (population dependent)
chr14 92071012 92071053 92537356 92537397 86300520 86300603 (CTG)28.0 SCA3_ATXN3 SCA3_MJD CTG CTG Spinocerebellar Ataxia Type 3/Machado-Joseph Disease ATXN3 CTG "(GCT)*" AD Coding Second last exon 12–44 12 44 45-59 45 59 60-87 60 87 14 3 10-50 typical 10 50 ref Polyglutamine Polyglutamine (doi.org/10.1038/nrg.2017.115) (doi.org/10.1007/s11604-022-01343-5) Hannan 2018, Mirkin 2007, GeneReviews, "SourceId": "NBK535148", s40478-021-01201-x "14:92071009-92071042" 41 AGC CTG OMIM:109150 1–5/100,000
chr3 63912685 63912716 63898361 63898392 63956303 63956334 (GCA)10.7 SCA7_ATXN7 SCA7 CAG GCA Spinocerebellar Ataxia Type 7 ATXN7 CAG "(GCA)*(GCC)+" AD Coding Exon 1, 2, or 3 (depending on isoform) 4–19 4 19 28-35 28 35 34–460 34 460 10.7 3 0-50 0 50 ref Polyglutamine Polyglutamine (doi.org/10.1038/nrg.2017.115) (doi.org/10.1007/s11604-022-01343-5) Hannan 2018, Mirkin 2007, GeneReviews, "SourceId": "NBK535148", s40478-021-01201-x 31 AGC CAG OMIM:164500 <1/300,000
chr13 70139383 70139429 70713515 70713561 69361244 69361271 (CTG)9.3 SCA8_ATXN8OS SCA8 CTG CTG Spinocerebellar Ataxia Type 8 ATXN8OS/ATXN8 CTG "(CTA)*(CTG)*" AD 3' UTR Exon 5, 3’ UTR? 15–50 15 50 50-70 50 70 71-1300 71 1300 15.3 3 20-50 typical 1 73 ref Polyglutamine/toxic gain-of-function; Unknown Polyglutamine/toxic gain-of-function; Unknown (OMIM) (doi.org/10.1007/s11604-022-01343-5) Hannan 2018, Mirkin 2007, GeneReviews, "SourceId": "NBK535148", s40478-021-01201-x Two genes span the CTG/CAG repeat and are expressed in opposite directions: ATXN8, which encodes a nearly pure polyglutamine expansion protein in the CAG direction, and ATXN8OS (603680), which, when transcribed, produces a noncoding CUG expansion RNA (Moseley et al., 2006). Roda et al. suggested that the ATXN8 or ATXN8OS gene should not be evaluated in isolation as a candidate gene for spinocerebellar degenerative disease 46 AGC CTG OMIM:608768 <1/100,000
chr16 66490397 66490466 66524300 66524369 72284667 72284761 (AATAA)19.4 SCA31_BEAN1 SCA31 TGGAA TGGAA/TAGAA Spinocerebellar Ataxia Type 31 BEAN1 AATAA "(TGGAA)*TAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA" AD Intronic Intron 4/4 0-10 0 10 >110 110 760 14.4 5 20-72 20 72 novel Epigenetic Role in heterochromatin or chromosomal structure theorized (OMIM) OMIM, Sato 2009, "SourceId": "19878914" (Pubmed), https://doi.org/10.1038/s41580-021-00382-6 Novel, STR-containing insertion, not present in reference genome: Reds disagree on normal/pathogenic sizes 69 AATGG TGGAA OMIM:117210 Unknown (more common in Japanese pop)
chr9 27573484 27573546 27573482 27573544 27584063 27584155 (GCCCCG)15.8 FTDALS1_C9orf72 FTDALS1 GGGGCC GGCCCC "In European populations, C9ORF72 repeat expansions were the most common (5.1 percent)" assessing genes in sporadic ALS C9orf72 GCCCCG "(GGCCCC)*" AD Intronic Intron 1 or 5' depending on transcript 3–25 (2-19 Reds) 2 20 20-60 20 60 250-2000 250 2000 10.8 6 27-85 27 85 ref RNA toxicity? "The HRE forms DNA and RNA G-quadruplexes with distinct structures and promotes RNA/DNA hybrids (R-loops). The structural polymorphism causes a repeat length-dependent accumulation of transcripts aborted in the HRE region." OMIM Hannan 2018, GeneReviews, OMIM, "SourceId": "NBK535148", s40478-021-01201-x 62 CCCCGG GGGGCC OMIM:105500 "The expansion of a hexanucleotide repeat GGGGCC in C9orf72 is the most common known cause of ALS accounting for ~ 40% familial cases and ~ 7% sporadic cases in the European population"
chr19 13207859 13207898 13318673 13318712 13333137 13333176 (CTG)13.3 SCA6_CACNA1A SCA6 CAG CTG Spinocerebellar Ataxia Type 6 CACNA1A CTG "(CTG)*" AD Coding Last Exon: 47 or 48 4–18 4 18 19 19 19 20–33 20 33 13.3 3 19-73 19 73 ref Polyglutamine Polyglutamine (doi.org/10.1038/nrg.2017.115) (doi.org/10.1007/s11604-022-01343-5) Hannan 2018, Mirkin 2007, GeneReviews, "SourceId": "NBK535148", s40478-021-01201-x 39 AGC CAG OMIM:183086 <1/1,000,000
chr11 119206289 119206322 119076999 119077032 119226663 119226696 (CGG)11.3 JBS_CBL2 JBS CCG CCG Jacobsen syndrome (FRAX11B fragile site) CBL2 CGG "(CGG)*" AD 5' UTR <79 11 79 >100 100 100 11.3 3 0 0 ref N/A No information found (OMIM) https://doi.org/10.1038/s41580-021-00382-6, " "SourceId": "7603564" (PubMed) 33 CCG OMIM:147791 1/100,000 births
chr19 18786034 18786049 18896844 18896859 18921630 18921645 EDM1-PSACH_COMP EDM1, PSACH GTC GTC Multiple epiphyseal dysplasia, Pseudoachondroplasia COMP GTC AD Coding 5 5 5 4 or 6-7 6 7 5 3 13 13 13 ref Protein LOF LOF, domain dependent (https://pubmed.ncbi.nlm.nih.gov/29530484/) Pathogenic Short Tandem Repeats Gnomad v3.1.2 Two diseases, same locus. Both expansions and contractions associated with disease 15 ACG OMIM:132400; OMIM:177170 9-16/100,000 births
chr1 57367044 57367125 57832716 57832797 57245936 57245977 (AAAAT)8.6 SCA37_DAB1 SCA37 ATTTC ATTTC Spinocerebellar Ataxia Type 37 DAB1 AAAAT "(AAAAT)*(GAAAT)*(AAAAT)*" AD Intronic Intron 1 (most isoforms) 0-16 0 16 31-75 31 75 16.6 5 18-64 18 64 novel Protein toxic GOF toxic gain-of-function mechanism (OMIM) Seixas et al 2017 AJHG, "SourceId": "NBK541729", s40478-021-01201-x Novel. Normal: [(ATTTT)7–400] Pathogenic: [(ATTTT)60–79(ATTTC)31–75(ATTTT)58–90], ATTTC within (ATTTT)7–400 repeat region 81 AAATG ATTTC OMIM:615945 <1/1,000,000
chr12 50505002 50505022 50898785 50898805 50468096 50468116 FRA12A_DIP2B FRA12A CGG GGC Intellectual developmental disorder, FRA12A type DIP2B CGG "(GGC)*" AD 5' UTR 6-23 6 23 ~139-206 139 206 ~273-306 273 306 7 3 1 1 ref Increased gene expression, methylation Increased gene expression, methylation (OMIM, https://www.medrxiv.org/content/10.1101/2022.09.12.22279739v3.full-text) OMIM, "SourceId": "NBK535148", path thresolds: https://www.medrxiv.org/content/10.1101/2022.09.12.22279739v3.full-text 20 CCG CGG OMIM:136630 N/A
chrX 31284557 31284605 31302674 31302722 30882695 30882743 (TTC)22.7 DMD_DMD DMD TTC TTC Duchenne muscular dystrophy DMD TTC XR Intronic <33 16 33 >59 59 59 16.7 3 dependent on repeat number (birth to adulthood) 0 3 ref Protein LOF Functional defect in dystrophin/dystroglycan (https://doi.org/10.1007/s10038-006-0056-7) "Pathogenic Short Tandem Repeats 48 AAG OMIM:310200 1 in 3,500-5,000 live male births
chr19 45770204 45770266 46273462 46273524 48597739 48597756 DM1_DMPK DM1 CAG CAG Myotonic Dystrophy Type 1 DMPK CAG "(CAG)*" AD 3' UTR Last exon 5–34 5 34 35-49 35 49 50-1000 50 1000 20.7 3 0-30, mild up to 70 0 70 ref RNA GOF RNA gain-of-function - RNA gelation leading to misregulation of alternative splicing (doi.org/10.1007/s11604-022-01343-5) Hannan 2018, Mirkin 2007, GeneReviews, "SourceId": "NBK1165", s40478-021-01201-x Interruptions: CCG 62 AGC CAG OMIM:160900 5-20/100,000
chrX 147912037 147912111 146993555 146993629 146176665 146176769 (GGC)35.0 FXS_FMR1 FXS/FXTAS/POF1 CGG CGG fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and fragile X-associated primary ovarian insufficiency FXPOI/POF1 FMR1 CGG "(CGG)*" XD 5' UTR Exon 2 5–44 5 44 45-200 45 200 200-2000 200 2000 20.6667 3 FXS 2, FXTAS 60-65 2 65 ref LOF via decreased gene expression in FXS, GOF in FXTAS Loss of function via transcriptional silencing in FXSRNA GOF in FXTAS (doi.org/10.1038/nrg1691) (doi.org/10.1007/s11604-022-01343-5) Hannan 2018, Mirkin 2007, "SourceId": "NBK1384" FXTAS/POI 55–200, FXS >200, late onset 74 CCG CGG OMIM:300624; OMIM:300623 16-25/100,000 males
chr3 138946020 138946062 138664862 138664904 141687014 141687051 (GCGGCTGCAGCCGCA)2.5 BPES_FOXL2 BPES GCN NGC Blepharophimosis, epicanthus inversus, and ptosis FOXL2 NGC "(NGC)*" AD Coding Exon 1 <14 14 14 >15 15 15 14 3 0, can have infertility in childbearing age 0 0 ref Polyalanine Polyalanine (doi.org/10.1038/nature05977) (doi.org/10.1007/s11604-022-01343-5) reds, "SourceId": "NBK535148" 42 CNG OMIM:110100 1 in 50,000 births globally
chr9 69037287 69037289 71652203 71652205 81210844 81210846 (AAG)9.7 FRDA_FXN FRDA AAG GAA Friedreich ataxia FXN GAA "(A)*(GAA)* AR Intronic Intron 1 5–33 5 33 34-65 34 65 66 to 1700 66 1700 6 3 5-25 5 25 ref LOF, reduced gene expression Loss of function via transcriptional silencing (doi.org/10.1038/nrg1691) (doi.org/10.1007/s11604-022-01343-5) Hannan 2018, Mirkin 2007, GeneReviews, "SourceId": "NBK535148" Not annotated by TRF? 2 AAG AAG OMIM:229300 1/50,000 (US), 1/40,000 (global)
chr19 14496041 14496074 14,606,853 14606886 14622656 14622702 (CCG)15.7 OPDM2_GIPC1 OPDM2 CGG CCG Oculopharyngodistal myopathy GIPC1 CCG "(CCG)*" AD 5' UTR Exon 1 6-29 6 29 70-138 70 138 14.7 3 10-29 10 29 ref RNA toxicity RNA mediated toxicity hypothesized; unknown (OMIM), (doi.org/10.1007/s11604-022-01343-5) reds; "Pathogenic Short Tandem Repeats Gnomad v3.1.2", "SourceId": "32413282" (Pubmed) 33 CCG OMIM:618940 Population dependent
chr2 190880873 190880920 191745599 191745646 191369983 191370024 (GCA)14.0 GDPAG_GLS GDPAG GCA GCA Glutaminase deficiency GLS GCA "(GCA)*" AR 5' UTR Exon 1 5-26 5 26 90 - 1500 90 1500 16 3 Early childhood 0 1 ref Decreased gene expression, methylation Change in histone modification decreases transcription (OMIM) van Kuilenburg 2019 NEJM, "SourceId": "30970188" (Pubmed) Several compound het cases reported 47 AGC GCA OMIM:618412 As of 2019, only 7 cases
chr7 27199678 27199732 27239297 27239351 27335815 27335849 (GCCGCGGCCGCCGCCG)1.9 HFG_HOXA13-III HFG GCN NGC Hand-foot-uterus syndrome HOXA13 NGC "(NGC)*" AD Coding Exon 1 8-18 8 18 24-32 24 32 18 3 0 0 0 ref Polyalanine Polyalanine (doi.org/10.1038/nature05977) (doi.org/10.1007/s11604-022-01343-5) reds; "Pathogenic Short Tandem Repeats Gnomad v3.1.2", "SourceId": "NBK1423" There are 3 pathogenic polyalanine tracts in this gene 54 CNG OMIM:140000 "Rare"
chr7 27199825 27199861 27239444 27239480 27335914 27335954 (GCAGCCGCCGCCGCT)2.9 HFG_HOXA13-II HFG GCN NGC Hand-foot-uterus syndrome HOXA13 NGC "(NGC)*" AD Coding Exon 1 12 12 12 18 18 18 12 3 0 0 0 ref Polyalanine Polyalanine (doi.org/10.1038/nature05977) (doi.org/10.1007/s11604-022-01343-5) reds; "Pathogenic Short Tandem Repeats Gnomad v3.1.2", "SourceId": "NBK1423" There are 3 pathogenic polyalanine tracts in this gene 36 CNG OMIM:140000 "Rare"
chr7 27199924 27199966 27239543 27239585 27335920 27335951 (GCAGCCGCCGCCGCT)2.7 HFG_HOXA13-I HFG GCN NGC Hand-foot-uterus syndrome HOXA13 NGC "(NGC)*" AD Coding Exon 1 14 14 14 22 22 22 14 3 0 0 0 ref Polyalanine Polyalanine (doi.org/10.1038/nature05977) (doi.org/10.1007/s11604-022-01343-5) reds; "Pathogenic Short Tandem Repeats, Gnomad v3.1.2" "SourceId": "NBK1423" There are 3 pathogenic polyalanine tracts in this gene 42 CNG OMIM:140000 "Rare"
chr2 176093058 176093103 176957786 17695783 176581179 176581220 (GGC)14.0 SD5_HOXD13 SD5 GCN GCG Syndactyly HOXD13 GCG "(GCN)*" AD Coding Exon 1 < 15 14 15 >22 22 22 14 3 0 0 0 ref Polyalanine Polyalanine (doi.org/10.1038/nature05977) (doi.org/10.1007/s11604-022-01343-5) reds; "Pathogenic Short Tandem Repeats Gnomad v3.1.2", "SourceId": "NBK535148" 45 CNG OMIM:186000 Unknown
chr4 3074877 3074940 3076604 3076667 3073604 3073694 (CAG)30.3 HD_HTT HD CAG CAG Huntington disease HTT CAG "(CAG)*CAACAG(CCG)*" AD Coding Exon 1 6–26 6 26 27-35 unstable, 36-39 reduced penetrance 27 39 40–250 (>60 assocated with onset age <20) 40 250 21.3 3 35-44 10 70 ref Polyglutamine Polyglutamine (doi.org/10.1038/nrg.2017.115) (doi.org/10.1007/s11604-022-01343-5) Hannan 2018, Mirkin 2007, GeneReviews CAG exp only pathogenic. Interruptions impact pathogenicity. Age 4 onset reported, not yet published 63 AGC CAG OMIM:143100 1/10,000
chr16 87604283 87604329 87637889 87637935 93675724 93675776 (GCT)17.3 HDL2_JPH3 HDL2 CAG CTG Huntington disease-like 2 JPH3 GCT "(CTG)*" AD Coding Exon 2 6–28 6 28 29-39 29 39 40–58 40 58 15.6667 3 12-66 12 66 ref ?? "unstable vertical transmission" (doi.org/10.1007/s11604-022-01343-5) Hannan 2018, Mirkin 2007, GeneReviews, "SourceId": "NBK1529" reflen + pos from HipSTR 46 AGC CAG OMIM:606438 <1/1,000,000
chr8 104,588,972 104,588,999 105,601,200 105,601,227 105,716,410 105,716,441 (CGC)10.7 OPDM1_LRP12 OPDM1 CGG CGC Oculopharyngodistal myopathy type 1 LRP12 CGC "(NCG)*" AD 5' UTR 13-45 13 45 90 90 90 11.7 3 Adult onset, variable (mean 22.1 in one study) 7 50 ref RNA toxicity RNA mediated toxicity hypothesized; unknown (OMIM), (doi.org/10.1007/s11604-022-01343-5) OMIM 164310, Ishiura et al [2019], Ehdn, "SourceId": "NBK535148", PMID 31332380 CGG/CGT 27 CCG OMIM:164310 Population dependent
chr5 10356339 10356411 10356451 10356523 10295521 10295593 (TTTTA)14.8 FAME3_MARCH6 FAME3 TTTCA ATTTC Familial adult myoclonic epilepsy type 3 MARCH6 TTTTA AD Intronic Intron 1 0 791-1,035 repeats 791 1035 14.8 5 10-40 10 40 novel Unknown Noted as unknown in literature (OMIM) Florian, R.T. Nat Comm. 2019 TTTTA + TTTCA 72 AAATG TTTTA + TTTCA OMIM:613608 ~<1/35,000
chr15 22786677 22786701 23086366 23086390 20458505 20458536 (GCG)10.7 ALS1_NIPA1 ALS1 GCG GCG Amyotrophic lateral sclerosis NIPA1 GCG "(CGC)*" AD Coding 6-10 6 10 > 11 11 56 10.7 3 Variable, 19-46 familial 19 46 ref N/A No information found N/A in GeneCard Pathogenic Short Tandem Repeats Gnomad v3.1.2, "SourceId": "30342764" (Pubmed), path range from gnomAD allele freqs Modifier for ALS? 24 CCG OMIM:105400 1.5-4.7 per 100,000 person-years (All ALS, Europe/NA) 2.7-7.4/100,000 (All ALS, not just this locus)
chr20 2652733 2652775 2633379 2633421 2683200 2683242 (GCCTGG)8.8 SCA36_NOP56 SCA36 GGCCTG GGCCTG Spinocerebellar ataxia type 36 NOP56 GGCCTG "(GGCCTG)*(CGCCTG)*" AD Intronic Intron 1 3 to 14 3 14 15-649 15 649 650-2500 650 2500 7.2 6 ~52 (mean) 48 57 ref Protein toxic GOF toxic gain-of-function mechanism (OMIM) GeneReviews, OMIM, "SourceId": "NBK231880" 42 AGGCCC GGCCTG OMIM:614153 Unknown
chr1 149390803 149390842 deletion/multiple? 148519696 148519738 (GGC)14.3 NIID_NOTCH2NLC NIID GGC GGC neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype NOTCH2NLC CGG AD 5' UTR 5' Region 7–39 7 39 66-517 66 517 13.3 3 16-76 16 76 ref Unknown May relate to methylation or RNA pathogenicity; Unknown (OMIM) (doi.org/10.1007/s11604-022-01343-5) doi: 10.1038/s41588-019-0458-z https://doi.org/10.1016/j.ajhg.2019.05.013, s40478-021-01201-x May be issues with parology between genes: C253572.1, NOTCH2, NOTCH2NL, NBPF14, NBPF19 ?? Motif variation in controls: (AGG)(CGG)n(AGG)0-3(CGG)0-2. Methylation involved 39 CCG OMIM:603472 Unknown
chr10 79826383 79826404 81586139 81586160 80695712 80695748 (GCG)12.7 OPML1_NUTM2B-AS1 OPML1 GGC GGC Oculopharyngeal myopathy with leukoencephalopathy 1 NUTM2B-AS1 GGC AD lncRNA Exon 1 (noncoding) 3-16 3 16 >700 700 700 7 3 15 40 ref RNA toxicity RNA mediated toxicity hypothesized, unknown (OMIM) (doi.org/10.1007/s11604-022-01343-5) Pathogenic Short Tandem Repeats Gnomad v3.1.2, Ishiura 2019 doi: 10.1038/s41588-019-0458-z, https://doi.org/10.1038/s41580-021-00382-6 Not in TRF annotation, alt transcript in opposite direction: LOC642361 21 CCG OMIM:618637 Couldn't find
chr14 23321472 23321492 23790681 23790701 17522488 17522508 OPMD_PABPN1 OPMD GCG GCG Oculopharyngeal muscular dystrophy PABPN1 CGG "(GCN)*" AD/AR Coding Exon 1 10 10 10 12-17 12 17 7 3 26-65 26 65 ref Polyalanine Polyalanine (doi.org/10.1038/nrg.2017.115) (doi.org/10.1007/s11604-022-01343-5) Mirkin 2007, GeneReviews, "SourceId": "NBK1126", s40478-021-01201-x AR for 11 repeats, AD >12 repeats. Most known patients have (GCG)+, but GCN or any polyalanine may be pathogenic 20 CCG CGN OMIM:164300 1/100,000 Western countries
chr4 41745976 41746022 41747993 41748039 41719749 41719795 (GCC)15.7 CCHS_PHOX2B CCHS GCN GCN Congenital central hypoventilation syndrome PHOX2B GCC "(GCN)*" AD Coding Exon 3 20 15 20 24 24 24 25-33 25 33 15.7 3 0-20 0 20 ref Polyalanine Polyalanine (doi.org/10.1038/nature05977) (doi.org/10.1007/s11604-022-01343-5) Mirkin 2007, GeneReviews, "SourceId": "NBK1427", s40478-021-01201-x "ReferenceRegion": "4:41745971-41746032", 46 CNG GCN OMIM:209880 1:148000-200000 births (Estimated)
chr15 89333589 89333629 89876820 89876860 87088412 87088452 (GCT)13.7 CPEO_POLG CPEO CTG GCT progressive external ophthalmoplegia, Parkinson’s disease POLG GCT "(CTG)*TTG(CTG)*" - 10-12, < 15 10 15 > 10000 10000 10000 13.7 3 23-87 23 87 ref N/A No information found N/A in GeneCard "SourceDisplay": "Research only - contact CMMS KUH regarding findings", PMC2905783 Unconfirmed association 40 AGC Disease association unclear?
chr5 146878728 146878759 146258291 146258322 147414734 147414765 (GCT)15.7 SCA12_PPP2R2B SCA12 CAG GCT Spinocerebellar ataxia type 12 PPP2R2B CAG "(GCT)*" AD Promoter 4–32 4 32 51–78 51 78 10.7 3 8-55 8 55 ref Unknown Noted as unknown in literature N/A in GeneCard, Hannan 2018, Mirkin 2007, OMIM, "SourceId": "NBK535148", s40478-021-01201-x (Roda et al. suggested that the ATXN8 or ATXN8OS gene should not be evaluated in isolation as a candidate gene for spinocerebellar degenerative disease) 31 AGC CAG OMIM:604326 Unknown
chr9 130681606 130681639 133556993 133557026 142886569 142886595 (CGC)9.0 HSAN-VIII_PRDM12 HSAN VIII GCC GCC Hereditary sensory and autonomic neuropathy type VIII PRDM12 GCC "(GCC)*" AR Coding Exon <14 12 14 >18 18 18 12 3 0 0 0 ref LOF, epigenetic "mutations abrogated the histone-modifying potential of PRDM12, consistent with a loss of function" OMIM Pathogenic Short Tandem Repeats Gnomad v3.1.2 33 CCG OMIM:616488 <1/1,000,000
chr4 159342527 159342618 160263679 160263770 162693304 162693405 (TTTTA)20.4 FAME7_ RAPGEF2 FAME7 TTTCA ATTTC Familial adult myoclonic epilepsy type 7 RAPGEF2 TTTTA "(TTTTA)*(TTTCA)*(TTTTA)*" AD Intronic Intron 14 0-1 0 1 >=60 60 60 17.4 5 ~18, 23-37 18 37 novel RNA toxicity RNA toxicity hypothesized (10.1038/s41588-018-0067-2) Ishiura 2018, "SourceId": "29507423" (Pubmed), https://sci-hub.hkvisa.net/10.1111/ene.13848 Novel, (TTTTA)exp(TTTCA)exp(TTTTA)n, but only the TTTCA is specific to affected individuals, Alu-associated repeat, incomplete penetrance 91 AAATG TTTCA OMIM:618075 ~<1/35,000
chr4 39348425 39348483 39350045 39350103 39318078 39318136 (AAAAG)11.8 CANVAS_RFC1 CANVAS AAGGG/ACAGG AAGGG Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome RFC1 AAAAG "(AARRG)*" AR Intronic Intron 2 0-11 0 11 >400 400 2000 11.8 5 33-71 33 71 novel N/A No information found N/A in GeneCard OMIM, Cortese 2019, "SourceId": "30926972" (Pubmed), https://actaneurocomms.biomedcentral.com/articles/10.1186/s40478-021-01201-x/tables/1, s40478-021-01201-x Novel, ref is AAAAG(11), path: (AAGGG)400–2000 or (ACAGG)exp 58 AAGGG AAGGG OMIM:614575 Unknown, <1/1,000,000
chr12 123533720 123533755 124018267 124018302 123532574 123532608 (GGC)11.7 OPDM4_RILPL1 OPDM4 CGG GGC oculopharyngodistal myopathy type 4 RILPL1 CGG AD 5' UTR 9-16 9 16 139 to 197 139 197 11.7 3 14 27 ref Protein toxic GOF toxic gain-of-function mechanism (Malacard) Yu 2022 AJHG toxic poly-glycine protein and/or toxic RNA gain-of-function effects 35 CCG Population dependent
chr6 45422750 45422792 45390487 45390529 45257567 45257611 (GGC)15.0 CCD_RUNX2 CCD GCN GCN Cleidocranial dysplasia RUNX2 GCN "(GCN)*" AD Coding Exon 3 <17 4 17 >27 27 27 15 3 0 0 0 ref Polyalanine Polyalanine (doi.org/10.1038/nature05977) (doi.org/10.1007/s11604-022-01343-5) reds; "Pathogenic Short Tandem Repeats Gnomad v3.1.2", "SourceId": "NBK535148" 42 CNG OMIM:119600 1/1,000,000 births (likely underdiagnosed)
chr8 118366813 118366918 119379052 119379157 119495248 119495353 (AAATA)21.6 FAME1_SAMD12 FAME1 TTTCA/TTTGA ATTTC Familial adult myoclonic epilepsy type 1 SAMD12 AAATA "(TAAAA)*(TGAAA)*(TAAAA)*" AD Intronic Intron 4/4 0 0 0 105–3680 105 3680 21.6 5 18-50 18 50 novel RNA molecules toxicity? RNA molecules (OMIM) Ishiura 2018. https://movementdisorders.onlinelibrary.wiley.com/doi/full/10.1002/mds.27832 reported TTTGA expansions in affected individuals: (TTTTA)114-123(TTTGA)108-116 Novel, pathogenic alleles include expansions of TTTTAn + TTTCAn, but only the TTTCA is specific to affected individuals, check reference and pathogenic sites with Stranger. TTTCA within TTTTA repeat region 105 AAATG TTTCA OMIM:601068 ~<1/35,000
chrX 140504316 140504361 139586481 139586526 138816205 138816239 (GCGGCAGCGGCGGCGG)1.9 XLMR_SOX3 XLMR GCN NGC X-linked panhypopituitarism ; X-linked mental retardation with isolated growth hormone SOX3 NGC "(NGC)*" XR Coding Exon 1 < 15 15 15 > 22 22 26 15 3 Infancy - childhood 0 9 ref Polyalanine Polyalanine (doi.org/10.1007/s11604-022-01343-5) reds; "Pathogenic Short Tandem Repeats Gnomad v3.1.2", "SourceId": "NBK535148" 45 CNG OMIM:300123
chr2 96197067 96197121 96862805 96862859 96703675 96703729 (AAAAT)11.6 FAME2_STARD7 FAME2 GAAAT ATTTC Familial adult myoclonic epilepsy 2 STARD7 AAAAT AD Intronic 0 0 0 >274 274 274 11.6 5 mean 25 5 60 novel RNA toxicity RNA toxicity (10.1038/s41467-019-12671-y) Pathogenic Short Tandem Repeats Gnomad v3.1.2 54 AAATG OMIM:607876 ~<1/35,000
chr6 170561907 170562017 170870995 170871105 171935459 171935569 (GCA)37.0 SCA17_TBP SCA17 CAG/CAA GCA Spinocerebellar ataxia type 17 TBP CAG "(GCA)*" AD Coding Exon 3 25–40 25 40 41–48 41 48 49 to 66 49 66 37 3 Most >30 3 55 ref Polyglutamine Polyglutamine (doi.org/10.1038/nrg.2017.115) (doi.org/10.1007/s11604-022-01343-5) Hannan 2018, Mirkin 2007, GeneReviews, "SourceId": "NBK1438" Parkinson disease,late-onset 110 AGC CAG/CAA OMIM:607136 Unknown (global), 0.47:1,000,000 (Japanese)
chr22 19766762 19766807 19754285 19754330 20143615 20143660 OTF_TBX1 OTF GCN GCN Tetralogy of Fallot TBX1 GCN "(GCN)*" AD Coding <15 15 15 >25 25 25 15 3 0 0 0 ref Polyalanine Polyalanine (OMIM) Pathogenic Short Tandem Repeats Gnomad v3.1.2, "SourceId": "NBK535148" 45 CNG OMIM:187500 Unknown for specific gene
chr18 55586155 55586227 53253386 53253458 55789234 55789288 (AGC)18.3 FECD3_TCF4 FECD3 CAG CAG Fuchs endothelial corneal dystrophy 3 TCF4 CAG "(CAG)*" AD Intronic Intron 1 10 - 40 10 40 >50 50 150 25.3 3 ~40 32 70 ref RNA toxicity? "sequestration of MBNL1 in RNA foci, similar to the mechanism underlying myotonic dystrophy-1 " (10.1074/jbc.M114.621607) reds; "Pathogenic Short Tandem Repeats Gnomad v3.1.2", "SourceId": "NBK535148" 72 AGC OMIM:613267 ~4/100 (over 40)
chr16 24613439 24613532 24624760 24624853 24890367 24890430 (ATTTT)12.8 FAME6_ TNRC6A FAME6 TTTCA ATTTC Familial adult myoclonic epilepsy type 6 TNRC6A ATTTT "(TTTTA)*(TTTCA)*(TTTTA)*" AD Intronic 0 0 0 >1100, >=10, 29 1100 1100 18.8 3 20s-70s 20 70 novel RNA toxicity RNA toxicity hypothesized (10.1038/s41588-018-0067-2) Ishiura 2018; gnomad v3.1.2, "SourceId": "29507423" (Pubmed), https://doi.org/10.1038/s41597-020-00633-9, https://stripy.org/database/TNRC6A Novel, reported pathogenic alleles: (TTTTA)22 (TTTCA)exp (TTTTA)exp, but only the TTTCA is specific to affected individuals, Alu-associated repeat. Non-pathogenic reference TTTTA repeat was expanded in nine healthy subjects 40-120 repeats and in two individuals potentially even longer (Ishiura et al., 2018). 93 AAATG TTTCA OMIM:618074 ~<1/35,000
chr16 17470921 17470922 17564778 17564779 17477910 17478013 (GCC)34.7 DBQD2_XYLT1 DBQD2, BSS CCG GCC Baratela-Scott Syndrome/Desbuquois dysplasia 2 XYLT1 CCG "(GGC)*" AR Promoter Intron 1 <20 0 20 >72 72 110 0 3 0 0 0 ref Methylation Methylation (doi.org/10.1016/j.ajhg.2018.11.005) LaCroix 2019; reds, gnomad v3.1.2, "SourceId": "30554721" Repeat is within a sequencing missing from hg38 1 CCG CCG OMIM:615777 <1 / 1,000,000 births
chr3 183712188 183712222 183429976 183430010 186521657 186521706 (ATTTT)10.0 FAME4_YEATS2 FAME4 TTTCA ATTTC Familial adult myoclonic epilepsy 4 YEATS2 TTTTA AD Intronic 0 0 0 >1000 1000 1000 10 5 19.5 years (range 10-33) for tremor and 25 years (range 19-33) for seizures 10 33 novel RNA toxicity RNA toxicity hypothesized (10.1093/brain/awz267) Pathogenic Short Tandem Repeats Gnomad v3.1.2 34 AAATG OMIM:615127 ~<1/35,000
chr13 99985448 99985493 100637702 100637747 99196359 99196404 (GCG)15.3 HPE5_ZIC2 HPE5 GCN GCN Holoprosencephaly-5 ZIC2 GCN "(GCN)*" AD Coding Exon 3 < 15 15 15 >25 25 25 15.3 3 0 0 0 ref Polyalanine Polyalanine (doi.org/10.1038/nature05977) (doi.org/10.1007/s11604-022-01343-5) reds; "Pathogenic Short Tandem Repeats Gnomad v3.1.2", "SourceId": "NBK535148" 45 CNG OMIM:609637 Unknown ZIC2 specific
chrX 137566826 137566856 136648985 136649015 135876774 135876800 (CGC)9.0 VACTERLX_ZIC3 VACTERLX GCN GCN X-linked VACTERL syndrome ZIC3 GCN "(GCN)*" XR Coding <10 9 10 11 11 11 >12 12 12 9 3 0 0 0 ref Polyalanine Polyalanine (doi.org/10.1038/nature05977) Pathogenic Short Tandem Repeats Gnomad v3.1.2, "SourceId": "NBK535148" 30 CNG OMIM:314390 Unknown
chr7 55887601 55887639 55955294 55955332 56047901 56047939 (GCG)15.0 FRA7A_ZNF713 FRA7A CGG CGG Autism spectrum disorder associated with fragile site FRA7A ZNF713 GCG AD Intronic 5-22 5 22 85 85 85 450 450 450 13 3 ref Methylation Methylation (OMIM) OMIM, https://pubmed.ncbi.nlm.nih.gov/25196122/ 38 CCG #616181 N/A
chr3 129172577 129172659 128891420 128891502 131917483 131917557 (CAGG)18.8 DM2_CNBP1 DM2 CCTG CAGG Myotonic Dystrophy Type 2 ZNF9 / CNBP1 CAGG "(CAGG)*(CAGA)*(CA)*" AD Intronic 11–26 11 26 27-74 27 74 75-11,000 75 11,000 20.8 4 ~30-40 30 40 ref Aberrant splicing Aberrant splicing (doi.org/10.1093/hmg/ddr568) Hannan 2018, Mirkin 2007, GeneReviews NBK1466, https://doi.org/10.1038/s41580-021-00382-6 (TG)n(TCTG)n(CCTG)n. CCTG expansion causes DM2 but the other repeat units are also variable. 82 AGGC CCTG OMIM:602668 2.29/100,000