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COL12A1 collagen type XII alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 1303, updated on 3-Apr-2024

Summary

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Official Symbol
COL12A1provided by HGNC
Official Full Name
collagen type XII alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:2188
See related
Ensembl:ENSG00000111799 MIM:120320; AllianceGenome:HGNC:2188
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
UCMD2; BTHLM2; EDSMYP; COL12A1L; BA209D8.1; DJ234P15.1
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 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]
Expression
Broad expression in endometrium (RPKM 41.5), ovary (RPKM 33.4) and 18 other tissues See more
Orthologs
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Genomic context

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See COL12A1 in Genome Data Viewer
Location:
6q13-q14.1
Exon count:
68
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (75084326..75206053, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (76261502..76383203, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (75794042..75915769, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928516 Neighboring gene uncharacterized LOC105377858 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:75490962-75491462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:75491463-75491963 Neighboring gene Sharpr-MPRA regulatory region 6905 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94546 Neighboring gene NUP50 pseudogene 4 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94569 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94572 Neighboring gene NANOG hESC enhancer GRCh37_chr6:75674378-75674954 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:75794417-75794939 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:75828643-75829842 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24756 Neighboring gene small nucleolar RNA, C/D box 156 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:75918738-75918943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24757 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24758 Neighboring gene uncharacterized LOC124901344 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:75981645-75982844 Neighboring gene cytochrome c oxidase subunit 7A2 Neighboring gene transmembrane protein 30A

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Temporal profiling of the breast tumour microenvironment reveals collagen XII as a driver of metastasis. Papanicolaou M, et al. Nat Commun, 2022 Aug 6. PMID 35933466, Free PMC Article
  2. COL12A1 Single Nucleotide Polymorphisms rs240736 and rs970547 Are Not Associated with Temporomandibular Joint Disc Displacement without Reduction. Dalewski B, et al. Genes (Basel), 2021 May 5. PMID 34062975, Free PMC Article
  3. A novel mutation in the COL12A1 gene. Araújo D, et al. Gene, 2021 Feb 5. PMID 33129849
  4. Integrated bioinformatics analysis of expression and gene regulation network of COL12A1 in colorectal cancer. Wu Y, et al. Cancer Med, 2020 Jul. PMID 32356618, Free PMC Article
  5. Dominant collagen XII mutations cause a distal myopathy. Mohassel P, et al. Ann Clin Transl Neurol, 2019 Oct. PMID 31509352, Free PMC Article

See all (67) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Whole exome sequencing identifies a novel variant in the COL12A1 gene in a family with Ullrich congenital muscular dystrophy 2.
    Title: Whole exome sequencing identifies a novel variant in the COL12A1 gene in a family with Ullrich congenital muscular dystrophy 2.
  2. PABPC1 promotes cell proliferation and metastasis in pancreatic adenocarcinoma by regulating COL12A1 expression.
    Title: PABPC1 promotes cell proliferation and metastasis in pancreatic adenocarcinoma by regulating COL12A1 expression.
  3. Epigenetic dysregulation-mediated COL12A1 upregulation predicts worse outcome in intrahepatic cholangiocarcinoma patients.
    Title: Epigenetic dysregulation-mediated COL12A1 upregulation predicts worse outcome in intrahepatic cholangiocarcinoma patients.
  4. Temporal profiling of the breast tumour microenvironment reveals collagen XII as a driver of metastasis.
    Title: Temporal profiling of the breast tumour microenvironment reveals collagen XII as a driver of metastasis.
  5. Collagen XII mediated cellular and extracellular mechanisms regulate establishment of tendon structure and function.
    Title: Collagen XII mediated cellular and extracellular mechanisms regulate establishment of tendon structure and function.
  6. Role of collagen XII in skin homeostasis and repair.
    Title: Role of collagen XII in skin homeostasis and repair.
  7. Bioinformatics analysis identified MMP14 and COL12A1 as immune-related biomarkers associated with pancreatic adenocarcinoma prognosis.
    Title: Bioinformatics analysis identified MMP14 and COL12A1 as immune-related biomarkers associated with pancreatic adenocarcinoma prognosis.
  8. COL12A1 Single Nucleotide Polymorphisms rs240736 and rs970547 Are Not Associated with Temporomandibular Joint Disc Displacement without Reduction.
    Title: COL12A1 Single Nucleotide Polymorphisms rs240736 and rs970547 Are Not Associated with Temporomandibular Joint Disc Displacement without Reduction.
  9. Integrated bioinformatics analysis of expression and gene regulation network of COL12A1 in colorectal cancer.
    Title: Integrated bioinformatics analysis of expression and gene regulation network of COL12A1 in colorectal cancer.
  10. A novel mutation in the COL12A1 gene.
    Title: A novel mutation in the COL12A1 gene.
Submit: New GeneRIF Correction See all GeneRIFs (30)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Bethlem myopathy 2
MedGen: C4225313 OMIM: 616471 GeneReviews: Not available
Compare labs
Ullrich congenital muscular dystrophy 2
MedGen: C4225314 OMIM: 616470 GeneReviews: Not available
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables extracellular matrix structural constituent conferring tensile strength NAS
Non-traceable Author Statement
more info
 PubMed 
enables extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in collagen fibril organization NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in endodermal cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endodermal cell differentiation IEP
Inferred from Expression Pattern
more info
 PubMed 
Component Evidence Code Pubs
part_of collagen type XII trimer NAS
Non-traceable Author Statement
more info
 PubMed 
colocalizes_with collagen-containing extracellular matrix HDA PubMed 
located_in collagen-containing extracellular matrix HDA PubMed 
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
located_in extracellular region HDA PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
  
located_in extracellular space HDA PubMed 
located_in extracellular vesicle HDA PubMed 

General protein information

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Preferred Names
collagen alpha-1(XII) chain
Names
collagen type XII proteoglycan
collagen, type XII, alpha 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_042181.1 RefSeqGene

    Range
    4855..126582
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001424113.1 → NP_001411042.1  collagen alpha-1(XII) chain isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) encodes the longest isoform (3).
    Source sequence(s)
    AL080250, AL096771, AL354664
    Related
    ENSP00000421216.1, ENST00000483888.6

  2. NM_001424114.1 → NP_001411043.1  collagen alpha-1(XII) chain isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AL080250, AL096771, AL354664

  3. NM_001424115.1 → NP_001411044.1  collagen alpha-1(XII) chain isoform 5 precursor

    Status: REVIEWED

    Source sequence(s)
    AL080250, AL096771, AL354664

  4. NM_001424116.1 → NP_001411045.1  collagen alpha-1(XII) chain isoform 6 precursor

    Status: REVIEWED

    Source sequence(s)
    AL080250, AL096771

  5. NM_004370.6 → NP_004361.3  collagen alpha-1(XII) chain long isoform precursor

    See identical proteins and their annotated locations for NP_004361.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (long) represents a transcript that encodes an isoform longer than that of the short isoform.
    Source sequence(s)
    AI752603, AL080250, AL096771, AL354664, BP286308, DA661773, U73778
    Consensus CDS
    CCDS43482.1
    UniProtKB/Swiss-Prot
    O43853, Q15955, Q5VYK1, Q5VYK2, Q71UR3, Q99715, Q99716
    UniProtKB/TrEMBL
    D6RGG3
    Related
    ENSP00000325146.8, ENST00000322507.13
    Conserved Domains (6) summary
    pfam01391
    Location:2765 → 2891
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:1474 → 1548
    FN3; Fibronectin type 3 domain
    smart00210
    Location:2520 → 2712
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:2118 → 2197
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd01482
    Location:1198 → 1361
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:1754 → 1834
    fn3; Fibronectin type III domain

  6. NM_080645.3 → NP_542376.2  collagen alpha-1(XII) chain short isoform precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (short) lacks multiple exons in the 5' coding region compared to the long variant. The encoded isoform (short) is shorter but has identical N-and C-termini compared to the long isoform.
    Source sequence(s)
    AI752603, AL080250, AL096771, DA661773, U73778
    Consensus CDS
    CCDS43481.1
    UniProtKB/TrEMBL
    B9EJB8
    Related
    ENSP00000305147.9, ENST00000345356.10
    Conserved Domains (6) summary
    pfam01391
    Location:1705 → 1733
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:310 → 384
    FN3; Fibronectin type 3 domain
    smart00210
    Location:1356 → 1548
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:954 → 1033
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd01482
    Location:34 → 197
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:590 → 670
    fn3; Fibronectin type III domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    75084326..75206053 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011535435.2 → XP_011533737.1  collagen alpha-1(XII) chain isoform X3

    UniProtKB/TrEMBL
    D6RGG3
    Conserved Domains (6) summary
    pfam01391
    Location:2674 → 2800
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:1383 → 1457
    FN3; Fibronectin type 3 domain
    smart00210
    Location:2429 → 2621
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:2027 → 2106
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd01482
    Location:1107 → 1270
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:1663 → 1743
    fn3; Fibronectin type III domain

  2. XM_047418186.1 → XP_047274142.1  collagen alpha-1(XII) chain isoform X6

  3. XM_047418184.1 → XP_047274140.1  collagen alpha-1(XII) chain isoform X1

  4. XM_017010252.3 → XP_016865741.1  collagen alpha-1(XII) chain isoform X2

    UniProtKB/TrEMBL
    D6RGG3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    76261502..76383203 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054354234.1 → XP_054210209.1  collagen alpha-1(XII) chain isoform X3

  2. XM_054354232.1 → XP_054210207.1  collagen alpha-1(XII) chain isoform X1

  3. XM_054354237.1 → XP_054210212.1  collagen alpha-1(XII) chain isoform X6

  4. XM_054354233.1 → XP_054210208.1  collagen alpha-1(XII) chain isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q99715.2 GenPept UniProtKB/Swiss-Prot:Q99715

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