Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs Other IDs Associated diseases
Entrez ID	1288
Gene name	Collagen type IV alpha 6 chain
Gene symbol	COL4A6
Synonyms (NCBI Gene)	CXDELq22.3DELXq22.3DFNX6
Chromosome	X
Chromosome location	Xq22.3
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 col

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs143895379	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, non coding transcript variant, coding sequence variant
rs769211787	A>C	Likely-pathogenic	Genic downstream transcript variant, terminator codon variant, stop lost
rs779748859	C>T	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant

Show/Hide all (29)

miRTarBase ID	miRNA	Experiments	Reference
MIRT048147	hsa-miR-197-3p	CLASH	23622248
MIRT053742	hsa-miR-29b-3p	Microarray	22942087
MIRT902994	hsa-miR-1252	CLIP-seq
MIRT902995	hsa-miR-1303	CLIP-seq
MIRT902996	hsa-miR-299-3p	CLIP-seq
MIRT902997	hsa-miR-3123	CLIP-seq
MIRT902998	hsa-miR-3190	CLIP-seq
MIRT902999	hsa-miR-3202	CLIP-seq
MIRT903000	hsa-miR-3622a-3p	CLIP-seq
MIRT903001	hsa-miR-3622b-3p	CLIP-seq
MIRT903002	hsa-miR-3911	CLIP-seq
MIRT903003	hsa-miR-3925-5p	CLIP-seq
MIRT903004	hsa-miR-4251	CLIP-seq
MIRT903005	hsa-miR-4303	CLIP-seq
MIRT903006	hsa-miR-4329	CLIP-seq
MIRT903007	hsa-miR-4533	CLIP-seq
MIRT903008	hsa-miR-4648	CLIP-seq
MIRT903009	hsa-miR-4654	CLIP-seq
MIRT903010	hsa-miR-4738-3p	CLIP-seq
MIRT903011	hsa-miR-4764-5p	CLIP-seq
MIRT903012	hsa-miR-4769-5p	CLIP-seq
MIRT903013	hsa-miR-539	CLIP-seq
MIRT903014	hsa-miR-595	CLIP-seq
MIRT903015	hsa-miR-619	CLIP-seq
MIRT1967769	hsa-miR-1294	CLIP-seq
MIRT1967770	hsa-miR-3942-3p	CLIP-seq
MIRT903005	hsa-miR-4303	CLIP-seq
MIRT1967771	hsa-miR-4316	CLIP-seq
MIRT1967772	hsa-miR-505	CLIP-seq

Show/Hide all (21)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005201	Function	Extracellular matrix structural constituent	IEA
GO:0005515	Function	Protein binding	IPI	32814053
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005581	Component	Collagen trimer	IEA
GO:0005587	Component	Collagen type IV trimer	IBA
GO:0005587	Component	Collagen type IV trimer	IEA
GO:0005587	Component	Collagen type IV trimer	NAS	8125972
GO:0005604	Component	Basement membrane	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0007155	Process	Cell adhesion	IEA
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	HDA	28344315
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	IBA
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	RCA	25037231, 28675934
GO:0030198	Process	Extracellular matrix organization	IEA
GO:0031012	Component	Extracellular matrix	HDA	25037231, 28344315, 28675934
GO:0031012	Component	Extracellular matrix	IBA
GO:0038063	Process	Collagen-activated tyrosine kinase receptor signaling pathway	IBA
GO:0038063	Process	Collagen-activated tyrosine kinase receptor signaling pathway	IEA
GO:0071230	Process	Cellular response to amino acid stimulus	IEA

MIM	HGNC	e!Ensembl
303631	2208	ENSG00000197565

Q14031

Protein name

Collagen alpha-6(IV) chain

Protein function

Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a 'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen.

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01391	Collagen	45 → 106	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	101 → 161	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	164 → 222	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	357 → 418	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	489 → 550	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	659 → 705	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	754 → 815	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	795 → 873	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	859 → 921	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	894 → 961	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	967 → 1027	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1011 → 1076	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1077 → 1136	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1133 → 1192	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1193 → 1252	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1254 → 1315	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1310 → 1372	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1375 → 1434	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1407 → 1468	Collagen triple helix repeat (20 copies)	Repeat
PF01413	C4	1468 → 1573	C-terminal tandem repeated domain in type 4 procollagen	Domain
PF01413	C4	1576 → 1689	C-terminal tandem repeated domain in type 4 procollagen	Domain

Sequence

MLINKLWLLLVTLCLTEELAAAGEKSYGKPCGGQDCSGSCQCFPEKGARGRPGPIGIQGP
TGPQGFTGSTGLSGLKGERGFPGLLGPYGPKGDKGPMGVPGFLGINGIPGHPGQPGPRGP
PGLDGCNGTQGAVGFPGPDGYPGLLGPPGLPGQKGSKGDPVLAPGSFKGMKGDPGLPGLD
GITGPQGAPGFPGAVGPAGPPGLQGPPGPPGPLGPDGNMGLGFQGEKGVKGDVGLPGPAG
PPPSTGELEFMGFPKGKKGSKGEPGPKGFPGISGPPGFPGLGTTGEKGEKGEKGIPGLPG
PRGPMGSEGVQGPPGQQGKKGTLGFPGLNGFQGIEGQKGDIGLPGPDVFIDIDGAVISGN
PGDPGVPGLPGLKGDEGIQGLRGPSGVPGLPALSGVPGALGPQGFPGLKGDQGNPGRTTI
GAAGLPGRDGLPGPPGPPGPPSPEFETETLHNKESGFPGLRGEQGPKGNLGLKGIKGDSG
FCACDGGVPNTGPPGEPGPPGPWGLIGLPGLKGARGDRGSGGAQGPAGAPGLVGPLGPSG
PKGKKGEPILSTIQGMPGDRGDSGSQGFRGVIGEPGKDGVPGLPGLPGLPGDGGQGFPGE
KGLPGLPGEKGHPGPPGLPGNGLPGLPGPRGLPGDKGKDGLPGQQGLPGSKGITLPCIIP
GSYGPSGFPGTPGFPGPKGSRGLPGTPGQPGSSGSKGEPGSPGLVHLPELPGFPGPRGEK
GLPGFPGLPGKDGLPGMIGSPGLPGSKGATGDIFGAENGAPGEQGLQGLTGHKGFLGDSG
LPGLKGVHGKPGLLGPKGERGSPGTPGQVGQPGTPGSSGPYGIKGKSGLPGAPGFPGISG
HPGKKGTRGKKGPPGSIVKKGLPGLKGLPGNPGLVGLKGSPGSPGVAGLPALSGPKGEKG
SVGFVGFPGIPGLPGIPGTRGLKGIPGSTGKMGPSGRAGTPGEKGDRGNPGPVGIPSPRR
PMSNLWLKGDKGSQGSAGSNGFPGPRGDKGEAGRPGPPGLPGAPGLPGIIKGVSGKPGPP
GFMGIRGLPGLKGSSGITGFPGMPGESGSQGIRGSPGLPGASGLPGLKGDNGQTVEISGS
PGPKGQPGESGFKGTKGRDGLIGNIGFPGNKGEDGKVGVSGDVGLPGAPGFPGVAGMRGE
PGLPGSSGHQGAIGPLGSPGLIGPKGFPGFPGLHGLNGLPGTKGTHGTPGPSITGVPGPA
GLPGPKGEKGYPGIGIGAPGKPGLRGQKGDRGFPGLQGPAGLPGAPGISLPSLIAGQPGD
PGRPGLDGERGRPGPAGPPGPPGPSSNQGDTGDPGFPGIPGPKGPKGDQGIPGFSGLPGE
LGLKGMRGEPGFMGTPGKVGPPGDPGFPGMKGKAGPRGSSGLQGDPGQTPTAEAVQVPPG
PLGLPGIDGIPGLTGDPGAQGPVGLQGSKGLPGIPGKDGPSGLPGPPGALGDPGLPGLQG
PPGFEGAPGQQGPFGMPGMPGQSMRVGYTLVKHSQSEQVPPCPIGMSQLWVGYSLLFVEG
QEKAHNQDLGFAGSCLPRFSTMPFIYCNINEVCHYARRNDKSYWLSTTAPIPMMPVSQTQ
IPQYISRCSVCEAPSQAIAVHSQDITIPQCPLGWRSLWIGYSFLMHTAAGAEGGGQSLVS
PGSCLEDFRATPFIECSGARGTCHYFANKYSFWLTTVEERQQFGELPVSETLKAGQLHTR
VSRCQVCMKSL

Sequence length

1691

Interactions

View interactions

145

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
COL4A6-related disorder	Likely pathogenic	rs769211787	RCV003965228
Hearing loss, X-linked 6	Likely pathogenic	rs779748859, rs2035656072	RCV000088659 RCV004585112

Show/Hide Unknown Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Clear cell carcinoma of kidney	Benign	rs143146797	RCV005907229
Gastric cancer	Likely benign	rs142593944	RCV005926624
Lung cancer	Benign	rs73636380	RCV005923546
Lymphedema	Benign; Likely benign	rs34740537	RCV005625700
Nonpapillary renal cell carcinoma	Conflicting classifications of pathogenicity; Uncertain significance	rs139988853, rs2522331599	RCV005922418 RCV005937378
Sarcoma	Benign	rs73636380	RCV005923545
Thyroid cancer, nonmedullary, 1	Uncertain significance; Benign; Likely benign	rs774796939, rs762403539, rs760496756, rs376450994	RCV005924176 RCV005930445 RCV005930293 RCV005899950

Show/Hide Text Mining Associations (20)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenocarcinoma	Associate	23301059, 34252262
Carcinogenesis	Associate	23301059
Carcinoma Basal Cell	Associate	34104083
Colorectal Neoplasms	Associate	16507901, 32945508
Fibromuscular Dysplasia	Associate	30045277
Genetic Diseases Inborn	Inhibit	26179878
Hearing Loss	Associate	33840813
Kidney Diseases	Associate	8587250
Labyrinth Diseases	Associate	33840813
Leiomyoma	Associate	23738515, 26787895, 9502408
Leiomyoma of vulva and esophagus	Associate	9502408
Leiomyomatosis esophageal and vulval with nephropathy	Associate	26179878, 8175748, 8587250, 9463311, 9915944
Neoplasms	Associate	16507901, 28072738, 35822448
Nephritis Hereditary	Associate	11096082, 7706490, 8587250, 9915944
Nonsyndromic Deafness	Associate	33840813
Peritoneal Neoplasms	Associate	26811494
Renal Insufficiency	Associate	7706490
Squamous Cell Carcinoma of Head and Neck	Associate	34999279
Stomach Neoplasms	Associate	26811494
Triple Negative Breast Neoplasms	Associate	34104083

COL4A6 (collagen type IV alpha 6 chain)