Gene Gene information from NCBI Gene database.
Entrez ID 1293
Gene name Collagen type VI alpha 3 chain
Gene symbol COL6A3
Synonyms (NCBI Gene)
BTHLM1BTHLM1CDYT27UCMD1UCMD1C
Chromosome 2
Chromosome location 2q37.3
Summary This gene encodes the alpha-3 chain, one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The alpha-3 chain of type VI collagen is much larger than the alpha-1 and -2 chains. This difference in si
SNPs SNP information provided by dbSNP.
193
SNP ID Visualize variation Clinical significance Consequence
rs34390834 G>A Conflicting-interpretations-of-pathogenicity Coding sequence variant, genic downstream transcript variant, synonymous variant
rs34741387 G>A Benign-likely-benign, conflicting-interpretations-of-pathogenicity Coding sequence variant, missense variant, intron variant
rs78365682 G>A Conflicting-interpretations-of-pathogenicity, likely-benign Coding sequence variant, intron variant, synonymous variant
rs111481402 G>A Uncertain-significance, conflicting-interpretations-of-pathogenicity, likely-benign Coding sequence variant, intron variant, synonymous variant
rs112181324 C>T Conflicting-interpretations-of-pathogenicity, likely-benign Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
402
miRTarBase ID miRNA Experiments Reference
MIRT756089 hsa-miR-202-3p Western blottingqRT-PCR 37226011
MIRT903151 hsa-miR-1207-5p CLIP-seq
MIRT903152 hsa-miR-1275 CLIP-seq
MIRT903153 hsa-miR-4488 CLIP-seq
MIRT903154 hsa-miR-4665-5p CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
27
GO ID Ontology Definition Evidence Reference
GO:0004867 Function Serine-type endopeptidase inhibitor activity IEA
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
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
120250 2213 ENSG00000163359
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P12111
Protein name Collagen alpha-3(VI) chain
Protein function Collagen VI acts as a cell-binding protein.
PDB 1KNT , 1KTH , 1KUN , 2KNT , 6SNK
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00092 VWA 39 212 von Willebrand factor type A domain Domain
PF00092 VWA 242 414 von Willebrand factor type A domain Domain
PF00092 VWA 445 616 von Willebrand factor type A domain Domain
PF00092 VWA 639 811 von Willebrand factor type A domain Domain
PF00092 VWA 837 1008 von Willebrand factor type A domain Domain
PF00092 VWA 1029 1200 von Willebrand factor type A domain Domain
PF00092 VWA 1233 1403 von Willebrand factor type A domain Domain
PF00092 VWA 1436 1608 von Willebrand factor type A domain Domain
PF00092 VWA 1639 1811 von Willebrand factor type A domain Domain
PF01391 Collagen 2036 2096 Collagen triple helix repeat (20 copies) Repeat
PF00092 VWA 2402 2579 von Willebrand factor type A domain Domain
PF00092 VWA 2619 2808 von Willebrand factor type A domain Domain
PF00014 Kunitz_BPTI 3111 3163 Kunitz/Bovine pancreatic trypsin inhibitor domain Domain
Sequence
MRKHRHLPLVAVFCLFLSGFPTTHAQQQQADVKNGAAADIIFLVDSSWTIGEEHFQLVRE
FLYDVVKSLAVGENDFHFALVQFNGNPHTEFLLNTYRTKQEVLSHISNMSYIGGTNQTGK
GLEYIMQSHLTKAAGSRAGDGVPQVIVVLTDGHSKDGLALPSAELKSADVNVFAIGVEDA
DEGALKEIASEPLNMHMFNLENFTSLHDIVGN
LVSCVHSSVSPERAGDTETLKDITAQDS
ADIIFLIDGSNNTGSVNFAVILDFLVNLLEKLPIGTQQIRVGVVQFSDEPRTMFSLDTYS
TKAQVLGAVKALGFAGGELANIGLALDFVVENHFTRAGGSRVEEGVPQVLVLISAGPSSD
EIRYGVVALKQASVFSFGLGAQAASRAELQHIATDDNLVFTVPEFRSFGDLQEK
LLPYIV
GVAQRHIVLKPPTIVTQVIEVNKRDIVFLVDGSSALGLANFNAIRDFIAKVIQRLEIGQD
LIQVAVAQYADTVRPEFYFNTHPTKREVITAVRKMKPLDGSALYTGSALDFVRNNLFTSS
AGYRAAEGIPKLLVLITGGKSLDEISQPAQELKRSSIMAFAIGNKGADQAELEEIAFDSS
LVFIPAEFRAAPLQGM
LPGLLAPLRTLSGTPEVHSNKRDIIFLLDGSANVGKTNFPYVRD
FVMNLVNSLDIGNDNIRVGLVQFSDTPVTEFSLNTYQTKSDILGHLRQLQLQGGSGLNTG
SALSYVYANHFTEAGGSRIREHVPQLLLLLTAGQSEDSYLQAANALTRAGILTFCVGASQ
ANKAELEQIAFNPSLVYLMDDFSSLPALPQQ
LIQPLTTYVSGGVEEVPLAQPESKRDILF
LFDGSANLVGQFPVVRDFLYKIIDELNVKPEGTRIAVAQYSDDVKVESRFDEHQSKPEIL
NLVKRMKIKTGKALNLGYALDYAQRYIFVKSAGSRIEDGVLQFLVLLVAGRSSDRVDGPA
SNLKQSGVVPFIFQAKNADPAELEQIVLSPAFILAAESLPKIGDLHPQ
IVNLLKSVHNGA
PAPVSGEKDVVFLLDGSEGVRSGFPLLKEFVQRVVESLDVGQDRVRVAVVQYSDRTRPEF
YLNSYMNKQDVVNAVRQLTLLGGPTPNTGAALEFVLRNILVSSAGSRITEGVPQLLIVLT
ADRSGDDVRNPSVVVKRGGAVPIGIGIGNADITEMQTISFIPDFAVAIPTFRQLGTVQQV

ISERVTQLTREELSRLQPVLQPLPSPGVGGKRDVVFLIDGSQSAGPEFQYVRTLIERLVD
YLDVGFDTTRVAVIQFSDDPKVEFLLNAHSSKDEVQNAVQRLRPKGGRQINVGNALEYVS
RNIFKRPLGSRIEEGVPQFLVLISSGKSDDEVDDPAVELKQFGVAPFTIARNADQEELVK
ISLSPEYVFSVSTFRELPSLEQK
LLTPITTLTSEQIQKLLASTRYPPPAVESDAADIVFL
IDSSEGVRPDGFAHIRDFVSRIVRRLNIGPSKVRVGVVQFSNDVFPEFYLKTYRSQAPVL
DAIRRLRLRGGSPLNTGKALEFVARNLFVKSAGSRIEDGVPQHLVLVLGGKSQDDVSRFA
QVIRSSGIVSLGVGDRNIDRTELQTITNDPRLVFTVREFRELPNIEER
IMNSFGPSAATP
APPGVDTPPPSRPEKKKADIVFLLDGSINFRRDSFQEVLRFVSEIVDTVYEDGDSIQVGL
VQYNSDPTDEFFLKDFSTKRQIIDAINKVVYKGGRHANTKVGLEHLRVNHFVPEAGSRLD
QRVPQIAFVITGGKSVEDAQDVSLALTQRGVKVFAVGVRNIDSEEVGKIASNSATAFRVG
NVQELSELSEQ
VLETLHDAMHETLCPGVTDAAKACNLDVILGFDGSRDQNVFVAQKGFES
KVDAILNRISQMHRVSCSGGRSPTVRVSVVANTPSGPVEAFDFDEYQPEMLEKFRNMRSQ
HPYVLTEDTLKVYLNKFRQSSPDSVKVVIHFTDGADGDLADLHRASENLRQEGVRALILV
GLERVVNLERLMHLEFGRGFMYDRPLRLNLLDLDYELAEQLDNIAEKACCGVPCKCSGQR
GDRGPIGSIGPKGIPGEDGYRGYPGDEGGPGERGPPGVNGTQGFQGCPGQRGVKGS
RGFP
GEKGEVGEIGLDGLDGEDGDKGLPGSSGEKGNPGRRGDKGPRGEKGERGDVGIRGDPGNP
GQDSQERGPKGETGDLGPMGVPGRDGVPGGPGETGKNGGFGRRGPPGAKGNKGGPGQPGF
EGEQGTRGAQGPAGPAGPPGLIGEQGISGPRGSGGAAGAPGERGRTGPLGRKGEPGEPGP
KGGIGNRGPRGETGDDGRDGVGSEGRRGKKGERGFPGYPGPKGNPGEPGLNGTTGPKGIR
GRRGNSGPPGIVGQKGDPGYPGPAGPKGNRGDSIDQCALIQSIKDKCPCCYGPLECPVFP
TELAFALDTSEGVNQDTFGRMRDVVLSIVNDLTIAESNCPRGARVAVVTYNNEVTTEIRF
ADSKRKSVLLDKIKNLQVALTSKQQSLETAMSFVARNTFKRVRNGFLMRKVAVFFSNTPT
RASPQLREAVLKLSDAGITPLFLTRQEDRQLINALQINNTAVGHALVLPAGRDLTDFLE
N
VLTCHVCLDICNIDPSCGFGSWRPSFRDRRAAGSDVDIDMAFILDSAETTTLFQFNEMKK
YIAYLVRQLDMSPDPKASQHFARVAVVQHAPSESVDNASMPPVKVEFSLTDYGSKEKLVD
FLSRGMTQLQGTRALGSAIEYTIENVFESAPNPRDLKIVVLMLTGEVPEQQLEEAQRVIL
QAKCKGYFFVVLGIGRKVNIKEVYTFASEPNDVFFKLVDKSTELNEEP
LMRFGRLLPSFV
SSENAFYLSPDIRKQCDWFQGDQPTKNLVKFGHKQVNVPNNVTSSPTSNPVTTTKPVTTT
KPVTTTTKPVTTTTKPVTIINQPSVKPAAAKPAPAKPVAAKPVATKMATVRPPVAVKPAT
AAKPVAAKPAAVRPPAAAAAKPVATKPEVPRPQAAKPAATKPATTKPMVKMSREVQVFEI
TENSAKLHWERAEPPGPYFYDLTVTSAHDQSLVLKQNLTVTDRVIGGLLAGQTYHVAVVC
YLRSQVRATYHGSFSTKKSQPPPPQPARSASSSTINLMVSTEPLALTETDICKLPKDEGT
CRDFILKWYYDPNTKSCARFWYGGCGGNENKFGSQKECEKVCA
PVLAKPGVISVMGT
Sequence length 3177
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  PI3K-Akt signaling pathway
Focal adhesion
ECM-receptor interaction
Cytoskeleton in muscle cells
Protein digestion and absorption
Human papillomavirus infection
  Collagen degradation
Collagen biosynthesis and modifying enzymes
Signaling by PDGF
Assembly of collagen fibrils and other multimeric structures
Integrin cell surface interactions
ECM proteoglycans
NCAM1 interactions
Collagen chain trimerization
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
78
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 the musculature Likely pathogenic rs2106314700, rs1395597644 RCV001814343
RCV001814348
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Bethlem myopathy 1A Pathogenic; Likely pathogenic rs398124126, rs398124128, rs886044593, rs2076974450, rs1323862623, rs2106341460, rs2106344225, rs948586287, rs2106324972, rs761453030, rs886043919, rs2106312317, rs2106324666, rs767654047, rs2106367443
View all (93 more)
RCV000817699
RCV001854427
RCV001327990
RCV001331208
RCV001384667
View all (112 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Bethlem myopathy 1C Pathogenic; Likely pathogenic rs398124126, rs139260335, rs2469819229, rs758626447, rs121434553, rs2469867055, rs121434555, rs2469799960, rs761796175 RCV005859498
RCV004589832
RCV004813234
RCV004595715
RCV003764588
View all (4 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
COL6A3-related disorder Likely pathogenic; Pathogenic rs139260335, rs780921503, rs2469883432, rs758626447, rs764193290, rs755382829 RCV003387788
RCV005230228
RCV004550569
RCV004554350
RCV004551575
View all (1 more)
★★★★★
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
Acute myeloid leukemia 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
AUTOSOMAL RECESSIVE DISTAL HEREDITARY MOTOR NEUROPATHY Disgenet
★★☆☆☆
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
Adamantinous Craniopharyngioma Adamantinous Craniopharyngioma BEFREE 29681617
★☆☆☆☆
Found in Text Mining only
Anaplasia Anaplasia BEFREE 28781950
★☆☆☆☆
Found in Text Mining only
Aortic Aneurysm Aortic aneurysm Pubtator 34968759 Associate
★☆☆☆☆
Found in Text Mining only
Aortic Aneurysm Abdominal Aortic aneurysm Pubtator 39895541 Associate
★☆☆☆☆
Found in Text Mining only
Autosomal Dominant Emery-Dreifuss Muscular Dystrophy (disorder) Emery-Dreifuss Muscular Dystrophy BEFREE 20576434
★☆☆☆☆
Found in Text Mining only
Bethlem myopathy Bethlem myopathy Pubtator 10419498, 11707460, 15689448, 19884007, 20882040, 22075033, 22226732, 29774307, 33596003, 39523858, 40225172, 40626679 Associate
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bethlem myopathy Bethlem Myopathy Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BETHLEM MYOPATHY 1 Bethlem Myopathy BEFREE 10399756, 15563506, 15689448, 15955946, 16141002, 18366090, 18378883, 19884007, 20882040, 21496625, 24334769, 28831785, 29894794, 8817344, 9536084
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BETHLEM MYOPATHY 1 Bethlem Myopathy UNIPROT_DG 10399756, 15689448, 17886299, 9536084
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BETHLEM MYOPATHY 1 Bethlem Myopathy CLINVAR_DG 15563506, 15689448, 17886299, 18366090, 18825676, 19344236, 20976770, 21280092, 24038877, 26004199, 26247046, 27447704, 27854218, 28688748, 7695699
View all (1 more)
★★☆☆☆
Found in Text Mining + Unknown/Other Associations