COL9A1

collagen type IX alpha 1 chain

Summary

This gene encodes one of the three alpha chains of type IX collagen, which is a minor (5-20%) collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

Known Variants1,039 total

rsidPosition (GRCh37)AllelesClassClinVar
rs10642506:70,926,334A/G—benign
rs24595556:70,926,371A/G—benign
rs7765150446:70,926,426A/G—uncertain significance
rs3745613986:70,926,605G/A—uncertain significance
rs3734300946:70,926,612C/T—likely benign
rs8989902806:70,926,615T/C—likely benign
rs21275439406:70,926,627T/C—likely benign
rs1452215436:70,926,629G/A—uncertain significance
rs13851929836:70,926,642C/T—uncertain significance
rs14122630116:70,926,643A/G—uncertain significance
rs5676062456:70,926,645G/A—likely benign
rs10288442096:70,926,655G/C—uncertain significance
rs12255812196:70,926,664C/T—uncertain significance
rs7705028316:70,926,671C/T—uncertain significance
rs3703247396:70,926,672G/A—likely benign
rs7589168846:70,926,682G/A—uncertain significance
rs1998451596:70,926,690C/T—likely benign
rs7606177136:70,926,691G/A—uncertain significance
rs7639701676:70,926,695G/A—uncertain significance
rs21275440556:70,926,711A/C—uncertain significance
rs10314137326:70,926,723C/T—likely benign
rs7505381596:70,926,729G/A—likely benign
rs11566056126:70,926,730G/T—uncertain significance
rs14080641186:70,926,736C/T—uncertain significance
rs7583887166:70,926,737G/A—uncertain significance
rs13362912426:70,926,738C/A—uncertain significance
rs21275440976:70,926,740C/G—uncertain significance
rs1995815936:70,926,743C/T—uncertain significance
rs1491398696:70,926,744G/A—likely benign
rs2015204376:70,926,748C/A—uncertain significance
rs2008292976:70,926,749G/C—uncertain significance
rs7738484656:70,926,753A/G—likely benign
rs21275441306:70,926,761C/G—uncertain significance
rs21275441346:70,926,769G/T—uncertain significance
rs17685631106:70,926,770C/T—uncertain significance
rs21275441416:70,926,772G/A—uncertain significance
rs12034777196:70,926,773G/A—uncertain significance
rs7454212866:70,926,776C/T—uncertain significance
rs2021767646:70,926,781T/G—conflicting classifications of pathogenicity
rs24830838816:70,926,783A/C—likely benign
rs7607044626:70,926,787G/A—conflicting classifications of pathogenicity
rs21275441766:70,926,795C/T—likely benign
rs24830839696:70,926,797G/A—likely benign
rs24830840056:70,926,800G/T—likely benign
rs94550046:70,926,887C/T—likely benign
rs12005696:70,926,898A/G—benign
rs28813436:70,926,933G/C—benign
rs94550056:70,926,948A/G—likely benign
rs778496716:70,927,015T/A—likely benign
rs1908245226:70,934,705T/Cintron variant—
rs17691955006:70,935,620A/G—likely benign
rs24831355776:70,935,626C/T—likely benign
rs7686420916:70,935,629A/G—uncertain significance
rs24831356456:70,935,630C/T—uncertain significance
rs14158590816:70,935,637G/C—uncertain significance
rs17691974906:70,935,644C/A—uncertain significance
rs7687375376:70,935,647T/C—conflicting classifications of pathogenicity
rs11350576:70,935,654A/G—conflicting classifications of pathogenicity
rs7617424496:70,935,655G/A—uncertain significance
rs8867022346:70,935,658A/G—uncertain significance
rs14403872296:70,935,662C/G—uncertain significance
rs5347523816:70,935,663G/A—likely benign
rs5780342236:70,935,664T/C—uncertain significance
rs17691996806:70,935,670C/T—uncertain significance
rs2019783696:70,935,679G/C—uncertain significance
rs7516602126:70,935,681A/G—likely benign
rs12255227946:70,935,684G/A—likely benign
rs5476181596:70,935,688C/T—uncertain significance
rs1432179386:70,935,689G/A—uncertain significance
rs12874086156:70,935,696C/T—likely benign
rs14137118346:70,935,706A/G—uncertain significance
rs5682959316:70,935,717A/G—likely benign
rs13859793336:70,935,723T/C—uncertain significance
rs24831367486:70,935,725A/G—likely benign
rs5372269886:70,935,731A/G—likely benign
rs792825546:70,935,759T/C—benign
rs132012246:70,937,177G/T——
rs746997446:70,942,217G/A—benign
rs24831746536:70,942,269T/G—likely benign
rs2011593656:70,942,294C/A—uncertain significance
rs7646249086:70,942,297C/T—uncertain significance
rs13373924846:70,942,300A/G—uncertain significance
rs24831751176:70,942,304C/T—uncertain significance
rs341195786:70,942,319G/T—likely benign
rs7576201856:70,942,332C/T—likely benign
rs1445816266:70,942,333G/A—conflicting classifications of pathogenicity
rs17696243056:70,942,335A/G—likely benign
rs14388567496:70,942,336A/T—uncertain significance
rs7512542456:70,942,338G/T—likely benign
rs21275576126:70,942,341A/G—likely benign
rs7545960576:70,942,342C/T—uncertain significance
rs7476529286:70,942,350C/T—uncertain significance
rs1418300606:70,942,353C/A—conflicting classifications of pathogenicity
rs13442397026:70,942,357C/T—uncertain significance
rs13915178756:70,942,373C/G—uncertain significance
rs21275576516:70,942,374T/C—likely benign
rs24831758296:70,942,377A/C—likely benign
rs7490742946:70,942,382G/A—uncertain significance
rs7707050236:70,942,383G/T—likely benign
rs7746108286:70,942,385C/T—uncertain significance

Showing 100 of 1,039 variants. Use the SNP search for the full list.

Gene information from NCBI Gene. Variant classifications from ClinVar.