COL2A1 collagen type II alpha 1 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL2A1provided by HGNC
Official Full Name: collagen type II alpha 1 chainprovided by HGNC
Primary source: HGNC:HGNC:2200
See related: Ensembl:ENSG00000139219 MIM:120140; AllianceGenome:HGNC:2200
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: AOM; ANFH; SEDC; STL1; COL11A3
Summary: This gene encodes the alpha-1 chain of type II collagen, a fibrillar collagen found in cartilage and the vitreous humor of the eye. Mutations in this gene are associated with achondrogenesis, chondrodysplasia, early onset familial osteoarthritis, SED congenita, Langer-Saldino achondrogenesis, Kniest dysplasia, Stickler syndrome type I, and spondyloepimetaphyseal dysplasia Strudwick type. In addition, defects in processing chondrocalcin, a calcium binding protein that is the C-propeptide of this collagen molecule, are also associated with chondrodysplasia. There are two transcripts identified for this gene. [provided by RefSeq, Jul 2008]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 12q13.11

Exon count:: 57

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (47972967..48006212, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (47934691..47967944, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (48366750..48398259, complement)

Chromosome 12 - NC_000012.12 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?

The molecular complexity of COL2A1 splicing variants and their significance in phenotype severity.
Title: The molecular complexity of COL2A1 splicing variants and their significance in phenotype severity.
Co-occurrence of Spondyloepiphyseal Dysplasia and X-Linked Hypophosphatemia in a Three-Generation Chinese Family.
Title: Co-occurrence of Spondyloepiphyseal Dysplasia and X-Linked Hypophosphatemia in a Three-Generation Chinese Family.
Characteristics of a Three-Generation Family with Stickler Syndrome Type I Carrying Two Different COL2A1 Mutations.
Title: Characteristics of a Three-Generation Family with Stickler Syndrome Type I Carrying Two Different COL2A1 Mutations.
Natural history and genetic spectrum of the Turkish metaphyseal dysplasia cohort, including rare types caused by biallelic COL10A1, COL2A1, and LBR variants.
Title: Natural history and genetic spectrum of the Turkish metaphyseal dysplasia cohort, including rare types caused by biallelic COL10A1, COL2A1, and LBR variants.
Severe foveal hypoplasia and macular degeneration in Stickler syndrome caused by missense mutation in COL2A1 gene.
Title: Severe foveal hypoplasia and macular degeneration in Stickler syndrome caused by missense mutation in COL2A1 gene.
Influence of COL2A1-G1405S polymorphism on mandibular skeletal malocclusions: A genetic association study and in silico analysis.
Title: Influence of COL2A1-G1405S polymorphism on mandibular skeletal malocclusions: A genetic association study and in silico analysis.
Hearing Outcomes in Stickler Syndrome: Variation Due to COL2A1 and COL11A1.
Title: Hearing Outcomes in Stickler Syndrome: Variation Due to COL2A1 and COL11A1.
Expanding the clinical spectrum of COL2A1 related disorders by a mass like phenotype.
Title: Expanding the clinical spectrum of COL2A1 related disorders by a mass like phenotype.
A Novel missense mutation of COL2A1 gene in a large family with stickler syndrome type I.
Title: A Novel missense mutation of COL2A1 gene in a large family with stickler syndrome type I.
Case report of the first molecular diagnosis of Stickler syndrome with a pathogenic COL2A1 variant in a Mongolia family.
Title: Case report of the first molecular diagnosis of Stickler syndrome with a pathogenic COL2A1 variant in a Mongolia family.

Submit: New GeneRIF Correction See all GeneRIFs (216)

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
Achondrogenesis type II MedGen: C0220685 OMIM: 200610 GeneReviews: Type II Collagen Disorders Overview	Compare labs
Avascular necrosis of femoral head, primary, 1 MedGen: C4551562 OMIM: 608805 GeneReviews: Type II Collagen Disorders Overview	Compare labs
Czech dysplasia, metatarsal type MedGen: C1836683 OMIM: 609162 GeneReviews: Not available	Compare labs
Kniest dysplasia MedGen: C0265279 OMIM: 156550 GeneReviews: Type II Collagen Disorders Overview	Compare labs
Legg-Calve-Perthes disease MedGen: C0023234 OMIM: 150600 GeneReviews: Not available	Compare labs
Multiple epiphyseal dysplasia, Beighton type MedGen: C1851536 OMIM: 132450 GeneReviews: Not available	Compare labs
Namaqualand hip dysplasia MedGen: C0432214 OMIM: 604864 GeneReviews: Type II Collagen Disorders Overview	Compare labs
Platyspondylic dysplasia, Torrance type MedGen: C1835437 OMIM: 151210 GeneReviews: Type II Collagen Disorders Overview	Compare labs
Spondyloepimetaphyseal dysplasia, Strudwick type MedGen: C0700635 OMIM: 184250 GeneReviews: Type II Collagen Disorders Overview	Compare labs
Spondyloepiphyseal dysplasia congenita MedGen: C2745959 OMIM: 183900 GeneReviews: Type II Collagen Disorders Overview	Compare labs
Spondyloepiphyseal dysplasia, Stanescu type MedGen: C4225273 OMIM: 616583 GeneReviews: Not available	Compare labs
Spondylometaphyseal dysplasia - Sutcliffe type MedGen: C0432221 OMIM: 184255 GeneReviews: Spondylometaphyseal Dysplasia, Corner Fracture Type	Compare labs
Spondyloperipheral dysplasia MedGen: C0796173 OMIM: 271700 GeneReviews: Type II Collagen Disorders Overview	Compare labs
Stickler syndrome type 1 MedGen: C2020284 OMIM: 108300 GeneReviews: Stickler Syndrome, Type II Collagen Disorders Overview	Compare labs
Stickler syndrome, type I, nonsyndromic ocular MedGen: C1836080 OMIM: 609508 GeneReviews: Not available	Compare labs
Vitreoretinopathy with phalangeal epiphyseal dysplasia MedGen: C1852989 OMIM: 619248 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2020-07-29) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2020-07-29) ClinGen Genome Curation PagePubMed

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

RH68551 (e-PCR)
- UniSTS:42512

D12S2021 (e-PCR)
- UniSTS:792

Col2a1 (e-PCR), detects polymorphism
- UniSTS:508440

MARC_24087-24088:1040064543:1 (e-PCR)
- UniSTS:268845

D12S1663 (e-PCR)
- UniSTS:48691

D12S85 (e-PCR), detects polymorphism
- UniSTS:47172

GDB:177727 (e-PCR)
- UniSTS:154955

GDB:177728 (e-PCR)
- UniSTS:154956

GDB:512193 (e-PCR)
- UniSTS:157522

GDB:577655 (e-PCR)
- UniSTS:157812

GDB:577659 (e-PCR)
- UniSTS:157813

GDB:577662 (e-PCR)
- UniSTS:157814

GDB:577664 (e-PCR)
- UniSTS:157815

GDB:577666 (e-PCR)
- UniSTS:157816

GDB:578728 (e-PCR)
- UniSTS:157817

GDB:578731 (e-PCR)
- UniSTS:157818

GDB:578732 (e-PCR)
- UniSTS:157819

GDB:578733 (e-PCR)
- UniSTS:157820

MARC_15881-15882:1015249633:1 (e-PCR)
- UniSTS:267914

COL2A1 (e-PCR)
- UniSTS:503994

GDB:626695 (e-PCR)
- UniSTS:158399

GDB:180356 (e-PCR)
- UniSTS:155083

COL2A1 (e-PCR)
- UniSTS:278221

SHGC-79734 (e-PCR)
- UniSTS:101073

GDB:177260 (e-PCR)
- UniSTS:154850

COL2A1 (e-PCR)
- UniSTS:258280

GDB:180743 (e-PCR)
- UniSTS:155118

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables MHC class II protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	HDA more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	IC Inferred by Curator more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables platelet-derived growth factor binding	IDA Inferred from Direct Assay more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables proteoglycan binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in anterior head development	IEA Inferred from Electronic Annotation more info
involved_in cartilage condensation	IEA Inferred from Electronic Annotation more info
involved_in cartilage development	TAS Traceable Author Statement more info	PubMed
involved_in cartilage development involved in endochondral bone morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cellular response to BMP stimulus	IEA Inferred from Electronic Annotation more info
involved_in central nervous system development	IEA Inferred from Electronic Annotation more info
involved_in chondrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in collagen fibril organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in collagen fibril organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in embryonic skeletal joint morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endochondral ossification	IEA Inferred from Electronic Annotation more info
involved_in extrinsic apoptotic signaling pathway in absence of ligand	IEA Inferred from Electronic Annotation more info
involved_in heart morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in inner ear morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in limb bud formation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of extrinsic apoptotic signaling pathway in absence of ligand	IEA Inferred from Electronic Annotation more info
involved_in notochord development	IBA Inferred from Biological aspect of Ancestor more info
involved_in otic vesicle development	IEA Inferred from Electronic Annotation more info
involved_in proteoglycan metabolic process	IEA Inferred from Electronic Annotation more info
involved_in regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in roof of mouth development	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tissue homeostasis	IEA Inferred from Electronic Annotation more info
involved_in visual perception	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in basement membrane	IEA Inferred from Electronic Annotation more info
part_of collagen type II trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type II trimer	IDA Inferred from Direct Assay more info	PubMed
part_of collagen type XI trimer	NAS Non-traceable Author Statement more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in collagen-containing extracellular matrix	NAS Non-traceable Author Statement more info	PubMed
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular region	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: collagen alpha-1(II) chain

Names: alpha-1 type II collagen; arthroophthalmopathy, progressive (Stickler syndrome); cartilage collagen; chondrocalcin; collagen II, alpha-1 polypeptide; collagen, type II, 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_008072.1 RefSeqGene

Range

5027..36536

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001844.5 → NP_001835.3 collagen alpha-1(II) chain isoform 1 precursor

See identical proteins and their annotated locations for NP_001835.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).

Source sequence(s)

AC004801

Consensus CDS

CCDS41778.1

UniProtKB/Swiss-Prot

A6NGA0, P02458, Q12985, Q14009, Q14044, Q14045, Q14046, Q14047, Q14056, Q14058, Q16672, Q1JQ82, Q2V4X7, Q6LBY1, Q6LBY2, Q6LBY3, Q96IT5, Q99227, Q9UE38, Q9UE39, Q9UE40, Q9UE41, Q9UE42, Q9UE43

Related

ENSP00000369889.3, ENST00000380518.8

Conserved Domains (3) summary

pfam01391
Location:801 → 860

Collagen; Collagen triple helix repeat (20 copies)

pfam00093
Location:34 → 89

VWC; von Willebrand factor type C domain

pfam01410
Location:1254 → 1486

COLFI; Fibrillar collagen C-terminal domain
NM_033150.3 → NP_149162.2 collagen alpha-1(II) chain isoform 2 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in a shorter protein. The resulting protein (isoform 2) lacks the von Willebrand factor type C (VWC) domain, compared to isoform 1.

Source sequence(s)

AC004801

Consensus CDS

CCDS8759.1

UniProtKB/Swiss-Prot

P02458

Related

ENSP00000338213.6, ENST00000337299.7

Conserved Domains (2) summary

pfam01391
Location:732 → 791

Collagen; Collagen triple helix repeat (20 copies)

pfam01410
Location:1185 → 1417

COLFI; Fibrillar collagen C-terminal 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

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

47972967..48006212 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017018830.1 → XP_016874319.1 collagen alpha-1(II) chain isoform X3
XM_017018829.1 → XP_016874318.1 collagen alpha-1(II) chain isoform X2

Conserved Domains (3) summary

pfam01391
Location:848 → 907

Collagen; Collagen triple helix repeat (20 copies)

pfam00093
Location:81 → 136

VWC; von Willebrand factor type C domain

pfam01410
Location:1301 → 1533

COLFI; Fibrillar collagen C-terminal domain
XM_017018828.1 → XP_016874317.1 collagen alpha-1(II) chain isoform X1

Conserved Domains (3) summary

pfam01391
Location:849 → 908

Collagen; Collagen triple helix repeat (20 copies)

pfam00093
Location:81 → 136

VWC; von Willebrand factor type C domain

pfam01410
Location:1302 → 1534

COLFI; Fibrillar collagen C-terminal domain
XM_047428315.1 → XP_047284271.1 collagen alpha-1(II) chain isoform X4
XM_017018831.3 → XP_016874320.1 collagen alpha-1(II) chain isoform X4