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

Gene Gene miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	1285
Gene name Gene Name - the full gene name approved by the HGNC.	Collagen type IV alpha 3 chain
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	COL4A3
Synonyms (NCBI Gene) Gene synonyms aliases	ATS2, ATS3, ATS3A, ATS3B, BFH2
Chromosome Chromosome number	2
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	2q36.3
Summary Summary of gene provided in NCBI Entrez Gene.	Type IV collagen, the major structural component of basement membranes, is a multimeric protein composed of 3 alpha subunits. These subunits are encoded by 6 different genes, alpha 1 through alpha 6, each of which can form a triple helix structure with 2

Show/Hide all(61)

miRTarBase ID	miRNA	Experiments	Reference
MIRT047553	hsa-miR-10a-5p	CLASH	23622248
MIRT527454	hsa-miR-548ac	PAR-CLIP	22012620
MIRT527453	hsa-miR-548bb-3p	PAR-CLIP	22012620
MIRT527452	hsa-miR-548d-3p	PAR-CLIP	22012620
MIRT527451	hsa-miR-548h-3p	PAR-CLIP	22012620
MIRT527450	hsa-miR-548z	PAR-CLIP	22012620
MIRT527449	hsa-miR-548ae-3p	PAR-CLIP	22012620
MIRT527448	hsa-miR-548ah-3p	PAR-CLIP	22012620
MIRT527447	hsa-miR-548aj-3p	PAR-CLIP	22012620
MIRT527446	hsa-miR-548am-3p	PAR-CLIP	22012620
MIRT527445	hsa-miR-548aq-3p	PAR-CLIP	22012620
MIRT527444	hsa-miR-548j-3p	PAR-CLIP	22012620
MIRT527443	hsa-miR-548x-3p	PAR-CLIP	22012620
MIRT527442	hsa-miR-548c-3p	PAR-CLIP	22012620
MIRT527441	hsa-miR-548aa	PAR-CLIP	22012620
MIRT527440	hsa-miR-548ap-3p	PAR-CLIP	22012620
MIRT527439	hsa-miR-548t-3p	PAR-CLIP	22012620
MIRT527438	hsa-miR-302b-5p	PAR-CLIP	22012620
MIRT527437	hsa-miR-302d-5p	PAR-CLIP	22012620
MIRT527454	hsa-miR-548ac	PAR-CLIP	22012620
MIRT527453	hsa-miR-548bb-3p	PAR-CLIP	22012620
MIRT527452	hsa-miR-548d-3p	PAR-CLIP	22012620
MIRT527451	hsa-miR-548h-3p	PAR-CLIP	22012620
MIRT527450	hsa-miR-548z	PAR-CLIP	22012620
MIRT527449	hsa-miR-548ae-3p	PAR-CLIP	22012620
MIRT527448	hsa-miR-548ah-3p	PAR-CLIP	22012620
MIRT527447	hsa-miR-548aj-3p	PAR-CLIP	22012620
MIRT527446	hsa-miR-548am-3p	PAR-CLIP	22012620
MIRT527445	hsa-miR-548aq-3p	PAR-CLIP	22012620
MIRT527444	hsa-miR-548j-3p	PAR-CLIP	22012620
MIRT527443	hsa-miR-548x-3p	PAR-CLIP	22012620
MIRT527442	hsa-miR-548c-3p	PAR-CLIP	22012620
MIRT527441	hsa-miR-548aa	PAR-CLIP	22012620
MIRT527440	hsa-miR-548ap-3p	PAR-CLIP	22012620
MIRT527439	hsa-miR-548t-3p	PAR-CLIP	22012620
MIRT527438	hsa-miR-302b-5p	PAR-CLIP	22012620
MIRT527437	hsa-miR-302d-5p	PAR-CLIP	22012620
MIRT902814	hsa-miR-196a	CLIP-seq
MIRT902815	hsa-miR-196b	CLIP-seq
MIRT902816	hsa-miR-3613-3p	CLIP-seq
MIRT902817	hsa-miR-3614-5p	CLIP-seq
MIRT902818	hsa-miR-3927	CLIP-seq
MIRT902819	hsa-miR-511	CLIP-seq
MIRT1967738	hsa-miR-3545-3p	CLIP-seq
MIRT1967739	hsa-miR-3622a-5p	CLIP-seq
MIRT902819	hsa-miR-511	CLIP-seq
MIRT1967740	hsa-miR-564	CLIP-seq
MIRT1967741	hsa-miR-583	CLIP-seq
MIRT2203570	hsa-miR-200b	CLIP-seq
MIRT2203571	hsa-miR-200c	CLIP-seq
MIRT2203572	hsa-miR-429	CLIP-seq
MIRT2203573	hsa-miR-489	CLIP-seq
MIRT2203574	hsa-miR-494	CLIP-seq
MIRT2203575	hsa-miR-514	CLIP-seq
MIRT2203576	hsa-miR-514b-3p	CLIP-seq
MIRT2203577	hsa-miR-519a	CLIP-seq
MIRT2203578	hsa-miR-519b-3p	CLIP-seq
MIRT2203579	hsa-miR-519c-3p	CLIP-seq
MIRT2678408	hsa-miR-4501	CLIP-seq
MIRT2678409	hsa-miR-568	CLIP-seq
MIRT2678410	hsa-miR-643	CLIP-seq

Transcription factors

Show/Hide all(1)

Transcription factor	Regulation	Reference
ZEB1	Unknown	22199242

Show/Hide all(34)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005178	Function	Integrin binding	IDA	12682293
GO:0005178	Function	Integrin binding	TAS	10766752
GO:0005198	Function	Structural molecule activity	NAS	3025878
GO:0005201	Function	Extracellular matrix structural constituent	IEA
GO:0005515	Function	Protein binding	IPI	10212244, 12682293
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	IDA	10766752
GO:0005587	Component	Collagen type IV trimer	IEA
GO:0005604	Component	Basement membrane	IDA	10766752
GO:0005604	Component	Basement membrane	IEA
GO:0005783	Component	Endoplasmic reticulum	IDA
GO:0005788	Component	Endoplasmic reticulum lumen	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0007155	Process	Cell adhesion	IEA
GO:0007166	Process	Cell surface receptor signaling pathway	IEA
GO:0007166	Process	Cell surface receptor signaling pathway	NAS	10766752
GO:0007605	Process	Sensory perception of sound	TAS	7987396
GO:0008191	Function	Metalloendopeptidase inhibitor activity	NAS	10766752
GO:0008285	Process	Negative regulation of cell population proliferation	TAS	10837460
GO:0016525	Process	Negative regulation of angiogenesis	IDA	10766752, 12682293
GO:0016525	Process	Negative regulation of angiogenesis	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:0031012	Component	Extracellular matrix	HDA	25037231, 28344315, 28675934
GO:0031012	Component	Extracellular matrix	IBA
GO:0032836	Process	Glomerular basement membrane development	IEA
GO:0032836	Process	Glomerular basement membrane development	ISS
GO:0038063	Process	Collagen-activated tyrosine kinase receptor signaling pathway	IEA
GO:0072577	Process	Endothelial cell apoptotic process	IDA	10766752
GO:1905563	Process	Negative regulation of vascular endothelial cell proliferation	IDA	10766752

MIM	HGNC	e!Ensembl
120070	2204	ENSG00000169031

Protein

UniProt ID

Q01955

Protein name

Collagen alpha-3(IV) chain (Goodpasture antigen) [Cleaved into: Tumstatin]

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.; Tumstatin, a cleavage fragment corresponding to t

PDB

5NB0 , 6WKU

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01391	Collagen	41 → 104	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	97 → 162	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	169 → 223	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	282 → 344	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	351 → 412	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	386 → 444	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	413 → 478	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	482 → 546	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	588 → 648	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	699 → 749	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	747 → 809	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	788 → 849	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	847 → 905	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	892 → 948	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	950 → 1009	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	997 → 1060	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1061 → 1122	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1119 → 1178	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1176 → 1235	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1292 → 1352	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	1379 → 1441	Collagen triple helix repeat (20 copies)	Repeat
PF01413	C4	1446 → 1553	C-terminal tandem repeated domain in type 4 procollagen	Domain
PF01413	C4	1556 → 1667	C-terminal tandem repeated domain in type 4 procollagen	Domain

Tissue specificity

TISSUE SPECIFICITY: Alpha 3 and alpha 4 type IV collagens are colocalized and present in kidney, eye, basement membranes of lens capsule, cochlea, lung, skeletal muscle, aorta, synaptic fibers, fetal kidney and fetal lung. PubMed:8083201 reports similar l

Sequence

MSARTAPRPQVLLLPLLLVLLAAAPAASKGCVCKDKGQCFCDGAKGEKGEKGFPGPPGSP
GQKGFTGPEGLPGPQGPKGFPGLPGLTGSKGVRGISGLPGFSGSPGLPGTPGNTGPYGLV
GVPGCSGSKGEQGFPGLPGTLGYPGIPGAAGLKGQKGAPAKEEDIELDAKGDPGLPGAPG
PQGLPGPPGFPGPVGPPGPPGFFGFPGAMGPRGPKGHMGERVIGHKGERGVKGLTGPPGP
PGTVIVTLTGPDNRTDLKGEKGDKGAMGEPGPPGPSGLPGESYGSEKGAPGDPGLQGKPG
KDGVPGFPGSEGVKGNRGFPGLMGEDGIKGQKGDIGPPGFRGPTEYYDTYQEKGDEGTPG
PPGPRGARGPQGPSGPPGVPGSPGSSRPGLRGAPGWPGLKGSKGERGRPGKDAMGTPGSP
GCAGSPGLPGSPGPPGPPGDIVFRKGPPGDHGLPGYLGSPGIPGVDGPKGEPGLLCTQCP
YIPGPPGLPGLPGLHGVKGIPGRQGAAGLKGSPGSPGNTGLPGFPGFPGAQGDPGLKGEK
GETLQPEGQVGVPGDPGLRGQPGRKGLDGIPGTPGVKGLPGPKGELALSGEKGDQGPPGD
PGSPGSPGPAGPAGPPGYGPQGEPGLQGTQGVPGAPGPPGEAGPRGELSVSTPVPGPPGP
PGPPGHPGPQGPPGIPGSLGKCGDPGLPGPDGEPGIPGIGFPGPPGPKGDQGFPGTKGSL
GCPGKMGEPGLPGKPGLPGAKGEPAVAMPGGPGTPGFPGERGNSGEHGEIGLPGLPGLPG
TPGNEGLDGPRGDPGQPGPPGEQGPPGRCIEGPRGAQGLPGLNGLKGQQGRRGKTGPKGD
PGIPGLDRSGFPGETGSPGIPGHQGEMGPLGQRGYPGNPGILGPPGEDGVIGMMGFPGAI
GPPGPPGNPGTPGQRGSPGIPGVKGQRGTPGAKGEQGDKGNPGPSEISHVIGDKGEPGLK
GFAGNPGEKGNRGVPGMPGLKGLKGLPGPAGPPGPRGDLGSTGNPGEPGLRGIPGSMGNM
GMPGSKGKRGTLGFPGRAGRPGLPGIHGLQGDKGEPGYSEGTRPGPPGPTGDPGLPGDMG
KKGEMGQPGPPGHLGPAGPEGAPGSPGSPGLPGKPGPHGDLGFKGIKGLLGPPGIRGPPG
LPGFPGSPGPMGIRGDQGRDGIPGPAGEKGETGLLRAPPGPRGNPGAQGAKGDRGAPGFP
GLPGRKGAMGDAGPRGPTGIEGFPGPPGLPGAIIPGQTGNRGPPGSRGSPGAPGPPGPPG
SHVIGIKGDKGSMGHPGPKGPPGTAGDMGPPGRLGAPGTPGLPGPRGDPGFQGFPGVKGE
KGNPGFLGSIGPPGPIGPKGPPGVRGDPGTLKIISLPGSPGPPGTPGEPGMQGEPGPPGP
PGNLGPCGPRGKPGKDGKPGTPGPAGEKGNKGSKGEPGPAGSDGLPGLKGKRGDSGSPAT
WTTRGFVFTRHSQTTAIPSCPEGTVPLYSGFSFLFVQGNQRAHGQDLGTLGSCLQRFTTM
PFLFCNVNDVCNFASRNDYSYWLSTPALMPMNMAPITGRALEPYISRCTVCEGPAIAIAV
HSQTTDIPPCPHGWISLWKGFSFIMFTSAGSEGTGQALASPGSCLEEFRASPFLECHGRG
TCNYYSNSYSFWLASLNPERMFRKPIPSTVKAGELEKIISRCQVCMKKRH

Sequence length

1670

Interactions

View interactions

	KEGG		Reactome
	PI3K-Akt signaling pathway Focal adhesion ECM-receptor interaction Cytoskeleton in muscle cells Relaxin signaling pathway AGE-RAGE signaling pathway in diabetic complications Protein digestion and absorption Amoebiasis Human papillomavirus infection Pathways in cancer Small cell lung cancer		Collagen degradation Extracellular matrix organization Collagen biosynthesis and modifying enzymes Signaling by PDGF Assembly of collagen fibrils and other multimeric structures Integrin cell surface interactions Anchoring fibril formation Crosslinking of collagen fibrils Laminin interactions Non-integrin membrane-ECM interactions NCAM1 interactions Collagen chain trimerization

Show/Hide Causal Diseases (5)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Alport Syndrome	autosomal recessive alport syndrome, autosomal dominant alport syndrome, alport syndrome, Alport syndrome 3b, autosomal recessive	rs1553750572, rs749383170, rs1574803208, rs1175052474, rs1574699806, rs781566652, rs121912824, rs1440033157, rs749390823, rs371334239, rs1274459294, rs1574698507, rs1559873550, rs748026887, rs1553751120 View all (105 more)	N/A
Benign Hematuria	Benign familial hematuria	rs869025328, rs1574813350, rs200287952, rs869025326, rs869025327, rs121912826, rs772708743	N/A
hematuria	Hematuria	rs1306992119	N/A
Nephrotic Syndrome	nephrotic syndrome	rs759043857	N/A
PILAROWSKI-BJORNSSON SYNDROME	pilarowski-bjornsson syndrome	rs1574823172	N/A

Show/Hide Unknown Diseases (7)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Dementia	Dementia	N/A	N/A	GWAS
focal segmental glomerulosclerosis	Focal segmental glomerulosclerosis	N/A	N/A	ClinVar
hearing impairment	Hearing impairment	N/A	N/A	ClinVar
Hemolytic Uremic Syndrome	Atypical hemolytic-uremic syndrome	N/A	N/A	ClinVar
Kidney Disease	Chronic kidney disease	N/A	N/A	ClinVar
Steroid resistant nephrotic syndrome	Steroid-resistant nephrotic syndrome	N/A	N/A	ClinVar
stickler syndrome	Stickler syndrome	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (61)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Albuminuria	Associate	31537649
Alzheimer Disease	Associate	11044206
Androgen Insensitivity Syndrome	Associate	11044206
Anti Glomerular Basement Membrane Disease	Associate	31686460, 36130833, 7783419
Asthma	Inhibit	28608951
Breast Neoplasms	Associate	23981902
Carcinoma Non Small Cell Lung	Associate	22473740, 23108892
Carcinoma Renal Cell	Associate	24002681, 33761933
Chronic Kidney Disease Mineral and Bone Disorder	Associate	31085678
Collagen Diseases	Associate	25514610, 30881523, 33159707
Colorectal Neoplasms	Associate	32945508
Corneal Dystrophy Posterior Polymorphous 3	Associate	22199242, 27537263
Corneal endothelial dystrophy type 2	Associate	22199242
Deafness	Associate	30881523, 34997062
Diabetic Nephropathies	Associate	30012629, 31537649
Down Syndrome	Associate	27487163
Epilepsy Benign Neonatal	Associate	19129241
Eye Abnormalities	Associate	24052634, 29551517, 30881523
Eye Infections Fungal	Associate	30881523
Fabry Disease	Associate	31840555
Genetic Diseases Inborn	Associate	18160688, 30881523
Glomerulonephritis IGA	Associate	34717572, 36130833
Glomerulosclerosis Focal Segmental	Associate	25229338, 25381091, 25407002, 25514610, 27469977, 28704582, 33305316, 36292665
Hearing Loss	Associate	24052634, 30881523, 34753855
Hearing Loss Sensorineural	Associate	29551517
Hematuria	Associate	11318937, 11473630, 12028435, 12631110, 14871398, 15882279, 25229338, 25381091, 25514610, 29551517, 30476138, 30881523, 33369211, 34400539, 35474271, 37872228 View all (1 more)
Hematuria Benign Familial	Associate	11318937, 11473630, 12028435, 12631110, 14871398, 17396119, 19675380, 23516419, 24854265, 25355442, 25514610, 26833262, 28704582, 29138824, 29764427 View all (6 more)
Hereditary renal agenesis	Associate	10200983
IgA Deficiency	Associate	34930753
Inflammation	Inhibit	28608951
Keratoconus	Associate	20029656, 20664914, 26040312, 32867823
Kidney Diseases	Associate	25229338, 25381091, 28117080, 29551517, 30881523, 31537649, 33095447, 33305316, 33369211, 34632641, 38317457, 39907758
Kidney Failure Chronic	Associate	15086897, 25381091, 25514610, 28704582, 29551517, 31144478, 33854215
Lupus Erythematosus Systemic	Associate	37841281
Mason Type Diabetes	Associate	30012629
Membranous Obstruction of Inferior Vena Cava	Associate	35151252
Neoplasm Metastasis	Associate	36407358
Neoplasms	Inhibit	22473740, 24002681
Neoplasms	Associate	33761933, 35361846
Neoplasms Adipose Tissue	Associate	31551515
Neoplastic Syndromes Hereditary	Associate	30881523
Nephritis Hereditary	Associate	10200983, 11044206, 11318937, 11473630, 12028435, 12631110, 15086897, 16252232, 17396119, 19675380, 21897443, 23297803, 24052634, 24854265, 25229338 View all (45 more)
Nephrotic Syndrome	Associate	25407002, 28117080, 34930753
Neuroma Acoustic	Associate	24030433
Noonan Syndrome	Associate	35151252
Osteogenesis Imperfecta Type IV	Associate	28704582
Ovarian Neoplasms	Associate	26260910
Proteinuria	Associate	14871398, 34930753, 37986374
Pulmonary Disease Chronic Obstructive	Associate	18385178, 22829758
Pulmonary edema of mountaineers	Associate	30053909
Renal Insufficiency	Associate	27627812, 28117080, 33305316, 33369211, 34930753
Renal Insufficiency Chronic	Associate	35325889, 38317457
Renal Nutcracker Syndrome	Associate	35151252
Respiratory Distress Syndrome	Associate	26507871
Respiratory Distress Syndrome Newborn	Associate	26507871
Scleroderma Diffuse	Associate	27111861
Status Asthmaticus	Inhibit	23483898
Status Asthmaticus	Associate	28608951
Thinness	Associate	25229338
Thyroid Cancer Papillary	Associate	28402931
Urofacial syndrome	Associate	35369551

COL4A3 (collagen type IV alpha 3 chain)