Loci
Tandem repeat loci associated with Mendelian diseases. Full Dataset
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Motif length–
Tags | Gene | Disease | Description | Position hg38 | Motif (len) | Inheritance | |
|---|---|---|---|---|---|---|---|
ABCD3 | OPDM5 | Oculopharyngodistal myopathy type 5 | GCC (3) | AD | |||
AFF2 | FRAXE | Intellectual developmental disorder, Fragile X intellectual disability | GCC (3) | XR | |||
AFF3 | FRA2A | Intellectual disability associated with fragile site FRA2A | GCC (3) | AD | |||
AR | SBMA | Spinal and bulbar muscular atrophy, Kennedy Disease | GCA (3) | XR | |||
ARX | EIEE1 | Early-infantile epileptic encephalopathy | NGC (3) | XR | |||
ARX | PRTS | Partington syndrome | NGC (3) | XR | |||
ATN1 | DRPLA | Dentatorubral-Pallidoluysian Atrophy | CAG (3) | AD | |||
ATXN1 | SCA1 | Spinocerebellar ataxia type 1 | CTG (3) | AD | |||
ATXN10 | SCA10 | Spinocerebellar ataxia type 10 | ATTCT (5) | AD | |||
ATXN2 | SCA2 | Spinocerebellar ataxia type 2 | CTG (3) | AD/AR | |||
ATXN3 | SCA3, MJD | Spinocerebellar ataxia type 3/Machado-Joseph disease | CTG (3) | AD | |||
ATXN7 | SCA7 | Spinocerebellar ataxia type 7 | CAG (3) | AD | |||
ATXN8OS | SCA8 | Spinocerebellar ataxia type 8 | CTG (3) | AD | |||
BEAN1 | SCA31 | Spinocerebellar ataxia type 31 | TGGAA, TAGAA (5, 5) | AD | |||
C9orf72 | FTDALS1 | Frontotemporal dementia (FTD) and/or amyotrophic lateral sclerosis (ALS) | GGCCCC (6) | AD | |||
CACNA1A | SCA6 | Spinocerebellar ataxia type 6 | CTG (3) | AD | |||
CBL | JBS | Jacobsen syndrome (FRAX11B fragile site) | CGG (3) | AD | |||
CEL | MODY8 | Maturity-Onset Diabetes of the Young Type 8 | GGCCCCCCCGTGCCGCCCACGGGTGACTCCGG (32) | AD | |||
CNBP | DM2 | Myotonic dystrophy type 2 | CAGG (4) | AD | |||
COMP | EDM1, PSACH | Multiple epiphyseal dysplasia, Pseudoachondroplasia | GTC (3) | AD | |||
CSNK1E | EPM, DEE | Progressive Myoclonic Epilepsy and Developmental and Epileptic Encephalopathy | CCG (3) | AR | |||
CSTB | EPM1 | Progressive Myoclonic Epilepsy Type 1 (EPM1), a.k.a Unverricht-Lundborg Disease (ULD) | CGCGGGGCGGGG (12) | AR | |||
DAB1 | SCA37 | Spinocerebellar ataxia type 37 | GAAAT (5) | AD | |||
DIP2B | FRA12A | Intellectual developmental disorder, FRA12A type | GGC (3) | AD | |||
DMD | DMD | Duchenne muscular dystrophy | TTC (3) | XR | |||
DMPK | DM1 | Myotonic dystrophy type 1 | CAG (3) | AD | |||
EIF4A3 | RCPS | Richieri-Costa-Pereira syndrome | CCTCGCTGTGCCGCTGCCGA (20) | AR | |||
FAM193B | OPDM | Oculopharyngodistal myopathy | GCC (3) | AD | |||
FGF14 | SCA27B | Spinocerebellar ataxia 27B | GAA (3) | AD | |||
FMR1 | FXS, FXTAS, POF1 | Fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and fragile X-associated primary ovarian insufficiency FXPOI/POF1 | CGG (3) | XD | |||
FOXL2 | BPES | Blepharophimosis, epicanthus inversus, and ptosis | NGC (3) | AD/AR | |||
FXN | FRDA | Friedreich ataxia | GAA (3) | AR | |||
GIPC1 | OPDM2 | Oculopharyngodistal myopathy type 2 | CCG (3) | AD | |||
GLS | GDPAG | Glutaminase deficiency | GCA (3) | AR | |||
GOLGA8A | aFTLD-U | Atypical frontotemporal lobar degeneration with ubiquitinated inclusions (aFTLD-U) | CT (2) | ||||
HOXA13 | HFG-I | Hand-foot-genital syndrome 1 | NGC (3) | AD | |||
HOXA13 | HFG-II | Hand-foot-genital syndrome 2 | NGC (3) | AD | |||
HOXA13 | HFG-III | Hand-foot-genital syndrome 3 | NGC (3) | AD | |||
HOXD13 | SD5 | Syndactyly | GCN (3) | AD | |||
HTT | HD | Huntington disease | CAG (3) | AD | |||
JPH3 | HDL2 | Huntington disease-like 2 | CTG (3) | AD | |||
LRP12 | OPDM1 | Oculopharyngodistal myopathy type 1 | CGC (3) | AD | |||
MARCHF6 | FAME3 | Familial adult myoclonic epilepsy type 3 | TTTCA (5) | AD | |||
MIR7-2 | CHNG3 | Nongoitrous congenital hypothyroidism-3 | TTTG (4) | AD | |||
MUC1 | ADTKD | Autosomal dominant tubulointerstitial kidney disease | GCCCACGGTGTCACCTCGGCCCCGGACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCA (61) | AD | |||
NAXE | NME | NAXE-related mitochondrial encephalopathy | GGGCC (5) | AR | |||
NIPA1 | ALS1 | Amyotrophic lateral sclerosis | GCG (3) | AD | |||
NOP56 | SCA36 | Spinocerebellar ataxia type 36 | GGCCTG (6) | AD | |||
NOTCH2NLC | NIID | Neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype, Oculopharyngodistal myopathy (OPDM) type 3, hereditary essential tremor type 6 | GGC (3) | AD | |||
NUTM2B-AS1 | OPML1 | Oculopharyngeal myopathy with leukoencephalopathy 1 | GGC (3) | AD | |||
PABPN1 | OPMD | Oculopharyngeal muscular dystrophy | GCN (3) | AD/AR | |||
PHOX2B | CCHS | Congenital central hypoventilation syndrome | GCN (3) | AD | |||
PLIN4 | MRUPAV | Myopathy with Rimmed Ubiquitin-Positive Autophagic Vacuolation, PLIN4-Related Myopathy | TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC (99) | AD | |||
POLG | CPEO | Progressive external ophthalmoplegia, Parkinson's disease | GCT (3) | ||||
PPP2R2B | SCA12 | Spinocerebellar ataxia type 12 | GCT (3) | AD | |||
PRDM12 | HSAN VIII | Hereditary sensory and autonomic neuropathy type VIII | GCC (3) | AR | |||
PRNP | CJD | Creutzfeldt-Jakob disease and Gerstmann-Straussler-Schneiker syndrome | CCTCATGGTGGTGGCTGGGGGCAG (24) | AD | |||
RAI1 | FAME8 | Familial adult myoclonic epilepsy type 8 | TTTCA (5) | AD | |||
RAPGEF2 | FAME7 | Familial adult myoclonic epilepsy type 7 | TTTCA (5) | AD | |||
RFC1 | CANVAS | Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome | AAGGG, ACAGG, AAAGG, AGGGC (5, 5, 5, 5) | AR | |||
RILPL1 | OPDM4 | Oculopharyngodistal myopathy type 4 | GGC (3) | AD | |||
RUNX2 | CCD | Cleidocranial dysplasia | GCN (3) | AD | |||
SAMD12 | FAME1 | Familial adult myoclonic epilepsy type 1 | TGAAA (5) | AD | |||
SOX3 | XLID, PHPX | X-linked intellectual developmental disorder with isolated growth hormone deficiency; X-linked panhypopituitarism (PHPX) | NGC (3) | XR | |||
STARD7 | FAME2 | Familial adult myoclonic epilepsy 2 | AAATG (5) | AD | |||
TAF1 | XDP | X-linked dystonia-parkinsonism (XDP) a.k.a. Dystonia 3, torsion, X-linked (DYT3) | AGAGGG (6) | XR | |||
TBC1D7 | OPDM | Oculopharyngodistal myopathy | GCC (3) | AD | |||
TBP | SCA17 | Spinocerebellar ataxia type 17 | CAG (3) | AD | |||
TBX1 | TOF | Tetralogy of Fallot | GCN (3) | AD | |||
TCF4 | FECD3 | Fuchs endothelial corneal dystrophy 3 | CAG (3) | AD | |||
THAP11 | SCA51 | Spinocerebellar ataxia 51 | CAG (3) | AD | |||
TNRC6A | FAME6 | Familial adult myoclonic epilepsy type 6 | TTTCA (5) | AD | |||
TYMS | CPUM | Congenital Progressive Universal Melanosis | GATGGT (6) | AR | |||
VWA1 | HMNR7 | Neuronopathy, distal hereditary motor, autosomal recessive 7 | GGCGCGGAGC (10) | AR | |||
XYLT1 | DBQD2, BSS | Baratela-Scott Syndrome/Desbuquois dysplasia 2 | GCC (3) | AR | |||
YEATS2 | FAME4 | Familial adult myoclonic epilepsy 4 | TTTCA (5) | AD | |||
ZFHX3 | SCA4 | Spinocerebellar ataxia 4 | GCC (3) | AD | |||
ZIC2 | HPE5 | Holoprosencephaly-5 | GCN (3) | AD | |||
ZIC3 | VACTERLX | X-linked VACTERL syndrome | GCN (3) | XR | |||
ZNF713 | FRA7A | Autism spectrum disorder associated with fragile site FRA7A | GCG (3) | AD |
Downloads
T2T-chm13 | hg19 | hg38 | |
|---|---|---|---|
General a general-purpose extended bed file for filtering and annotating loci | |||
TRGT for genotyping full allele sequences in PacBio HiFi reads | |||
Atarva ⚠️ for genotyping full allele sequences in long-read data | |||
LongTR ⚠️ for genotyping full allele sequences in long-read data | |||
Straglr ⚠️ for genotyping allele sizes in long read-data | |||
Stranger ⚠️ for annotating TRGT or ExpansionHunter allele sizes with pathologic implications. |
⚠️ Still under development, use with caution
Plots
High-level, visual overview of loci.