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Aliases for COL12A1 Gene

Aliases for COL12A1 Gene

  • Collagen Type XII Alpha 1 Chain 2 3 5
  • Collagen Type XII Proteoglycan 2 3
  • Collagen, Type XII, Alpha 1 2 3
  • COL12A1L 3 4
  • Collagen, Type XII, Alpha 1-Like 2
  • Collagen Alpha-1(XII) Chain 3
  • DJ234P15.1 3
  • BA209D8.1 3
  • BTHLM2 3
  • UCMD2 3

External Ids for COL12A1 Gene

Previous HGNC Symbols for COL12A1 Gene

  • COL12A1L

Previous GeneCards Identifiers for COL12A1 Gene

  • GC06M075743
  • GC06M075789
  • GC06M075850
  • GC06M072993

Summaries for COL12A1 Gene

Entrez Gene Summary for COL12A1 Gene

  • 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 is thought to modify the interactions between collagen I fibrils and the surrounding matrix. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

GeneCards Summary for COL12A1 Gene

COL12A1 (Collagen Type XII Alpha 1 Chain) is a Protein Coding gene. Diseases associated with COL12A1 include Bethlem Myopathy 2 and Ullrich Congenital Muscular Dystrophy 2. Among its related pathways are Degradation of the extracellular matrix and Phospholipase-C Pathway. GO annotations related to this gene include extracellular matrix structural constituent conferring tensile strength. An important paralog of this gene is COL14A1.

UniProtKB/Swiss-Prot for COL12A1 Gene

  • 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.

Gene Wiki entry for COL12A1 Gene

Additional gene information for COL12A1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL12A1 Gene

Genomics for COL12A1 Gene

Regulatory Elements for COL12A1 Gene

Enhancers for COL12A1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06H075200 1.6 FANTOM5 ENCODE dbSUPER 12.1 +1.2 1240 8.5 SIN3A FEZF1 ZNF2 ZNF143 FOS DEK SP3 REST SMARCB1 ZNF592 SENP6 COL12A1 LOC100506804 TMEM30A GC06P075070
GH06H075242 1.1 ENCODE 10.7 -37.7 -37687 2.3 PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF143 DEK TMEM30A LOC100506804 FILIP1 SENP6 COL12A1 COX7A2
GH06H075267 1 Ensembl ENCODE 11 -62.2 -62164 1.8 CTCF PKNOX1 ETV1 FEZF1 REST ZNF843 BRCA1 PRDM6 ZNF791 HMBOX1 SENP6 COL12A1 RNU6-1016P TMEM30A COX7A2
GH06H075144 0.7 FANTOM5 dbSUPER 14.3 +62.3 62267 0.3 ZNF600 COL12A1 GC06P075070
GH06H075170 0.8 ENCODE dbSUPER 11.9 +34.7 34727 2.5 RFX1 MAX MNT BMI1 COL12A1 GC06P075070
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around COL12A1 on UCSC Golden Path with GeneCards custom track

Promoters for COL12A1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000199008 902 2201 FEZF1 BRCA1 ZNF2 GLIS2 ZNF143 FOS DEK SP3 TSHZ1 REST

Genomic Locations for COL12A1 Gene

Genomic Locations for COL12A1 Gene
121,877 bases
Minus strand

Genomic View for COL12A1 Gene

Genes around COL12A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL12A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL12A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL12A1 Gene

Proteins for COL12A1 Gene

  • Protein details for COL12A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Collagen alpha-1(XII) chain
    Protein Accession:
    Secondary Accessions:
    • O43853
    • Q15955
    • Q5VYK1
    • Q5VYK2
    • Q71UR3
    • Q99716

    Protein attributes for COL12A1 Gene

    3063 amino acids
    Molecular mass:
    333147 Da
    Quaternary structure:
    • Trimer of identical chains each containing 190 kDa of non-triple-helical sequences.

    Alternative splice isoforms for COL12A1 Gene


neXtProt entry for COL12A1 Gene

Post-translational modifications for COL12A1 Gene

  • Hydroxylation on proline residues within the sequence motif, GXPG, is most likely to be 4-hydroxy as this fits the requirement for 4-hydroxylation in vertebrates.
  • Isoform 1 O-glycosylation; glycosaminoglycan of chondroitin-sulfate type.
  • The triple-helical tail is stabilized by disulfide bonds at each end.
  • Glycosylation at posLast=700700, posLast=798798, Ser889, Ser981, posLast=10991099, posLast=11061106, Thr1120, Thr1124, Thr1748, posLast=17631763, posLast=22062206, posLast=23032303, posLast=25282528, and posLast=26792679
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for COL12A1 Gene

Domains & Families for COL12A1 Gene

Gene Families for COL12A1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted secreted proteins

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
genes like me logo Genes that share domains with COL12A1: view

Function for COL12A1 Gene

Molecular function for COL12A1 Gene

GENATLAS Biochemistry:
collagen,type XII,alpha 1,extracellular matrix protein,fibril associated collagen with interrupted triple helices (FACIT),with two splice variants 330.8,203.2kDa,respectively,expressed in collagen I-containing tissues
UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for COL12A1 Gene

Gene Ontology (GO) - Molecular Function for COL12A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030020 extracellular matrix structural constituent conferring tensile strength NAS 1427837
genes like me logo Genes that share ontologies with COL12A1: view
genes like me logo Genes that share phenotypes with COL12A1: view

Human Phenotype Ontology for COL12A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for COL12A1 Gene

MGI Knock Outs for COL12A1:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for COL12A1 Gene

Localization for COL12A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL12A1 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COL12A1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
plasma membrane 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for COL12A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005581 collagen trimer IEA --
GO:0005595 collagen type XII trimer NAS,TAS 1427837
GO:0005615 extracellular space IDA 20551380
genes like me logo Genes that share ontologies with COL12A1: view

Pathways & Interactions for COL12A1 Gene

genes like me logo Genes that share pathways with COL12A1: view

Gene Ontology (GO) - Biological Process for COL12A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 3476925
GO:0007155 cell adhesion IEA --
GO:0030199 collagen fibril organization NAS 1427837
GO:0030574 collagen catabolic process TAS --
GO:0035987 endodermal cell differentiation IEP 23154389
genes like me logo Genes that share ontologies with COL12A1: view

No data available for SIGNOR curated interactions for COL12A1 Gene

Drugs & Compounds for COL12A1 Gene

No Compound Related Data Available

Transcripts for COL12A1 Gene

Unigene Clusters for COL12A1 Gene

Collagen, type XII, alpha 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL12A1 Gene

No ASD Table

Relevant External Links for COL12A1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for COL12A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COL12A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for COL12A1 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (39.3) and Breast (10.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for COL12A1 Gene

Protein tissue co-expression partners for COL12A1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of COL12A1 Gene:


SOURCE GeneReport for Unigene cluster for COL12A1 Gene:


mRNA Expression by UniProt/SwissProt for COL12A1 Gene:

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 in lung, placenta, kidney and a squamous cell carcinoma cell line. Isoform 1 is also present in the corneal epithelial Bowmans membrane (BM) and the interfibrillar matrix of the corneal stroma, but it is not detected in the limbal BM.

Evidence on tissue expression from TISSUES for COL12A1 Gene

  • Liver(4.5)
  • Eye(4.2)
  • Pancreas(3.3)
  • Adrenal gland(3.1)
  • Intestine(3)
  • Kidney(3)
  • Lung(2.5)
  • Gall bladder(2.4)
  • Bone(2.2)
  • Heart(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for COL12A1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • outer ear
  • skull
  • bronchus
  • chest wall
  • clavicle
  • diaphragm
  • heart
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • kidney
  • pelvis
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • sweat gland
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with COL12A1: view

No data available for mRNA differential expression in normal tissues for COL12A1 Gene

Orthologs for COL12A1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for COL12A1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia COL12A1 33 34
  • 99.58 (n)
(Canis familiaris)
Mammalia COL12A1 33 34
  • 91.86 (n)
(Monodelphis domestica)
Mammalia COL12A1 34
  • 90 (a)
(Bos Taurus)
Mammalia COL12A1 33 34
  • 89.53 (n)
(Mus musculus)
Mammalia Col12a1 33 16 34
  • 87.75 (n)
(Rattus norvegicus)
Mammalia Col12a1 33
  • 87.46 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 73 (a)
(Gallus gallus)
Aves COL12A1 33 34
  • 75.96 (n)
(Anolis carolinensis)
Reptilia COL12A1 34
  • 77 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia col12a1 33
  • 70.9 (n)
Str.12198 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.23790 33
(Danio rerio)
Actinopterygii col12a1a 33 34
  • 62.69 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3872 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10963 34
  • 19 (a)
Species where no ortholog for COL12A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for COL12A1 Gene

Gene Tree for COL12A1 (if available)
Gene Tree for COL12A1 (if available)

Paralogs for COL12A1 Gene

(4) SIMAP similar genes for COL12A1 Gene using alignment to 6 proteins: Pseudogenes for COL12A1 Gene

genes like me logo Genes that share paralogs with COL12A1: view

Variants for COL12A1 Gene

Sequence variations from dbSNP and Humsavar for COL12A1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs200487396 Pathogenic, Bethlem myopathy 2 (BTHLM2) [MIM:616471] 75,131,984(+) AACGC(A/G)ATATT reference, missense
rs796052093 Pathogenic, Bethlem myopathy 2 (BTHLM2) [MIM:616471] 75,121,387(-) GAGCA(C/T)TGGGG reference, missense
rs796052094 Pathogenic, Bethlem myopathy 2 (BTHLM2) [MIM:616471] 75,102,655(-) TCCAG(A/G)CCCCC reference, missense
rs875989819 Pathogenic 75,113,601(-) AGATC(A/G)TAAGA splice-donor-variant
rs141517088 Likely benign 75,177,825(+) AACTG(A/G)TCTAT intron-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for COL12A1 Gene

Variant ID Type Subtype PubMed ID
nsv830697 CNV gain+loss 17160897
nsv603762 CNV loss 21841781
nsv475786 CNV novel sequence insertion 20440878
esv3609570 CNV loss 21293372

Variation tolerance for COL12A1 Gene

Residual Variation Intolerance Score: 9.57% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.18; 80.87% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL12A1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL12A1 Gene

Disorders for COL12A1 Gene

MalaCards: The human disease database

(9) MalaCards diseases for COL12A1 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards


  • Bethlem myopathy 2 (BTHLM2) [MIM:616471]: A form of Bethlem myopathy, a benign proximal myopathy characterized by early childhood onset and joint contractures most frequently affecting the elbows and ankles. {ECO:0000269 PubMed:24334604, ECO:0000269 PubMed:24334769}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Ullrich congenital muscular dystrophy 2 (UCMD2) [MIM:616470]: A form of Ullrich muscular dystrophy, a congenital myopathy characterized by muscle weakness and multiple joint contractures, generally noted at birth or early infancy. The clinical course is more severe than in Bethlem myopathy. {ECO:0000269 PubMed:24334604}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for COL12A1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with COL12A1: view

No data available for Genatlas for COL12A1 Gene

Publications for COL12A1 Gene

  1. Complete primary structure of two splice variants of collagen XII, and assignment of alpha 1(XII) collagen (COL12A1), alpha 1(IX) collagen (COL9A1), and alpha 1(XIX) collagen (COL19A1) to human chromosome 6q12-q13. (PMID: 9143499) Gerecke DR … Burgeson RE (Genomics 1997) 2 3 4 22 60
  2. The COL12A1 and COL14A1 genes and Achilles tendon injuries. (PMID: 17960519) September AV … Collins M (International journal of sports medicine 2008) 3 22 45 60
  3. The mouse alpha 1(XII) and human alpha 1(XII)-like collagen genes are localized on mouse chromosome 9 and human chromosome 6. (PMID: 1427837) Oh SP … Olsen BR (Genomics 1992) 3 4 22 60
  4. Mutations in the collagen XII gene define a new form of extracellular matrix-related myopathy. (PMID: 24334769) Hicks D … Straub V (Human molecular genetics 2014) 3 4 60
  5. A Large-scale genetic association study of esophageal adenocarcinoma risk. (PMID: 20453000) Liu CY … Christiani DC (Carcinogenesis 2010) 3 45 60

Products for COL12A1 Gene

Sources for COL12A1 Gene

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