Gene Gene information from NCBI Gene database.
Entrez ID 1305
Gene name Collagen type XIII alpha 1 chain
Gene symbol COL13A1
Synonyms (NCBI Gene)
CMS19COLXIIIA1
Chromosome 10
Chromosome location 10q22.1
Summary This gene encodes the alpha chain of one of the nonfibrillar collagens. The function of this gene product is not known, however, it has been detected at low levels in all connective tissue-producing cells so it may serve a general function in connective t
SNPs SNP information provided by dbSNP.
7
SNP ID Visualize variation Clinical significance Consequence
rs375471249 T>C Likely-pathogenic Splice donor variant, intron variant
rs763281993 A>- Pathogenic Non coding transcript variant, coding sequence variant, frameshift variant
rs769426298 C>G,T Pathogenic Stop gained, 5 prime UTR variant, coding sequence variant, missense variant, non coding transcript variant
rs864309662 G>- Pathogenic Non coding transcript variant, coding sequence variant, frameshift variant
rs864309663 G>- Pathogenic Non coding transcript variant, coding sequence variant, 5 prime UTR variant, splice acceptor variant
miRNA miRNA information provided by mirtarbase database.
64
miRTarBase ID miRNA Experiments Reference
MIRT706674 hsa-miR-124-3p HITS-CLIP 21572407
MIRT706695 hsa-miR-3714 HITS-CLIP 21572407
MIRT706696 hsa-miR-3910 HITS-CLIP 21572407
MIRT706694 hsa-miR-3664-5p HITS-CLIP 21572407
MIRT706693 hsa-miR-6808-5p HITS-CLIP 21572407
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
24
GO ID Ontology Definition Evidence Reference
GO:0001503 Process Ossification IEA
GO:0001763 Process Morphogenesis of a branching structure ISS
GO:0001958 Process Endochondral ossification ISS
GO:0005515 Function Protein binding IPI 11956183
GO:0005576 Component Extracellular region TAS
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
120350 2190 ENSG00000197467
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q5TAT6
Protein name Collagen alpha-1(XIII) chain (COLXIIIA1)
Protein function Involved in cell-matrix and cell-cell adhesion interactions that are required for normal development. May participate in the linkage between muscle fiber and basement membrane. May play a role in endochondral ossification of bone and branching m
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF01391 Collagen 156 216 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 257 322 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 285 340 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 318 383 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 382 441 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 463 522 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 506 567 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 566 625 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 643 712 Collagen triple helix repeat (20 copies) Repeat
Tissue specificity TISSUE SPECIFICITY: Widely expressed in both fetal and adult ocular tissues (at protein level). In the eye, expression is accentuated in the ciliary muscle, optic nerve and the neural retina. In early placenta, localized to fibroblastoid stromal cells of
Sequence
MVAERTHKAAATGARGPGELGAPGTVALVAARAERGARLPSPGSCGLLTLALCSLALSLL
AHFRTAELQARVLRLEAERGEQQMETAILGRVNQLLDEKWKLHSRRRREAPKTSPGCNCP
PGPPGPTGRPGLPGDKGAIGMPGRVGSPGDAGLSIIGPRGPPGQPGTRGFPGFPGPIGLD
GKPGHPGPKGDMGLTGPPGQPGPQGQKGEKGQCGEY
PHRECLSSMPAALRSSQIIALKLL
PLLNSVRLAPPPVIKRRTFQGEQSQASIQGPPGPPGPPGPSGPLGHPGLPGPMGPPGLPG
PPGPKGDPGIQGYHGRK
GERGMPGMPGKHGAKGAPGIAVAGMKGEPGIPGTKGEKGAEGS
PGLPGLLGQKGEKGDAGNSIGGGRGEPGPPGLPGPPGPKGEAGVDGQVGPPGQPGDKGER
GAAGEQGPDGPKGSKGEPGKG
EMVDYNGNINEALQEIRTLALMGPPGLPGQIGPPGAPGI
PGQKGEIGLPGPPGHDGEKGPRGKP
GDMGPPGPQGPPGKDGPPGVKGENGHPGSPGEKGE
KGETGQAGSPGEKGEAGEKGNPGAEVPGLPGPEGPPGPPGLQGVPGPKGEAGLDGAKGEK
GFQGEKGDRGPLGLPGASGLDGRPG
PPGTPGPIGVPGPAGPKGERGSKGDPGMTGPTGAA
GLPGLHGPPGDKGNRGERGKKGSRGPKGDKGDQGAPGLDAPCPLGEDGLPVQ
GCWNK
Sequence length 717
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
Integrin cell surface interactions
Collagen chain trimerization
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
32
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
Congenital myasthenic syndrome 19 Likely pathogenic; Pathogenic rs763197055, rs2136077497, rs2134842358, rs2135829327, rs769673346, rs1480562957, rs864309662, rs864309663, rs2544717844, rs763281993, rs1057204973, rs2545815673, rs1554943789, rs2064735979, rs1564932829
View all (2 more)
RCV003136050
RCV001543594
RCV001543595
RCV001543596
RCV001780804
View all (12 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Thyroid cancer, nonmedullary, 1 Likely pathogenic rs894208635 RCV005928392
★★★★☆
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 Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CIRRHOSIS OF LIVER GWAS catalog
★★☆☆☆
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
Arthrogryposis Arthrogryposis multiplex congenita HPO_DG
★☆☆☆☆
Found in Text Mining only
Bladder Neoplasm Bladder Neoplasm BEFREE 28415608, 28837258
★☆☆☆☆
Found in Text Mining only
Blepharoptosis Ptosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Bulbar palsy Bulbar palsy HPO_DG
★☆☆☆☆
Found in Text Mining only
Byzanthine arch palate High palate HPO_DG
★☆☆☆☆
Found in Text Mining only
Carcinoma of bladder Bladder carcinoma BEFREE 28837258
★☆☆☆☆
Found in Text Mining only
Clumsiness - motor delay Motor delay HPO_DG
★☆☆☆☆
Found in Text Mining only
Congenital Dysplasia Of The Hip Developmental dysplasia of the hip HPO_DG
★☆☆☆☆
Found in Text Mining only
Congenital kyphoscoliosis Congenital kyphoscoliosis HPO_DG
★☆☆☆☆
Found in Text Mining only