CleftGeneDB-Search

Gene: Col4a3

Basic information

Tag	Content
Uniprot ID	Q9QZS0; Q61430; Q61435; Q8CCD6;
Entrez ID	12828
Genbank protein ID	BAC28260.1; CAA84529.1; CAA57689.1; AAD50449.1;
Genbank nucleotide ID	NM_007734.2
Ensembl protein ID	ENSMUSP00000109084
Ensembl nucleotide ID	ENSMUSG00000079465
Gene name	Collagen alpha-3(IV) chain
Gene symbol	Col4a3
Organism	Mus musculus
NCBI taxa ID	10090
Cleft type
Developmental stage
Data sources	Homology search
Reference
Functional description	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.
Sequence	MHSKTAPRFL VFLLLTLLLL LAASPVASKG CVCKGKGQCL CAGTKGEKGE KGVPGSPGFP 60 GQKGFPGPEG LPGPQGPKGS PGLPGLTGPK GIRGITGLPG FAGPPGLPGL PGHPGPRGLA 120 GLPGCNGSKG EQGFPGFPGT PGYAGLPGPD GLKGQKGEPA QGEDRGFNGK GDPGPPGVPG 180 FQGFPGLPGF PGPAGPPGPP GFFGLPGAMG PRGPKGHMGD SVIGQKGERG MKGLTGPPGP 240 PGTVIFTLTQ PYNKSDFKGE KGDEGERGEP GPPGPSGPPG DSYGSEKGAP GEPGPRGKPG 300 KDGAPGFPGT EGAKGNRGFP GLRGEAGIKG RKGDIGPPGF PGPTEYYDAY LEKGERGMPG 360 LPGPKGARGP QGPSGPPGVP GSPGLSRPGL RGPIGWPGLK GSKGERGPPG KDTVGPPGPL 420 GCPGSPGPPG PPGPPGCPGD IVFKCSPGEH GMPGDTGPPG VPGLDGPKGE PGSPCTECHC 480 FPGPPGVPGF PGLDGIKGIP GGRGVPGLKG NPGSPGSAGL PGFAGFPGDQ GHPGLKGDKG 540 DTPLPWGQVG NPGDPGLRGL PGRKGFDGTP GGPGAKGPPG PQGEPALSGR KGDQGPPGPP 600 GFPGPPGPAG PAGPPGYGPQ GEPGPKGAQG VPGVLGPPGE AGLKGEPSTS TPDLGPPGPP 660 GPPGQAGPRG LPGLPGPVGK CDPGLPGPDG EPGIPEAGCP GPPGPKGNQG FPGTKGSPGC 720 PGEMGKPGRP GEPGIPGAKG EPSVGRPGKP GKPGFPGERG NAGENGDIGL PGLPGLPGTP 780 GRGGLDGPPG DPGQPGSPGA KGSPGRCIPG PRGTQGLPGL NGLKGQPGRR GDTGPKGDPG 840 IPGMDRSGVP GDPGPPGTPG CPGEMGPPGQ KGYPGAPGFP GPPGEKGEVG MMGYPGTTGP 900 PGLPGKPGSQ GQRGSLGIPG MKGEKGRPGA KGERGEKGKP GPSQTTLLKG DKGEPGLKGF 960 VGNPGEKGNR GNPGLPGPKG LEGLPGLPGP PGPRGDTGSR GNPGRPGPHG MPGSMGIMGV 1020 PGPKGRKGTS GLPGLAGRPG LTGIHGPQGD KGEPGYSEGA RPGPPGPKGD PGLPGDKGKK 1080 GERGVPGPPG QSGPAGPDGA PGSPGSPGHP GKPGPAGDLG LKGQKGFPGP PGSTGPPGPP 1140 GLPGLPGPMG MRGDQGRDGI PGPPGEKGET GLLGAYPGPK GSPGVPGAKG DRGVPGLSGL 1200 PGRKGVMGDV GPQGPPGTAG LPGPPGLPGA IIPGPKGDRG LPGLRGNPGE PGPPGPPGPI 1260 GKGIKGDKGF MGPPGPKGLP GTVGDMGPPG FPGAPGTPGL PGVRGDPGFP GFPGIKGEKG 1320 NPGFLGPIGH PGPVGPKGPP GPRGKPGTLK VISLPGSPGP PGVPGQPGMK GDPGPLGLPG 1380 IPGPCGPRGK PGKDGKPGTP GPAGTKGNKG LKGQQGPPGL DGLPGLKGNP GDRGTPATGT 1440 RMRGFIFTRH SQTTAIPSCP EGTQPLYSGF SLLFVQGNKR AHGQDLGTLG SCLQRFTTMP 1500 FLFCNINNVC NFASRNDYSY WLSTPALMPM DMAPISGRAL EPYISRCTVC EGPAMAIAVH 1560 SQTTAIPPCP QDWVSLWKGF SFIMFTSAGS EGAGQALASP GSCLEEFRAS PFIECHGRGT 1620 CNYYSNSYSF WLASLNPERM FRKPIPSTVK AGDLEKIISR CQVCMKKRH 1669

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Relation	Gene symbol	Entrez ID	UniProt ID	Cleft type	Species	Evidence	Details
1:1 ortholog	COL4A3		F1MZU6		Bos taurus	Prediction	More>>
1:1 ortholog	COL4A3	1285	Q01955	CPO,CL/P	Homo sapiens	Publication	More>>
1:1 ortholog	Col4a3	12828	Q9QZS0		Mus musculus	Prediction	More>>
1:1 ortholog	COL4A3	459988	H2QJJ5		Pan troglodytes	Prediction	More>>
1:1 ortholog	COL4A3		G1SCM1		Oryctolagus cuniculus	Prediction	More>>
1:1 ortholog	Col4a3	363265	F1LRJ1		Rattus norvegicus	Prediction	More>>

Identified variants/mutations related to cleft phenotype

Gene symbol	Significant Variants/SNPS	Methods	PubMed ID
COL4A3	c.4243G>D; p.G1415R and c.4216G>A; p.G1406R (compound heterozygous)	WES and Sanger sequencing	33524082

Other genetic variants/mutations

ID	Variant	Type	Disease	Chromosome\Coordinate	Evidence
rs265374672	p.Phe12Leu	missense variant	-	NC_000067.6:g.82587378T>C	UniProt
rs221147853	p.Thr16Ile	missense variant	-	NC_000067.6:g.82587391C>T	UniProt
rs230323041	p.Ser24Pro	missense variant	-	NC_000067.6:g.82587414T>C	UniProt
rs251256168	p.Ser221Arg	missense variant	-	NC_000067.6:g.82656868C>A	UniProt
rs248113040	p.Val222Met	missense variant	-	NC_000067.6:g.82656869G>A	UniProt
rs245786693	p.Thr249Ile	missense variant	-	NC_000067.6:g.82657204C>T	UniProt
rs215381176	p.Gln250His	missense variant	-	NC_000067.6:g.82657208G>C	UniProt
rs255139027	p.Lys258Gln	missense variant	-	NC_000067.6:g.82660230A>C	UniProt
rs30248150	p.Ser276Leu	missense variant	-	NC_000067.6:g.82660285C>T	UniProt
rs30245872	p.Ala304Gly	missense variant	-	NC_000067.6:g.82662224C>G	UniProt
rs232544217	p.Asn316Ser	missense variant	-	NC_000067.6:g.82662909A>G	UniProt
rs216193221	p.Met358Thr	missense variant	-	NC_000067.6:g.82666564T>C	UniProt
rs255757380	p.Ile394Thr	missense variant	-	NC_000067.6:g.82668950T>C	UniProt
rs229309822	p.Val505Ala	missense variant	-	NC_000067.6:g.82671319T>C	UniProt
rs30240545	p.Asn551Asp	missense variant	-	NC_000067.6:g.82672675A>G	UniProt
rs229497087	p.Ala575Val	missense variant	-	NC_000067.6:g.82672748C>T	UniProt
rs226440295	p.Val634Ile	missense variant	-	NC_000067.6:g.82674123G>A	UniProt
rs219747888	p.Asp653Val	missense variant	-	NC_000067.6:g.82675942A>T	UniProt
rs30243082	p.Val744Ile	missense variant	-	NC_000067.6:g.82679091G>A	UniProt
rs226745634	p.Lys749Glu	missense variant	-	NC_000067.6:g.82679106A>G	UniProt
rs30243081	p.Glu764Asp	missense variant	-	NC_000067.6:g.82679153A>T	UniProt
rs246416154	p.Arg782Lys	missense variant	-	NC_000067.6:g.82679206G>A	UniProt
rs244422697	p.Gly783Asp	missense variant	-	NC_000067.6:g.82679209G>A	UniProt
rs30243076	p.Ser797Pro	missense variant	-	NC_000067.6:g.82679569T>C	UniProt
rs248764669	p.Pro809Ser	missense variant	-	NC_000067.6:g.82679605C>T	UniProt
rs30241519	p.Asp852Glu	missense variant	-	NC_000067.6:g.82680753T>G	UniProt
rs255861884	p.Phe879Ser	missense variant	-	NC_000067.6:g.82680833T>C	UniProt
rs239467142	p.Pro900Ser	missense variant	-	NC_000067.6:g.82682333C>T	UniProt
rs218956785	p.Lys925Arg	missense variant	-	NC_000067.6:g.82682736A>G	UniProt
rs227539857	p.Thr945Ile	missense variant	-	NC_000067.6:g.82682796C>T	UniProt
rs30244767	p.Asn972Ser	missense variant	-	NC_000067.6:g.82689146A>G	UniProt
rs30242860	p.Thr997Met	missense variant	-	NC_000067.6:g.82690001C>T	UniProt
rs230825959	p.Thr997Ser	missense variant	-	NC_000067.6:g.82690000A>T	UniProt
rs247645821	p.Met1015Val	missense variant	-	NC_000067.6:g.82690054A>G	UniProt
rs228389366	p.Met1018Ile	missense variant	-	NC_000067.6:g.82690065G>T	UniProt
rs6185983	p.Thr1042Pro	missense variant	-	NC_000067.6:g.82690580A>C	UniProt
rs30241249	p.Val1085Leu	missense variant	-	NC_000067.6:g.82693467G>C	UniProt
rs245218272	p.Met1149Ile	missense variant	-	NC_000067.6:g.82696714G>T	UniProt
rs215287375	p.Val1206Phe	missense variant	-	NC_000067.6:g.82700294G>T	UniProt
rs30239356	p.Ile1232Val	missense variant	-	NC_000067.6:g.82700372A>G	UniProt
rs227916390	p.Val1283Ile	missense variant	-	NC_000067.6:g.82700858G>A	UniProt
rs250629567	p.Pro1322Ser	missense variant	-	NC_000067.6:g.82710814C>T	UniProt
rs214316835	p.Pro1336Leu	missense variant	-	NC_000067.6:g.82710857C>T	UniProt
rs218566067	p.Leu1378Pro	missense variant	-	NC_000067.6:g.82711070T>C	UniProt
rs227478258	p.Leu1411Ser	missense variant	-	NC_000067.6:g.82711924T>C	UniProt
rs257630165	p.Met1442Ile	missense variant	-	NC_000067.6:g.82715321G>T	UniProt
rs30242570	p.Lys1479Glu	missense variant	-	NC_000067.6:g.82715430A>G	UniProt
rs30242569	p.Met1530Val	missense variant	-	NC_000067.6:g.82716140A>G	UniProt

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID	GO Term	Evidence
GO:0005178	integrin binding	ISS
GO:0005178	integrin binding	ISO
GO:0005201	extracellular matrix structural constituent	IBA
GO:0030020	extracellular matrix structural constituent conferring tensile strength	RCA

GO:Biological Process

GO ID	GO Term	Evidence
GO:0006919	activation of cysteine-type endopeptidase activity involved in apoptotic process	ISS
GO:0006919	activation of cysteine-type endopeptidase activity involved in apoptotic process	ISO
GO:0007155	cell adhesion	IEA
GO:0007166	cell surface receptor signaling pathway	IDA
GO:0009749	response to glucose	IEA
GO:0016525	negative regulation of angiogenesis	ISO
GO:0016525	negative regulation of angiogenesis	IDA
GO:0030198	extracellular matrix organization	IBA
GO:0032836	glomerular basement membrane development	IMP
GO:0038063	collagen-activated tyrosine kinase receptor signaling pathway	IGI
GO:0072577	endothelial cell apoptotic process	ISS
GO:0072577	endothelial cell apoptotic process	ISO
GO:1905563	negative regulation of vascular endothelial cell proliferation	ISS
GO:1905563	negative regulation of vascular endothelial cell proliferation	ISO

GO:Cellular Component

GO ID	GO Term	Evidence
GO:0005587	collagen type IV trimer	ISO
GO:0005587	collagen type IV trimer	IDA
GO:0005587	collagen type IV trimer	IBA
GO:0005604	basement membrane	ISS
GO:0005604	basement membrane	ISO
GO:0005604	basement membrane	IDA
GO:0005615	extracellular space	IBA
GO:0005783	endoplasmic reticulum	ISO
GO:0031012	extracellular matrix	IBA
GO:0043231	intracellular membrane-bounded organelle	ISO
GO:0062023	collagen-containing extracellular matrix	HDA

Reactome Pathway

Reactome ID	Reactome Term	Evidence
R-MMU-1266738	Developmental Biology	IEA
R-MMU-1442490	Collagen degradation	IEA
R-MMU-1474228	Degradation of the extracellular matrix	IEA
R-MMU-1474244	Extracellular matrix organization	IEA
R-MMU-1474290	Collagen formation	IEA
R-MMU-162582	Signal Transduction	IEA
R-MMU-1650814	Collagen biosynthesis and modifying enzymes	IEA
R-MMU-186797	Signaling by PDGF	IEA
R-MMU-2022090	Assembly of collagen fibrils and other multimeric structures	IEA
R-MMU-216083	Integrin cell surface interactions	IEA
R-MMU-2214320	Anchoring fibril formation	IEA
R-MMU-2243919	Crosslinking of collagen fibrils	IEA
R-MMU-3000157	Laminin interactions	IEA
R-MMU-3000171	Non-integrin membrane-ECM interactions	IEA
R-MMU-375165	NCAM signaling for neurite out-growth	IEA
R-MMU-419037	NCAM1 interactions	IEA
R-MMU-422475	Axon guidance	IEA
R-MMU-8948216	Collagen chain trimerization	IEA
R-MMU-9006934	Signaling by Receptor Tyrosine Kinases	IEA

Functional annotations

Keywords

Keyword ID	Keyword Term
KW-0084	Basement membrane
KW-0130	Cell adhesion
KW-0176	Collagen
KW-1015	Disulfide bond
KW-0272	Extracellular matrix
KW-0325	Glycoprotein
KW-0597	Phosphoprotein
KW-1185	Reference proteome
KW-0677	Repeat
KW-0964	Secreted
KW-0732	Signal

Interpro

InterPro ID	InterPro Term
IPR008160	Collagen
IPR001442	Collagen_IV_NC
IPR036954	Collagen_IV_NC_sf
IPR016187	CTDL_fold

PROSITE

PROSITE ID	PROSITE Term
PS51403	NC1_IV

Pfam

Pfam ID	Pfam Term
PF01413	C4
PF01391	Collagen

Gene: Col4a3

Basic information

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Identified variants/mutations related to cleft phenotype

Other genetic variants/mutations

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO:Biological Process

GO:Cellular Component

Reactome Pathway

Functional annotations

Keywords

Interpro

PROSITE

Pfam

Protein-miRNA interaction