Gene Gene information from NCBI Gene database.
Entrez ID 1303
Gene name Collagen type XII alpha 1 chain
Gene symbol COL12A1
Synonyms (NCBI Gene)
BA209D8.1BTHLM2COL12A1LDJ234P15.1EDSMYPUCMD2
Chromosome 6
Chromosome location 6q13-q14.1
Summary This gene encodes the alpha chain of type XII collagen, a member of the FACIT (fibril-associated collagens with interrupted triple helices) collagen family. Type XII collagen is a homotrimer found in association with type I collagen, an association that i
SNPs SNP information provided by dbSNP.
33
SNP ID Visualize variation Clinical significance Consequence
rs41266761 C>T Likely-benign, conflicting-interpretations-of-pathogenicity Coding sequence variant, missense variant
rs151324784 C>T Conflicting-interpretations-of-pathogenicity Coding sequence variant, missense variant
rs200201449 C>T Conflicting-interpretations-of-pathogenicity Coding sequence variant, missense variant
rs200443479 G>A,T Conflicting-interpretations-of-pathogenicity Coding sequence variant, intron variant, missense variant
rs200487396 G>A,T Uncertain-significance, pathogenic Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
546
miRTarBase ID miRNA Experiments Reference
MIRT020009 hsa-miR-375 Microarray 20215506
MIRT021464 hsa-miR-9-5p Microarray 17612493
MIRT023070 hsa-miR-124-3p Proteomics;Microarray 18668037
MIRT024050 hsa-miR-1-3p Proteomics;Microarray 18668037
MIRT438071 hsa-miR-26b-5p pSILAC 23939832
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
20
GO ID Ontology Definition Evidence Reference
GO:0005576 Component Extracellular region HDA 27068509
GO:0005576 Component Extracellular region IEA
GO:0005576 Component Extracellular region TAS
GO:0005581 Component Collagen trimer IEA
GO:0005595 Component Collagen type XII trimer NAS 1427837
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
120320 2188 ENSG00000111799
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q99715
Protein name Collagen alpha-1(XII) chain
Protein function Type XII collagen interacts with type I collagen-containing fibrils, the COL1 domain could be associated with the surface of the fibrils, and the COL2 and NC3 domains may be localized in the perifibrillar matrix.
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00041 fn3 26 105 Fibronectin type III domain Domain
PF00092 VWA 140 311 von Willebrand factor type A domain Domain
PF00041 fn3 335 416 Fibronectin type III domain Domain
PF00092 VWA 440 611 von Willebrand factor type A domain Domain
PF00041 fn3 633 712 Fibronectin type III domain Domain
PF00041 fn3 724 801 Fibronectin type III domain Domain
PF00041 fn3 815 894 Fibronectin type III domain Domain
PF00041 fn3 906 986 Fibronectin type III domain Domain
PF00041 fn3 999 1077 Fibronectin type III domain Domain
PF00041 fn3 1088 1168 Fibronectin type III domain Domain
PF00092 VWA 1199 1370 von Willebrand factor type A domain Domain
PF00041 fn3 1386 1465 Fibronectin type III domain Domain
PF00041 fn3 1475 1556 Fibronectin type III domain Domain
PF00041 fn3 1567 1646 Fibronectin type III domain Domain
PF00041 fn3 1656 1734 Fibronectin type III domain Domain
PF00041 fn3 1754 1835 Fibronectin type III domain Domain
PF00041 fn3 1845 1926 Fibronectin type III domain Domain
PF00041 fn3 1937 2016 Fibronectin type III domain Domain
PF00041 fn3 2026 2108 Fibronectin type III domain Domain
PF00041 fn3 2117 2195 Fibronectin type III domain Domain
PF00041 fn3 2205 2283 Fibronectin type III domain Domain
PF00092 VWA 2323 2495 von Willebrand factor type A domain Domain
PF01391 Collagen 2745 2802 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 2800 2853 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 2844 2902 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 2937 2994 Collagen triple helix repeat (20 copies) Repeat
Tissue specificity TISSUE SPECIFICITY: Found in collagen I-containing tissues: both isoform 1 and isoform 2 appear in amnion, chorion, skeletal muscle, small intestine, and in cell culture of dermal fibroblasts, keratinocytes and endothelial cells. Only isoform 2 is found i
Sequence
MRSRLPPALAALGAALLLSSIEAEVDPPSDLNFKIIDENTVHMSWAKPVDPIVGYRITVD
PTTDGPTKEFTLSASTTETLLSELVPETEYVVTITSYDEVEESVP
VIGQLTIQTGSSTKP
VEKKPGKTEIQKCSVSAWTDLVFLVDGSWSVGRNNFKYILDFIAALVSAFDIGEEKTRVG
VVQYSSDTRTEFNLNQYYQRDELLAAIKKIPYKGGNTMTGDAIDYLVKNTFTESAGARVG
FPKVAIIITDGKSQDEVEIPARELRNVGVEVFSLGIKAADAKELKQIASTPSLNHVFNVA
NFDAIVDIQNE
IISQVCSGVDEQLGELVSGEEVVEPPSNLIAMEVSSKYVKLNWNPSPSP
VTGYKVILTPMTAGSRQHALSVGPQTTTLSVRDLSADTEYQISVSAMKGMTSSEPI
SIME
KTQPMKVQVECSRGVDIKADIVFLVDGSYSIGIANFVKVRAFLEVLVKSFEISPNRVQIS
LVQYSRDPHTEFTLKKFTKVEDIIEAINTFPYRGGSTNTGKAMTYVREKIFVPSKGSRSN
VPKVMILITDGKSSDAFRDPAIKLRNSDVEIFAVGVKDAVRSELEAIASPPAETHVFTVE
DFDAFQRISFE
LTQSICLRIEQELAAIKKKAYVPPKDLSFSEVTSYGFKTNWSPAGENVF
SYHITYKEAAGDDEVTVVEPASSTSVVLSSLKPETLYLVNVTAEYEDGFSIP
LAGEETTE
EVKGAPRNLKVTDETTDSFKITWTQAPGRVLRYRIIYRPVAGGESREVTTPPNQRRRTLE
NLIPDTKYEVSVIPEYFSGPG
TPLTGNAATEEVRGNPRDLRVSDPTTSTMKLSWSGAPGK
VKQYLVTYTPVAGGETQEVTVRGDTTNTVLQGLKEGTQYALSVTALYASGAGDA
LFGEGT
TLEERGSPQDLVTKDITDTSIGAYWTSAPGMVRGYRVSWKSLYDDVDTGEKNLPEDAIHT
MIENLQPETKYRISVFATYSSGEGEP
LTGDATTELSQDSKTLKVDEETENTMRVTWKPAP
GKVVNYRVVYRPHGRGKQMVAKVPPTVTSTVLKRLQPQTTYDITVLPIYKMGEGKLR
QGS
GTTASRFKSPRNLKTSDPTMSSFRVTWEPAPGEVKGYKVTFHPTGDDRRLGELVVGPYDN
TVVLEELRAGTTYKVNVFGMFDGGESSP
LVGQEMTTLSDTTVMPILSSGMECLTRAEADI
VLLVDGSWSIGRANFRTVRSFISRIVEVFDIGPKRVQIALAQYSGDPRTEWQLNAHRDKK
SLLQAVANLPYKGGNTLTGMALNFIRQQNFRTQAGMRPRARKIGVLITDGKSQDDVEAPS
KKLKDEGVELFAIGIKNADEVELKMIATDPDDTHAYNVADFESLSRIVDD
LTINLCNSVK
GPGDLEAPSNLVISERTHRSFRVSWTPPSDSVDRYKVEYYPVSGGKRQEFYVSRMETSTV
LKDLKPETEYVVNVYSVVEDEYSEP
LKGTEKTLPVPVVSLNIYDVGPTTMHVQWQPVGGA
TGYILSYKPVKDTEPTRPKEVRLGPTVNDMQLTDLVPNTEYAVTVQAVLHDLTSEP
VTVR
EVTLPLPRPQDLKLRDVTHSTMNVFWEPVPGKVRKYIVRYKTPEEDVKEVEVDRSETSTS
LKDLFSQTLYTVSVSAVHDEGESPPV
TAQETTRPVPAPTNLKITEVTSEGFRGTWDHGAS
DVSLYRITWAPFGSSDKMETILNGDENTLVFENLNPNTIYEVSITAIYPDESES
DDLIGS
ERTLPILTTQAPKSGPRNLQVYNATSNSLTVKWDPASGRVQKYRITYQPSTGEGNEQTTT
IGGRQNSVVLQKLKPDTPYTITVSSLYPDGEGGRM
TGRGKTKPLNTVRNLRVYDPSTSTL
NVRWDHAEGNPRQYKLFYAPAAGGPEELVPIPGNTNYAILRNLQPDTSYTVTVVPVYTEG
DGGRTS
DTGRTLMRGLARNVQVYNPTPNSLDVRWDPAPGPVLQYRVVYSPVDGTRPSESI
VVPGNTRMVHLERLIPDTLYSVNLVALYSDGEGNPS
PAQGRTLPRSGPRNLRVFGETTNS
LSVAWDHADGPVQQYRIIYSPTVGDPIDEYTTVPGRRNNVILQPLQPDTPYKITVIAVYE
DGDGGHLT
GNGRTVGLLPPQNIHISDEWYTRFRVSWDPSPSPVLGYKIVYKPVGSNEPME
AFVGEMTSYTLHNLNPSTTYDVNVYAQYDSGLSVP
LTDQGTTLYLNVTDLKTYQIGWDTF
CVKWSPHRAATSYRLKLSPADGTRGQEITVRGSETSHCFTGLSPDTDYGVTVFVQTPNLE
GPG
VSVKEHTTVKPTEAPTEPPTPPPPPTIPPARDVCKGAKADIVFLTDASWSIGDDNFN
KVVKFIFNTVGGFDEISPAGIQVSFVQYSDEVKSEFKLNTYNDKALALGALQNIRYRGGN
TRTGKALTFIKEKVLTWESGMRKNVPKVLVVVTDGRSQDEVKKAALVIQQSGFSVFVVGV
ADVDYNELANIASKPSERHVFIVDDFESFEKIEDN
LITFVCETATSSCPLIYLDGYTSPG
FKMLEAYNLTEKNFASVQGVSLESGSFPSYSAYRIQKNAFVNQPTADLHPNGLPPSYTII
LLFRLLPETPSDPFAIWQITDRDYKPQVGVIADPSSKTLSFFNKDTRGEVQTVTFDTEEV
KTLFYGSFHKVHIVVTSKSVKIYIDCYEIIEKDIKEAGNITTDGYEILGKLLKGERKSAA
FQIQSFDIVCSPVWTSRDRCCDIPSRRDEGKCPAFPNSCTCTQDSVGPPGPPGPAGGPGA
KGPRGERGISGAIGPPGPRGDIGPPGPQGPPGPQGPNGL
SIPGEQGRQGMKGDAGEPGLP
GRTGTPGLPGPPGPMGPPGDRGFTGKDGAMGPRGPPGPPGSPGSPGVTGPSGKPGKPGDH
GRPGPSGLKGEKGDRGDIASQN
MMRAVARQVCEQLISGQMNRFNQMLNQIPNDYQSSRNQ
PGPPGPPGPPGSAGARGEPGPGGRPGFPGTPGMQGPPGERGLPGEKGERGTGSS
GPRGLP
GPPGPQGESRTGPPGSTGSRGPPGPPGRPGNSGIRGPPGPPGYCDSSQCASIPYNGQGYP
GSG
Sequence length 3063
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Protein digestion and absorption   Collagen degradation
Collagen biosynthesis and modifying enzymes
Assembly of collagen fibrils and other multimeric structures
Collagen chain trimerization
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
50
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Abnormality of connective tissue Likely pathogenic rs1582025807 RCV000850300
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Bethlem myopathy 2 Likely pathogenic; Pathogenic rs2149352927, rs2149372690, rs2149337320, rs2149369481, rs1266090046, rs2149347624, rs984784417, rs2149373593, rs2149344192, rs2149492561, rs1765881602, rs1766437216, rs2149349312, rs1766404539, rs1178118885
View all (59 more)
RCV001372379
RCV001378005
RCV001381736
RCV001382528
RCV005225442
View all (70 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
COL12A1-related disorder Likely pathogenic; Pathogenic rs2533398364, rs1064796670 RCV003399561
RCV003915338
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay Likely pathogenic rs1554168326 RCV001526658
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Adrenocortical carcinoma, hereditary Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ASTHMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bartter disease type 4B Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acquired Kyphoscoliosis Acquired Kyphoscoliosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Alzheimer`s Disease Alzheimer disease GWASCAT_DG 26830138
★☆☆☆☆
Found in Text Mining only
Arthritis Rheumatoid Rheumatoid arthritis Pubtator 26191188 Associate
★☆☆☆☆
Found in Text Mining only
Bethlem myopathy Bethlem Myopathy Orphanet
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
Bethlem myopathy Bethlem myopathy Pubtator 27348394, 31273343 Associate
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
BETHLEM MYOPATHY 1 Bethlem Myopathy GENOMICS_ENGLAND_DG 24334604
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BETHLEM MYOPATHY 1 Bethlem Myopathy ORPHANET_DG 24334604, 24334769
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BETHLEM MYOPATHY 1 Bethlem Myopathy BEFREE 29342313
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BETHLEM MYOPATHY 1 Bethlem Myopathy CTD_human_DG
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BETHLEM MYOPATHY 2 Bethlem Myopathy CLINVAR_DG 24334604, 24334769, 27159402, 27348394
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)