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
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Genomic context

Location:: 1p21.1

Exon count:: 71

Annotation release	Status	Assembly	Chr	Location
109.20210226	current	GRCh38.p13 (GCF_000001405.39)	1	NC_000001.11 (102876473..103108580, complement)
105.20201022	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (103342029..103574078, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Expanding the phenotype spectrum associated with pathogenic variants in the COL2A1 and COL11A1 genes.
Title: Expanding the phenotype spectrum associated with pathogenic variants in the COL2A1 and COL11A1 genes.
Mutation Spectrum and De Novo Mutation Analysis in Stickler Syndrome Patients with High Myopia or Retinal Detachment.
Title: Mutation Spectrum and De Novo Mutation Analysis in Stickler Syndrome Patients with High Myopia or Retinal Detachment.
Homozygous variants in AMPD2 and COL11A1 lead to a complex phenotype of pontocerebellar hypoplasia type 9 and Stickler syndrome type 2.
Title: Homozygous variants in AMPD2 and COL11A1 lead to a complex phenotype of pontocerebellar hypoplasia type 9 and Stickler syndrome type 2.
Multifactor dimensionality reduction reveals a strong gene-gene interaction between STC1 and COL11A1 genes as a possible risk factor of knee osteoarthritis.
Title: Multifactor dimensionality reduction reveals a strong gene-gene interaction between STC1 and COL11A1 genes as a possible risk factor of knee osteoarthritis.
Influence of genetic factors in elbow tendon pathology: a case-control study.
Title: Influence of genetic factors in elbow tendon pathology: a case-control study.
A Meta-analysis Assessing the Association Between COL11A1 and GDF5 Genetic Variants and Intervertebral Disc Degeneration Susceptibility.
Title: A Meta-analysis Assessing the Association Between COL11A1 and GDF5 Genetic Variants and Intervertebral Disc Degeneration Susceptibility.
overexpression of stromal COL11A1 is associated with invasive recurrence in DCIS and is a potential marker to predict the response to radiotherapy.
Title: Collagen (XI) alpha-1 chain is an independent prognostic factor in breast ductal carcinoma in situ.
we revealed that COL11A1 and TWIST1 were significantly upregulated at the mRNA and protein levels within rightsided colon cancer compared with in leftsided colon cancer samples (P<0.05), consistent with bioinformatical analysis. Furthermore, a positive correlation between COL11A1 and TWIST1 protein expression was observed (P<0.0276). Collectively
Title: Microarray‑based analysis of COL11A1 and TWIST1 as important differentially‑expressed pathogenic genes between left and right‑sided colon cancer.
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.

Submit: New GeneRIF Correction See all GeneRIFs (70)

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
A genome-wide association study identifies protein quantitative trait loci (pQTLs). GeneReviews: Not available
Deafness, autosomal dominant 37 MedGen: C4760307 OMIM: 618533 GeneReviews: Not available	Compare labs
Fibrochondrogenesis 1 MedGen: C3278138 OMIM: 228520 GeneReviews: Not available	Compare labs
Genome-wide association analyses identify three new susceptibility loci for primary angle closure glaucoma. GeneReviews: Not available
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. GeneReviews: Not available
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	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

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

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: 330 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-macromolecule adaptor activity	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

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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)

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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_008033.2 RefSeqGene

Range

5001..237030

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001190709.2 → 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_080629.3 → 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