COL9A3 collagen type IX alpha 3 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL9A3provided by HGNC
Official Full Name: collagen type IX alpha 3 chainprovided by HGNC
Primary source: HGNC:HGNC:2219
See related: Ensembl:ENSG00000092758 MIM:120270; AllianceGenome:HGNC:2219
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: IDD; MED; EDM3; STL6; DJ885L7.4.1
Summary: This gene encodes one of the three alpha chains of type IX collagen, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. Mutations in this gene are associated with multiple epiphyseal dysplasia type 3. [provided by RefSeq, Jan 2010]
Expression: Broad expression in thyroid (RPKM 8.5), salivary gland (RPKM 6.2) and 17 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 20q13.33

Exon count:: 33

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (62816213..62841159)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (64616007..64640720)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (61448402..61472511)

Chromosome 20 - NC_000020.11 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 missense COL9A3 variant in a pedigree with multiple lumbar disc herniation.
Title: A novel missense COL9A3 variant in a pedigree with multiple lumbar disc herniation.
Identification of three novel homozygous variants in COL9A3 causing autosomal recessive Stickler syndrome.
Title: Identification of three novel homozygous variants in COL9A3 causing autosomal recessive Stickler syndrome.
Heterozygous COL9A3 variants cause severe peripheral vitreoretinal degeneration and retinal detachment.
Title: Heterozygous COL9A3 variants cause severe peripheral vitreoretinal degeneration and retinal detachment.
Whole exome sequencing reveals pathogenic variants in MYO3A, MYO15A and COL9A3 and differential frequencies in ancestral alleles in hearing impairment genes among individuals from Cameroon.
Title: Whole exome sequencing reveals pathogenic variants in MYO3A, MYO15A and COL9A3 and differential frequencies in ancestral alleles in hearing impairment genes among individuals from Cameroon.
Multiple variants in collagen genes are associated with the susceptibility to lumbar disc herniation in the Chinese population.
Title: Multiple variants in collagen genes are associated with the susceptibility to lumbar disc herniation in the Chinese population.
Homozygous type IX collagen variants, COL9A1, COL9A2, and COL9A3, causing recessive Stickler syndrome, expand the disease phenotype.
Title: Homozygous Type IX collagen variants (COL9A1, COL9A2, and COL9A3) causing recessive Stickler syndrome-Expanding the phenotype.
we report the second family with autosomal recessive Stickler syndrome due to homozygosity for a loss-of-function mutation in COL9A3 and further establish the phenotype associated with mutations in this gene
Title: Autosomal recessive Stickler syndrome resulting from a COL9A3 mutation.
Study results suggest that the COL9A3 trp3 polymorphism might not be associated with intervertebral disk degeneration. [meta-analysis]
Title: Association of COL9A3 trp3 polymorphism with intervertebral disk degeneration: a meta-analysis.
rs61734651 variant in COL9A3 was not significantly associated with a predisposition to lumbar disc degeneration.
Title: Collagen IX gene polymorphisms and lumbar disc degeneration: a systematic review and meta-analysis.
In an Iranian population, we observed a 5.8-fold increase in the odds of degenerative disc disease in males when the Trp3 allele was present
Title: MRI Phenotyping of COL9A2/Trp2 and COL9A3/Trp3 Alleles in Lumbar Disc Disease: A Case-control Study in South-Western Iranian Population Reveals a Significant Trp3-Disease Association in Males.

Submit: New GeneRIF Correction See all GeneRIFs (24)

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Epiphyseal dysplasia, multiple, 3 MedGen: C1832998 OMIM: 600969 GeneReviews: Multiple Epiphyseal Dysplasia, Dominant	Compare labs
Intervertebral disc disorder MedGen: C0158252 OMIM: 603932 GeneReviews: Not available	Compare labs
Stickler syndrome, IIa 6 MedGen: C5774207 OMIM: 620022 GeneReviews: Not available	Compare labs

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

SHGC-35186 (e-PCR)
- UniSTS:83479

RH36237 (e-PCR)
- UniSTS:84091

COL9A3_1612 (e-PCR)
- UniSTS:277122

PMC15572P1 (e-PCR)
- UniSTS:271347

PMC15572P2 (e-PCR)
- UniSTS:271348

RH16374 (e-PCR)
- UniSTS:87796

PMC15572P3 (e-PCR)
- UniSTS:271349

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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 protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type IX trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type IX trimer	IDA Inferred from Direct Assay more info	PubMed
part_of collagen type IX trimer	IPI Inferred from Physical Interaction 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 region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

Go to the top of the page Help

Preferred Names: collagen alpha-3(IX) chain

Names: collagen IX, alpha-3 polypeptide; collagen type IX proteoglycan; collagen, type IX, alpha 3

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.