COL9A1 collagen type IX alpha 1 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL9A1provided by HGNC
Official Full Name: collagen type IX alpha 1 chainprovided by HGNC
Primary source: HGNC:HGNC:2217
See related: Ensembl:ENSG00000112280 MIM:120210; AllianceGenome:HGNC:2217
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: MED; EDM6; STL4; DJ149L1.1.2
Summary: This gene encodes one of the three alpha chains of type IX collagen, which is a minor (5-20%) collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
Expression: Biased expression in prostate (RPKM 6.1), testis (RPKM 1.3) and 6 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6q13

Exon count:: 43

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (70215061..70303084, complement)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (71395620..71483638, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (70924764..71012787, 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?

Relationship of COL9A1 and SOX9 Genes with Genetic Susceptibility of Postmenopausal Osteoporosis.
Title: Relationship of COL9A1 and SOX9 Genes with Genetic Susceptibility of Postmenopausal Osteoporosis.
Gene Environment Interactions Between the COL9A1 Gene and Maternal Drinking of Alcohol Contribute to the Risk of Congenital Talipes Equinovarus.
Title: Gene Environment Interactions Between the <i>COL9A1</i> Gene and Maternal Drinking of Alcohol Contribute to the Risk of Congenital Talipes Equinovarus.
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.
The present study emphasizes the importance of exome-wide copy number variation analysis in molecular diagnosis and provides supporting evidence to associate COL9A1 with autosomal recessive non-syndromic HL.
Title: Exome-wide copy number variation analysis identifies a COL9A1 in frame deletion that is associated with hearing loss.
Two tagSNPs, rs28647489 in FAT1 gene and rs550675 in COL9A1 gene, were significantly associated with the risk of oral malignancy.
Title: Variants in FAT1 and COL9A1 genes in male population with or without substance use to assess the risk factors for oral malignancy.
Whole-genome sequencing reveals possible role of deleterious mutation of COL9A1 in ossification of the posterior longitudinal ligament of the thoracic spine in the Chinese population.
Title: Whole-genome sequencing reveals novel genes in ossification of the posterior longitudinal ligament of the thoracic spine in the Chinese population.
the COL9A1 rs35470562 variant may contribute to congenital talipes equinovarus susceptibility in the Chinese population examined.
Title: Role of COL9A1 genetic polymorphisms in development of congenital talipes equinovarus in a Chinese population.
We observed a significant association between rs6910140 of COL9A1 and KBD, suggesting a role of COL9A1 in the development of KBD.
Title: COL9A1 gene polymorphism is associated with Kashin-Beck disease in a northwest Chinese Han population.
The study demonstrated that hypermethylation is associated with down-regulation of COL9A1 expression in osteoarthritic (OA) cartilage and highlights the pivotal role of epigenetics in OA.
Title: Association of reduced type IX collagen gene expression in human osteoarthritic chondrocytes with epigenetic silencing by DNA hypermethylation.
The NC2 domain of type IX collagen determines the chain composition but also the chain register of the triple helix.
Title: The NC2 domain of type IX collagen determines the chain register of the triple helix.

Submit: New GeneRIF Correction See all GeneRIFs (27)

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
Epiphyseal dysplasia, multiple, 6 MedGen: C2675767 OMIM: 614135 GeneReviews: Multiple Epiphyseal Dysplasia, Dominant	Compare labs
Stickler syndrome, type 4 MedGen: C3279941 OMIM: 614134 GeneReviews: Stickler Syndrome	Compare labs

Copy number response

Description
Copy number response Haploinsufficency No evidence available (Last evaluated 2013-11-06) ClinGen Genome Curation Page Triplosensitivity No evidence available (Last evaluated 2013-11-06) ClinGen Genome Curation Page

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

D6S313 (e-PCR), detects polymorphism
- UniSTS:62477

SHGC-852 (e-PCR)
- UniSTS:22883

D10S16 (e-PCR)
- UniSTS:155756

STS-X54412 (e-PCR)
- UniSTS:76405

GDB:249306 (e-PCR)
- UniSTS:156278

G35510 (e-PCR)
- UniSTS:44150

RH46227 (e-PCR)
- UniSTS:30088

GDB:335751 (e-PCR)
- UniSTS:156601

D6S1557 (e-PCR), detects polymorphism
- UniSTS:67834

Homology

Homologs of the COL9A1 gene: The COL9A1 gene is conserved in chimpanzee, Rhesus monkey, dog, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 438 organisms have orthologs with human gene COL9A1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables carbohydrate binding	EXP Inferred from Experiment more info	PubMed
enables carbohydrate binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables carbohydrate binding	IPI Inferred from Physical Interaction more info	PubMed
enables extracellular matrix structural constituent	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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 protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in animal organ morphogenesis	TAS Traceable Author Statement more info	PubMed
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Component	Evidence Code	Pubs
part_of collagen type IX trimer	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of collagen type IX trimer	IDA Inferred from Direct Assay more info	PubMed
part_of collagen type IX trimer	TAS Traceable Author Statement more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
is_active_in extracellular matrix	IBA Inferred from Biological aspect of Ancestor 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	PubMed

General protein information

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Preferred Names: collagen alpha-1(IX) chain

Names: alpha-1(IX) collagen chain; cartilage-specific short collagen; collagen IX, alpha-1 polypeptide; collagen, type IX, 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_011654.1 RefSeqGene

Range

5000..91958

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001377289.1 → NP_001364218.1 collagen alpha-1(IX) chain isoform 3 precursor

Status: REVIEWED

Source sequence(s)

AL080275, AL160262

Consensus CDS

CCDS93940.1

UniProtKB/TrEMBL

A0A804HIB6

Related

ENSP00000506990.1, ENST00000683980.2

Conserved Domains (1) summary

pfam01391
Location:253 → 309

Collagen; Collagen triple helix repeat (20 copies)
NM_001377290.1 → NP_001364219.1 collagen alpha-1(IX) chain isoform 4 precursor

Status: REVIEWED

Source sequence(s)

AL080275, AL160262

Related

ENSP00000508147.1, ENST00000683758.1

Conserved Domains (1) summary

pfam01391
Location:244 → 298

Collagen; Collagen triple helix repeat (20 copies)
NM_001377291.1 → NP_001364220.1 collagen alpha-1(IX) chain isoform 5 precursor

Status: REVIEWED

Source sequence(s)

AL080275

Consensus CDS

CCDS93941.1

Related

ENSP00000359527.3, ENST00000370496.3

Conserved Domains (1) summary

smart00210
Location:50 → 244

TSPN; Thrombospondin N-terminal -like domains
NM_001851.6 → NP_001842.3 collagen alpha-1(IX) chain isoform 1 precursor

See identical proteins and their annotated locations for NP_001842.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1, also known as the long form).

Source sequence(s)

AL080275, AL160262

Consensus CDS

CCDS4971.1

UniProtKB/Swiss-Prot

P20849, Q9Y6P3

Related

ENSP00000349790.6, ENST00000357250.11

Conserved Domains (2) summary

pfam01391
Location:493 → 552

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:50 → 244

TSPN; Thrombospondin N-terminal -like domains
NM_078485.4 → NP_511040.2 collagen alpha-1(IX) chain isoform 2 precursor

See identical proteins and their annotated locations for NP_511040.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and lacks several exons in the 5' coding region, compared to variant 1. These differences cause translation initiation at a unique AUG and an isoform (2, also known as the short form) with a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AL160262, AW021120, BC063646, BF196880, CA392556, X54412

Consensus CDS

CCDS47447.1

UniProtKB/Swiss-Prot

P20849

Related

ENSP00000315252.7, ENST00000320755.12

Conserved Domains (1) summary

pfam01391
Location:250 → 309

Collagen; Collagen triple helix repeat (20 copies)

RNA

NR_165185.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL080275, AL160262

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...

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

70215061..70303084 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011535429.4 → XP_011533731.1 collagen alpha-1(IX) chain isoform X1

Conserved Domains (2) summary

pfam01391
Location:493 → 552

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:50 → 244

TSPN; Thrombospondin N-terminal -like domains
XM_017010246.3 → XP_016865735.1 collagen alpha-1(IX) chain isoform X2
XM_047418180.1 → XP_047274136.1 collagen alpha-1(IX) chain isoform X4
XM_047418179.1 → XP_047274135.1 collagen alpha-1(IX) chain isoform X3
XM_017010247.3 → XP_016865736.1 collagen alpha-1(IX) chain isoform X5