COL11A1 collagen type XI alpha 1 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL11A1provided by HGNC
Official Full Name: collagen type XI alpha 1 chainprovided by HGNC
Primary source: HGNC:HGNC:2186
See related: Ensembl:ENSG00000060718 MIM:120280
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: STL2; COLL6; CO11A1; DFNA37
Summary: This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Mutations in this gene are associated with type II Stickler syndrome and with Marshall syndrome. A single-nucleotide polymorphism in this gene is also associated with susceptibility to lumbar disc herniation. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Nov 2009]
Expression: Biased expression in placenta (RPKM 6.4), gall bladder (RPKM 1.9) and 4 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 1p21.1

Exon count:: 71

Annotation release	Status	Assembly	Chr	Location
109.20191205	current	GRCh38.p13 (GCF_000001405.39)	1	NC_000001.11 (102876467..103108580, complement)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (103342023..103574052, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A novel splice variant (c.2556+1G>A) of the COL11A1 gene has been identified in a pedigree affected with congenital high myopia
Title: [Genetic analysis of a pedigree affected with congenital high myopia caused by a novel splice site variant of COL11A1 gene].
We have identified COL11A1 as the gene responsible for deafness at the DFNA37 locus. Previously, COL11A1 was solely associated with Marshall and Stickler syndromes. This study expands its phenotypic spectrum to include nonsyndromic deafness. The implications of this discovery are valuable in the clinical diagnosis, prognosis, and treatment of patients with COL11A1 pathogenic variants.
Title: Splice-altering variant in COL11A1 as a cause of nonsyndromic hearing loss DFNA37.
The SNP rs3753841 in COL11A1, rs1258267 in CHAT and rs736893 in GLIS3 are associated with PACG in northern Chinese people, and the association of genetic markers manifests a tendency of ethnic diversity. Larger population-based studies are warranted to reveal additional primary angle-closure glaucoma loci and ethnic aspects of primary angle-closure glaucoma.
Title: Genotype-ocular biometry correlation analysis of eight primary angle closure glaucoma susceptibility loci in a cohort from Northern China.
COL11A1 confers cisplatin resistance in ovarian cancer.
Title: Inhibitor of apoptosis proteins (IAPs) mediate collagen type XI alpha 1-driven cisplatin resistance in ovarian cancer.
COL11A1 4603C/T gene polymorphism is associated with an increased risk of cervical disc degeneration, but not lumbar disc degeneration, in Japanese collegiate wrestlers.
Title: Association of COL11A1 4603C/T polymorphism with cervical disc degeneration in collegiate wrestlers.
In summary, it is not easy to differentiate stickler syndrome (STL) from early-onset high myopia with routine ocular examination in outpatient clinics. Awareness of atypical phenotypes and newly recognized signs may be of help in identifying atypical STL, especially in children at eye clinics.
Title: Phenotypic characterization of patients with early-onset high myopia due to mutations in <i>COL2A1</i> or <i>COL11A1</i>: Why not Stickler syndrome?
Plasma samples from lung cancer patients and healthy heavy-smokers controls were tested for levels of COL11A1 and COL10A1 (n = 57 each) and SPARC (n = 90 each). Higher plasma levels of COL10A1 were detected in patients (p </= 0.001), a difference that was driven specifically by females (p < 0.001). No difference in COL11A1 levels between patients and controls was found
Title: Diagnostic role of circulating extracellular matrix-related proteins in non-small cell lung cancer.
results suggested that common polymorphisms in these two candidate genes were unlikely to play major roles in the genetic susceptibility to HM. Nevertheless, to avoid filtering real myopia genes, the role of COL11A1 and COL18A1 in the pathogenesis of myopia requires more refinement in both animal models and human genetic epidemiological studies
Title: Genetic Association Study Between the COL11A1 and COL18A1 Genes and High Myopia in a Han Chinese Population.
These results showed that the frequency distribution of genotypes of the rs2229783 polymorphism in COL11A1 was significantly different between the Kashin-Beck Disease (KBD) and control groups; the expression level of COL11A in cartilage was significantly lower in the KBD group, but no association was found between the rs2229783 and the severity of KBD.
Title: Polymorphism in rs2229783 of the Alpha 1(XI) Collagen Gene Is Associated with Susceptibility to but not Severity of Kashin-Beck Disease in a Northwest Chinese Han Population.
We confirmed that the rs1676486 of COL11A may be functionally associated with lumbar disc herniation (LDH) in the Chinese population. Extracellular matrix related proteins may play an important role in the pathogenesis of LDH. Our findings shed light on a better understanding of the pathogenesis of LDH, which could be a promising target for a novel treatment modality of LDH.
Title: A genetic variant in COL11A1 is functionally associated with lumbar disc herniation in Chinese population.

Submit: New GeneRIF Correction See all GeneRIFs (62)

Phenotypes

Go to the top of the page Help

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
DEAFNESS, AUTOSOMAL DOMINANT 37 MedGen: CN262182 OMIM: 618533 GeneReviews: Not available	not available
Fibrochondrogenesis 1 MedGen: C3278138 OMIM: 228520 GeneReviews: Not available	Compare labs
Intervertebral disc disorder MedGen: C0158252 OMIM: 603932 GeneReviews: Not available	Compare labs
Marshall syndrome MedGen: C0265235 OMIM: 154780 GeneReviews: Not available	Compare labs
Stickler syndrome, type 2 MedGen: C1858084 OMIM: 604841 GeneReviews: Stickler Syndrome	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated (2011-10-19) ClinGen Genome Curation Page Haploinsufficency Little evidence for dosage pathogenicity (Last evaluated (2011-10-19) ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A genome-wide association study identifies protein quantitative trait loci (pQTLs). NHGRI GWA Catalog NHGRI GWA CatalogPubMed
Genome-wide association analyses identify three new susceptibility loci for primary angle closure glaucoma. NHGRI GWA Catalog NHGRI GWA CatalogPubMed
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. NHGRI GWA Catalog NHGRI GWA CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

WI-15584 (e-PCR)
- UniSTS:47123

RH98519 (e-PCR)
- UniSTS:90929

SHGC-75227 (e-PCR)
- UniSTS:40016

AL034233 (e-PCR)
- UniSTS:94050

SHGC-75242 (e-PCR)
- UniSTS:26770

Cda1db02 (e-PCR)
- UniSTS:48817

AL033959 (e-PCR)
- UniSTS:93371

SHGC-35204 (e-PCR)
- UniSTS:26060

D1S3215 (e-PCR)
- UniSTS:56272

Homology

Homologs of the COL11A1 gene: The COL11A1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 263 organisms have orthologs with human gene COL11A1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
extracellular matrix binding	NAS Non-traceable Author Statement more info	PubMed
extracellular matrix structural constituent	IBA Inferred from Biological aspect of Ancestor more info	PubMed
extracellular matrix structural constituent	NAS Non-traceable Author Statement more info	PubMed
extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
heparan sulfate binding	IEA Inferred from Electronic Annotation more info
heparin binding	IEA Inferred from Electronic Annotation more info
metal ion binding	IEA Inferred from Electronic Annotation more info
protein binding, bridging	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
cartilage condensation	IEA Inferred from Electronic Annotation more info
chondrocyte development	IEA Inferred from Electronic Annotation more info
collagen fibril organization	NAS Non-traceable Author Statement more info	PubMed
detection of mechanical stimulus involved in sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed
embryonic skeletal system morphogenesis	IEA Inferred from Electronic Annotation more info
endodermal cell differentiation	IEP Inferred from Expression Pattern more info	PubMed
extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info	PubMed
extracellular matrix organization	NAS Non-traceable Author Statement more info	PubMed
inner ear morphogenesis	IEA Inferred from Electronic Annotation more info
ossification	IEA Inferred from Electronic Annotation more info
proteoglycan metabolic process	IEA Inferred from Electronic Annotation more info
sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed
tendon development	IEA Inferred from Electronic Annotation more info
ventricular cardiac muscle tissue morphogenesis	IEA Inferred from Electronic Annotation more info
visual perception	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
collagen type XI trimer	IBA Inferred from Biological aspect of Ancestor more info	PubMed
collagen type XI trimer	IDA Inferred from Direct Assay more info	PubMed
collagen type XI trimer	NAS Non-traceable Author Statement more info	PubMed
collagen-containing extracellular matrix	HDA more info	PubMed
endoplasmic reticulum lumen	TAS Traceable Author Statement more info
extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info	PubMed
extracellular region	TAS Traceable Author Statement more info
extracellular space	IBA Inferred from Biological aspect of Ancestor more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: collagen alpha-1(XI) chain

Names: collagen XI, alpha-1 polypeptide; collagen, type XI, alpha 1; deafness, autosomal dominant 37

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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_008033.2 RefSeqGene

Range

5001..237030

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001190709.1 → NP_001177638.1 collagen alpha-1(XI) chain isoform E preproprotein

Status: REVIEWED

Description

Transcript Variant: This variant (E, previously referred to as C) does not utilize either alternate exon 6A or 6B. The encoded isoform (E, previously referred to as C) is shorter than isoform A. There are no publicly available transcripts representing this variant; it is supported by mRNA annotation on DNA accession AF101112.1, protein AAF04724.1, submitted by the authors of PMID:10486316.

Source sequence(s)

AB208844, AC093150, AC099567, BU159588, BX476821, CA448616, J04177

Consensus CDS

CCDS53348.1

UniProtKB/Swiss-Prot

P12107

UniProtKB/TrEMBL

Q59HB5

Related

ENSP00000302551.6, ENST00000353414.8

Conserved Domains (3) summary

pfam01391
Location:802 → 861

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:38 → 229

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1539 → 1765

COLFI; Fibrillar collagen C-terminal domain
NM_001854.4 → NP_001845.3 collagen alpha-1(XI) chain isoform A preproprotein

See identical proteins and their annotated locations for NP_001845.3

Status: REVIEWED

Description

Transcript Variant: This variant (A) utilizes alternate exon 6, designated exon 6A. The encoded isoform (A) has a 39 aa region specified by exon 6A, that differs from the corresponding 51 aa region encoded by exon 6B in isoform B.

Source sequence(s)

AB208844, AC093150, AC099567, BU159588, BX476821, J04177

Consensus CDS

CCDS778.1

UniProtKB/Swiss-Prot

P12107

UniProtKB/TrEMBL

Q59HB5

Related

ENSP00000359114.3, ENST00000370096.9

Conserved Domains (3) summary

pfam01391
Location:841 → 900

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:38 → 229

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1578 → 1804

COLFI; Fibrillar collagen C-terminal domain
NM_080629.2 → NP_542196.2 collagen alpha-1(XI) chain isoform B preproprotein

See identical proteins and their annotated locations for NP_542196.2

Status: REVIEWED

Description

Transcript Variant: This variant (B) utilizes alternate exon 6, designated exon 6B, and encodes the longest isoform (B). There are no publicly available transcripts representing this variant; it is supported by mRNA annotation on DNA accession AF101112.1, protein AAF04726.1, submitted by the authors of PMID:10486316.

Source sequence(s)

AB208844, AC093150, AC099567, BU159588, BX476821, J04177

UniProtKB/Swiss-Prot

P12107

UniProtKB/TrEMBL

Q59HB5

Related

ENSP00000351163.2, ENST00000358392.6

Conserved Domains (3) summary

pfam01391
Location:853 → 912

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:38 → 229

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1590 → 1816

COLFI; Fibrillar collagen C-terminal domain
NM_080630.4 → NP_542197.3 collagen alpha-1(XI) chain isoform C preproprotein

See identical proteins and their annotated locations for NP_542197.3

Status: REVIEWED

Description

Transcript Variant: This variant (C, previously referred to as D) includes alternate exon 6A but lacks two other alternate exons, resulting in the loss of an in-frame segment in the coding region, compared to variant A. The encoded isoform (C, previously referred to as D) is shorter than isoform A.

Source sequence(s)

AC093150, AC099567, BC117697, CA448616

Consensus CDS

CCDS780.2

UniProtKB/Swiss-Prot

P12107

Related

ENSP00000426533.1, ENST00000512756.5

Conserved Domains (3) summary

pfam01391
Location:725 → 784

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:38 → 229

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1462 → 1688

COLFI; Fibrillar collagen C-terminal domain

RNA

NR_134980.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (F) contains an alternate internal exon compared to variant A. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AB208844, AC093150, AC099567, BC117697, CA448616