COL4A6 collagen, type IV, alpha 6 [Homo sapiens] - Gene

Help top of page

Summary

Official Symbol: COL4A6provided by HGNC
Official Full Name: collagen, type IV, alpha 6provided by HGNC
Primary source: HGNC:2208
Locus tag: RP5-889N15.4
See related: Ensembl:ENSG00000197565; HPRD:02364; MIM:303631; Vega:OTTHUMG00000022179
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: DELXq22.3; CXDELq22.3; MGC88184
Summary: This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene, alpha 5 type IV collagen, so that the gene pair shares a common promoter. Deletions in the alpha 5 gene that extend into the alpha 6 gene result in diffuse leiomyomatosis accompanying the X-linked Alport syndrome caused by the deletion in the alpha 5 gene. Two splice variants have been identified for this gene. [provided by RefSeq, Jul 2008]

Help top of page

Genomic context

Location :: Xq22

Sequence :: Chromosome: X; NC_000023.10 (107398837..107682704, complement)

See COL4A6 in Epigenomics, MapViewer

Chromosome X - NC_000023.10 Genomic Context describing neighboring genes

Help top of page

Genomic regions, transcripts, and products

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Help top of page

Bibliography

GeneRIFs: Gene References Into Functions What's a GeneRIF?

In this paper we improve the definition of the COL4A5/COL4A6 deletions in three Alport syndrome with diffuse leiomyomatosis.
Title: Alport syndrome and leiomyomatosis: the first deletion extending beyond COL4A6 intron 2.
The expression of Col I, Col IV and Fn was closely related to tumor invasion, the regional lymph node metastasis and other pathological features in laryngeal squamous cell carcinoma.
Title: [Expression and pathobiological significance of Col I, Col IV and Fn in laryngeal squamous cell carcinomas].
expression of collagen type IV alpha6 chain in the smooth muscle BM of the gastrointestinal tract is restricted to the esophagus in humans
Title: Clonal overgrowth of esophageal smooth muscle cells in diffuse leiomyomatosis-Alport syndrome caused by partial deletion in COL4A5 and COL4A6 genes.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: A genetic association study of maternal and fetal candidate genes that predispose to preterm prelabor rupture of membranes (PROM).
The expression of collagen type IV was significantly decreased in colorectal cancer tissues.
Title: [Expression of MMP-2, MMP-9 and collagen type IV and their relationship in colorectal carcinomas].
Results suggest that the down-regulation of alpha 6(IV) mRNA coincides with the acquisition of invasive growth properties, whereas alpha1(IV) and alpha1(VII) mRNAs were up-regulated already in dysplastic tissue.
Title: Collagen mRNA levels changes during colorectal cancer carcinogenesis.
Type IV collagen alpha6 chain-derived noncollagenous domain 1 (alpha6NC1) is an endogenous inhibitor of angiogenesis and tumor growth.
Title: Type IV collagen alpha6 chain-derived noncollagenous domain 1 (alpha6(IV)NC1) inhibits angiogenesis and tumor growth.
Meningiomas increase in size through increased production of extracellular matrix; furthermore, the proliferation of cells typically associated with neoplasia requires considerable interaction with the extracellular matrix.
Title: Immunohistochemical study of the extracellular matrix proteins laminin, fibronectin and type IV collagen in secretory meningiomas.
This study showed that in some cases of esophageal squamous cell carcinoma the alpha5/alpha6 (IV) chains are expressed linearly around the cancer cell nests and the alpha5/alpha6 (IV) chain expression is one prognostic factor of ESCC.
Title: The expression of type IV collagen alpha6 chain is related to the prognosis in patients with esophageal squamous cell carcinoma.

Submit: New GeneRIF Correction See all (14)

Help top of page

Phenotypes

Review eQTL and phenotype association data in this region using PheGenI

Leiomyomatosis, diffuse, with Alport syndrome

MIM: 308940

Help top of page

Products	Interactant	Other Gene	Source	Pubs	Description
Q14031	P05067	APP	HPRD	PubMed
Q14031	Q9NPY3	CD93	HPRD	PubMed
Q14031	P07585	DCN	HPRD	PubMed
Q14031	P98095	FBLN2	HPRD	PubMed
Q14031	P02751	FN1	HPRD	PubMed
Q14031	Q14520	HABP2	HPRD	PubMed
Q14031	O00339	MATN2	HPRD	PubMed
Q14031	P14780	MMP9	HPRD	PubMed
Q14031	P13725	OSM	HPRD	PubMed
Q14031	P07093	SERPINE2	HPRD	PubMed
BioGRID:107685	BioGRID:113269	VHL	BioGRID	PubMed	Affinity Capture-MS

Function	Evidence Code	Pubs
binding	IEA Inferred from Electronic Annotation more info
extracellular matrix structural constituent	NAS Non-traceable Author Statement more info

Process	Evidence Code	Pubs
cell adhesion	IEA Inferred from Electronic Annotation more info
cellular response to amino acid stimulus	IEA Inferred from Electronic Annotation more info
extracellular matrix organization	NAS Non-traceable Author Statement more info

Component	Evidence Code	Pubs
collagen	IEA Inferred from Electronic Annotation more info
collagen type IV	NAS Non-traceable Author Statement more info	PubMed
extracellular region	IEA Inferred from Electronic Annotation more info

General protein information

Preferred Names: collagen alpha-6(IV) chain

Names: collagen alpha-6(IV) chain; collagen alpha 6 type IV; collagen IV, alpha-6 polypeptide; dJ889N15.4 (Collagen Alpha 6(IV)); collagen of basement membrane, alpha-6

Help top of page

NCBI Reference Sequences (RefSeq)

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_012059.2 RefSeqGene

Range

5001..288868

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001847.2 → NP_001838.2 collagen alpha-6(IV) chain isoform A precursor

Status: REVIEWED

Description

Transcript Variant: This variant (A) utilizes alternative exon 1A resulting in a different 5'UTR and signal peptide.

Source sequence(s)

AL136080, BC005305, BF726518, BQ331638, CB050016, D21337, U04845

Consensus CDS

CCDS14541.1

UniProtKB/Swiss-Prot

Q14031

UniProtKB/TrEMBL

Q9BS57

Related

ENSP00000361290, OTTHUMP00000023834, ENST00000372216, OTTHUMT00000057875

Conserved Domains (2) summary

cl02467
Location:1467 – 1574
Blast Score: 519

C4; C-terminal tandem repeated domain in type 4 procollagen

pfam01391
Location:1316 – 1367
Blast Score: 82

Collagen; Collagen triple helix repeat (20 copies)
NM_033641.2 → NP_378667.1 collagen alpha-6(IV) chain isoform B precursor

Status: REVIEWED

Description

Transcript Variant: This variant (B) utilizes alternative exon 1B resulting in a different 5'UTR and signal peptide.

Source sequence(s)

AL136080, BF726518, BQ331638, CB050016, CN313347, D21337, U04845

Consensus CDS

CCDS14542.1

UniProtKB/Swiss-Prot

Q14031

Related

ENSP00000334733, OTTHUMP00000023835, ENST00000334504, OTTHUMT00000057876

Conserved Domains (1) summary

cl02467
Location:1466 – 1573
Blast Score: 519

C4; C-terminal tandem repeated domain in type 4 procollagen

RefSeqs of Annotated Genomes: Build 37.3

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh37.p5 Primary Assembly

Genomic

NC_000023.10 Reference GRCh37.p5 Primary Assembly

Range

107398837..107682704, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000155.1 Alternate HuRef

Range

97021267..97304612, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Help top of page

Related Sequences

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	AL031177.1	CAI43139.1
		CAI43140.1
genomic	AL034369.1	CAI42045.1
		CAI42047.1
genomic	AL109943.18	CAI42993.1
		CAI42995.1
genomic	AL136080.6	CAI40756.1
		CAI40758.1
genomic	CH471120.2	EAX02687.1
		EAX02688.1
genomic	D28116.1	None
genomic	D63562.2	BAA09791.1
genomic	U47004.1	AAB19038.1
		AAB19039.1
mRNA	AK300502.1	BAG62216.1
mRNA	BC000874.1	None
mRNA	BC005305.1	AAH05305.1
mRNA	BC070203.1	AAH70203.1
mRNA	BC140855.1	AAI40856.1
mRNA	BC144669.1	AAI44670.1
mRNA	BF726518.1	None
mRNA	BQ331638.1	None
mRNA	BT007228.1	AAP35892.1
mRNA	CB050016.1	None
mRNA	CN313347.1	None
mRNA	D21337.1	BAA04809.1
mRNA	EU182215.1	ABW24668.1
mRNA	L22763.1	AAA16338.1
mRNA	U04845.1	AAA19569.2

Protein Accession	Links
Protein Accession	GenPept Link	UniProtKB Link
Q14031.3	GenPept	UniProtKB/Swiss-Prot:Q14031
Q6NSE8	GenPept	UniProtKB/TrEMBL:Q6NSE8
Q9BS57	GenPept	UniProtKB/TrEMBL:Q9BS57
Q9UEH6	GenPept	UniProtKB/TrEMBL:Q9UEH6