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

Summary

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: mouse all
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Genomic context

Location:: 6q13-q14.1

Exon count:: 68

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (75084326..75206053, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (76261502..76383203, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (75794042..75915769, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
Role of collagen XII in skin homeostasis and repair.
Title: Role of collagen XII in skin homeostasis and repair.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH47329 (e-PCR)
- UniSTS:14917

COL12A1_1592 (e-PCR)
- UniSTS:277111

COL12A1_v565 (e-PCR)
- UniSTS:277111

RH48075 (e-PCR)
- UniSTS:6026

STS-W72891 (e-PCR)
- UniSTS:69267

SHGC-33702 (e-PCR)
- UniSTS:82841

SHGC-112458 (e-PCR)
- UniSTS:168610

STS-U73778 (e-PCR)
- UniSTS:53183

D6S1478 (e-PCR)
- UniSTS:29657

SHGC-84655 (e-PCR)
- UniSTS:103142

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 more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	HDA more info	PubMed
located_in extracellular vesicle	HDA more info	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

NG_042181.1 RefSeqGene

Range

4855..126582

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Status: REVIEWED

Source sequence(s)

AL080250, AL096771, AL354664
NM_001424115.1 → NP_001411044.1 collagen alpha-1(XII) chain isoform 5 precursor

Status: REVIEWED

Source sequence(s)

AL080250, AL096771, AL354664
NM_001424116.1 → NP_001411045.1 collagen alpha-1(XII) chain isoform 6 precursor

Status: REVIEWED

Source sequence(s)

AL080250, AL096771
NM_004370.6 → NP_004361.3 collagen alpha-1(XII) chain long isoform precursor

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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

75084326..75206053 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
XM_047418186.1 → XP_047274142.1 collagen alpha-1(XII) chain isoform X6
XM_047418184.1 → XP_047274140.1 collagen alpha-1(XII) chain isoform X1
XM_017010252.3 → XP_016865741.1 collagen alpha-1(XII) chain isoform X2

UniProtKB/TrEMBL

D6RGG3