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

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
COL4A6-related disorder	Likely pathogenic	rs769211787	RCV003965228	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hearing loss, X-linked 6	Likely pathogenic	rs779748859, rs2035656072	RCV000088659 RCV004585112	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (14)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Clear cell carcinoma of kidney	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, X-LINKED 6	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEIOMYOMA, EPITHELIOID	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphedema	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PREMATURE OVARIAN FAILURE 1	—	Disgenet, GenCC Disgenet, GenCC	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance; Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED ALPORT SYNDROME-DIFFUSE LEIOMYOMATOSIS	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED DIFFUSE LEIOMYOMATOSIS WITH ALPORT SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED ISOLATED SENSORINEURAL HEARING LOSS TYPE DFN	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED NONSYNDROMIC HEARING LOSS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (47)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Adenocarcinoma	Adenocarcinoma	LHGDN	15211113		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adenocarcinoma	Adenocarcinoma	BEFREE	23301059		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adenoma	Adenoma	BEFREE	23301059		★★★★★ ★☆☆☆☆ Found in Text Mining only
Alport Syndrome	Alport Syndrome	BEFREE	11208731, 11773466, 16114791, 17069596, 18616531, 21380622, 23958657, 28275241, 31630709, 7711741, 7833948, 8599366, 8661006, 8738805, 9195222, 9463311, 9465897, 9562604, 9915944 View all (4 more)		★★★★★ ★☆☆☆☆ Found in Text Mining only
Alport Syndrome, Autosomal Recessive	Alport Syndrome	BEFREE	27377778		★★★★★ ★☆☆☆☆ Found in Text Mining only
Alport Syndrome, X-Linked	Alport Syndrome, X-Linked	BEFREE	10499074, 16114791, 23714752, 23958657, 8587250, 9463311		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	23301059	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Basal Cell	Basal cell carcinoma	Pubtator	34104083	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	BEFREE	23714752		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colon Carcinoma	Colon Carcinoma	BEFREE	16507901		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	UNIPROT_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal Neoplasms	LHGDN	16507901		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	16507901, 32945508	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
DEAFNESS, X-LINKED 6	Deafness, X-Linked	CLINGEN_DG	23714752		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, X-LINKED 6	Deafness, X-Linked	UNIPROT_DG	23714752		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, X-LINKED 6	Deafness, X-Linked	GENOMICS_ENGLAND_DG	26350204, 9463311		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, X-LINKED 6	Deafness, X-Linked	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, X-LINKED 6	Deafness, X-Linked	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Diffuse leiomyomatosis	Diffuse leiomyomatosis	BEFREE	10499074, 11773466, 14517961, 17069596, 23958657, 9465897, 9562604, 9915944		★★★★★ ★☆☆☆☆ Found in Text Mining only
Fibroid Tumor	Leiomyoma	BEFREE	9502408		★★★★★ ★☆☆☆☆ Found in Text Mining only
Fibromuscular Dysplasia	Fibromuscular Dysplasia	BEFREE	30045277		★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	29422532		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	33840813	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney Disease	BEFREE	11773466, 23714752, 8587250		★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney disease	Pubtator	8587250	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Failure	Kidney Failure	BEFREE	7706490		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leiomyoma	Leiomyoma	Pubtator	23738515, 26787895, 9502408	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Leiomyoma, Epithelioid	Leiomyoma	CTD_human_DG	17069596		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Leiomyomatosis, esophageal and vulval, with nephropathy	Leiomyosarcoma	ORPHANET_DG	20951201		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leiomyomatosis, esophageal and vulval, with nephropathy	Leiomyosarcoma	BEFREE	23958657		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leiomyomatosis, esophageal and vulval, with nephropathy	Leiomyosarcoma	GENOMICS_ENGLAND_DG	9463311		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	23621580		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	16507901, 30800594		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	16507901		★★★★★ ★☆☆☆☆ Found in Text Mining only
Miscarriage	Miscarriage	CTD_human_DG	18539642		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	7711741		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nonsyndromic Deafness	Nonsyndromic Deafness	BEFREE	23714752		★★★★★ ★☆☆☆☆ Found in Text Mining only
Peritoneal Neoplasms	Peritoneal neoplasm	Pubtator	26811494	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	23621580		★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	LHGDN	17955302		★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	34999279	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	26811494	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple negative breast cancer	Pubtator	34104083	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uterine Fibroids	Uterine Fibroids	BEFREE	30376129, 9502408		★★★★★ ★☆☆☆☆ Found in Text Mining only
X-linked Alport syndrome-diffuse leiomyomatosis	Alport Syndrome, X-Linked	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-linked hydrocephalus syndrome	Hydrocephalus Syndrome, X-Linked	BEFREE	10499074, 9749944		★★★★★ ★☆☆☆☆ Found in Text Mining only
X-linked non-syndromic sensorineural deafness type DFN	Deafness, X-Linked	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only

COL4A6 (collagen type IV alpha 6 chain)