COL4A2 (collagen type IV alpha 2 chain)

Gene

• Entrez ID: 1284
• Gene name: Collagen type IV alpha 2 chain
• Gene symbol: COL4A2
• Synonyms: BSVD2, ICH, POREN2
• Chromosome: 13
• Chromosome location: 13q34
• Summary: This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. The C-terminal portion of the protein, known as canstatin, is an inhibitor of angiogenesis and tumor growth. 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 so that each gene pair shares a common promoter. [provided by RefSeq, Jul 2008]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs12877501	G>A,C	Likely-pathogenic, likely-benign	Missense variant, coding sequence variant
rs62621875	C>A	Risk-factor, benign, likely-benign	Missense variant, coding sequence variant
rs117412802	A>G	Likely-benign, risk-factor, benign	Missense variant, coding sequence variant
rs201105747	G>A,T	Risk-factor, likely-benign, benign	Coding sequence variant, missense variant
rs387906602	G>A	Pathogenic	Coding sequence variant, missense variant
rs387906603	G>A	Pathogenic	Coding sequence variant, missense variant
rs776550709	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs969435078	->C	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1057519090	G>A	Pathogenic	Coding sequence variant, missense variant
rs1057523764	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1064797180	G>A	Likely-pathogenic	Splice acceptor variant
rs1085307983	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1555331796	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1566525717	G>C	Pathogenic	Splice acceptor variant
rs1594088780	G>A	Likely-pathogenic	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT000099	hsa-miR-29b-3p	Luciferase reporter assay	22745231
MIRT000099	hsa-miR-29b-3p	qRT-PCR	25744716
MIRT001926	hsa-miR-29c-3p	Luciferase reporter assay, Reporter assay;Other	18390668
MIRT001926	hsa-miR-29c-3p	Luciferase reporter assay	22745231
MIRT003220	hsa-miR-29a-3p	Luciferase reporter assay, qRT-PCR, Western blot	20067797
MIRT003220	hsa-miR-29a-3p	qRT-PCR	22864815
MIRT003220	hsa-miR-29a-3p	Luciferase reporter assay	22745231
MIRT003220	hsa-miR-29a-3p	Western blot, Luciferase reporter assay, Immunofluorescence	25241894
MIRT020729	hsa-miR-155-5p	Proteomics	18668040
MIRT029546	hsa-miR-26b-5p	Microarray	19088304
MIRT040463	hsa-miR-615-3p	CLASH	23622248
MIRT047706	hsa-miR-10a-5p	CLASH	23622248
MIRT049302	hsa-miR-92a-3p	CLASH	23622248
MIRT051129	hsa-miR-16-5p	CLASH	23622248
MIRT054207	hsa-miR-210-3p	Luciferase reporter assay, Microarray, qRT-PCR, Western blot	23028679
MIRT054216	hsa-miR-147b	Luciferase reporter assay, Microarray, qRT-PCR, Western blot	23028679
MIRT437565	hsa-miR-767-5p	Luciferase reporter assay	22745231

Transcription factors

Transcription factor	Regulation	Reference
VHL	Unknown	17700531

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001525	Process	Angiogenesis	IEA
GO:0005201	Function	Extracellular matrix structural constituent	IBA	21873635
GO:0005201	Function	Extracellular matrix structural constituent	TAS	8317999
GO:0005515	Function	Protein binding	IPI	12011424
GO:0005576	Component	Extracellular region	TAS
GO:0005587	Component	Collagen type IV trimer	IBA	21873635
GO:0005587	Component	Collagen type IV trimer	TAS	2846280, 3345760
GO:0005615	Component	Extracellular space	IBA	21873635
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0006351	Process	Transcription, DNA-templated	IEA
GO:0007568	Process	Aging	IEA
GO:0014823	Process	Response to activity	IEA
GO:0016525	Process	Negative regulation of angiogenesis	IDA	10625665
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	HDA	28344315
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	ISS
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	RCA	20551380, 23979707, 25037231, 27068509, 27559042, 28327460, 28675934
GO:0030198	Process	Extracellular matrix organization	IBA	21873635
GO:0030198	Process	Extracellular matrix organization	NAS	8317999
GO:0030198	Process	Extracellular matrix organization	TAS
GO:0031012	Component	Extracellular matrix	IBA	21873635
GO:0035987	Process	Endodermal cell differentiation	IEP	23154389
GO:0038063	Process	Collagen-activated tyrosine kinase receptor signaling pathway	IBA	21873635
GO:0062023	Component	Collagen-containing extracellular matrix	HDA	23658023, 23979707, 25037231, 27068509, 27559042, 28327460, 28344315, 28675934
GO:0062023	Component	Collagen-containing extracellular matrix	HDA	20551380
GO:0062023	Component	Collagen-containing extracellular matrix	ISS	22261194
GO:0062023	Component	Collagen-containing extracellular matrix	TAS	22261194
GO:0070062	Component	Extracellular exosome	HDA	23533145
GO:0071560	Process	Cellular response to transforming growth factor beta stimulus	IEA

Other IDs

• MIM: 120090
• HGNC: 2203
• e!Ensembl: ENSG00000134871

Protein

• UniProt ID: P08572
• Protein name: Collagen alpha-2(IV) chain [Cleaved into: Canstatin]
• 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.; Canstatin, a cleavage product corresponding to the collagen alpha 2(IV) NC1 domain, possesses both anti-angiogenic and anti-tumor cell activity. It inhibits proliferation and migration of endothelial cells, reduces mitochondrial membrane potential, and induces apoptosis. Specifically induces Fas-dependent apoptosis and activates procaspase-8 and -9 activity. Ligand for alphavbeta3 and alphavbeta5 integrins.
• PDB: 1LI1, 5NAX, 5NB2, 6MPX
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01391	Collagen	56 → 118	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	112 → 173	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	182 → 234	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	291 → 353	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	423 → 483	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	491 → 552	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	679 → 740	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	720 → 778	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	777 → 838	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	812 → 892	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	862 → 938	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	920 → 981	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	1032 → 1096	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	1098 → 1157	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	1152 → 1214	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	1278 → 1340	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	1332 → 1396	Collagen triple helix repeat (20 copies)	Repeat
  PF01413	C4	1490 → 1595	C-terminal tandem repeated domain in type 4 procollagen	Domain
  PF01413	C4	1598 → 1710	C-terminal tandem repeated domain in type 4 procollagen	Domain

• Sequence:

  MGRDQRAVAGPALRRWLLLGTVTVGFLAQSVLAGVKKFDVPCGGRDCSGGCQCYPEKGGR
  GQPGPVGPQGYNGPPGLQGFPGLQGRKGDKGERGAPGVTGPKGDVGARGVSGFPGADGIP
  GHPGQGGPRGRPGYDGCNGTQGDSGPQGPPGSEGFTGPPGPQGPKGQKGEPYALPKEERD
  RYRGEPGEPGLVGFQGPPGRPGHVGQMGPVGAPGRPGPPGPPGPKGQQGNRGLGFYGVKG
  EKGDVGQPGPNGIPSDTLHPIIAPTGVTFHPDQYKGEKGSEGEPGIRGISLKGEEGIMGF
  PGLRGYPGLSGEKGSPGQKGSRGLDGYQGPDGPRGPKGEAGDPGPPGLPAYSPHPSLAKG
  ARGDPGFPGAQGEPGSQGEPGDPGLPGPPGLSIGDGDQRRGLPGEMGPKGFIGDPGIPAL
  YGGPPGPDGKRGPPGPPGLPGPPGPDGFLFGLKGAKGRAGFPGLPGSPGARGPKGWKGDA
  GECRCTEGDEAIKGLPGLPGPKGFAGINGEPGRKGDRGDPGQHGLPGFPGLKGVPGNIGA
  PGPKGAKGDSRTITTKGERGQPGVPGVPGMKGDDGSPGRDGLDGFPGLPGPPGDGIKGPP
  GDPGYPGIPGTKGTPGEMGPPGLGLPGLKGQRGFPGDAGLPGPPGFLGPPGPAGTPGQID
  CDTDVKRAVGGDRQEAIQPGCIGGPKGLPGLPGPPGPTGAKGLRGIPGFAGADGGPGPRG
  LPGDAGREGFPGPPGFIGPRGSKGAVGLPGPDGSPGPIGLPGPDGPPGERGLPGEVLGAQ
  PGPRGDAGVPGQPGLKGLPGDRGPPGFRGSQGMPGMPGLKGQPGLPGPSGQPGLYGPPGL
  HGFPGAPGQEGPLGLPGIPGREGLPGDRGDPGDTGAPGPVGMKGLSGDRGDAGFTGEQGH
  PGSPGFKGIDGMPGTPGLKGDRGSPGMDGFQGMPGLKGRPGFPGSKGEAGFFGIPGLKGL
  AGEPGFKGSRGDPGPPGPPPVILPGMKDIKGEKGDEGPMGLKGYLGAKGIQGMPGIPGLS
  GIPGLPGRPGHIKGVKGDIGVPGIPGLPGFPGVAGPPGITGFPGFIGSRGDKGAPGRAGL
  YGEIGATGDFGDIGDTINLPGRPGLKGERGTTGIPGLKGFFGEKGTEGDIGFPGITGVTG
  VQGPPGLKGQTGFPGLTGPPGSQGELGRIGLPGGKGDDGWPGAPGLPGFPGLRGIRGLHG
  LPGTKGFPGSPGSDIHGDPGFPGPPGERGDPGEANTLPGPVGVPGQKGDQGAPGERGPPG
  SPGLQGFPGITPPSNISGAPGDKGAPGIFGLKGYRGPPGPPGSAALPGSKGDTGNPGAPG
  TPGTKGWAGDSGPQGRPGVFGLPGEKGPRGEQGFMGNTGPTGAVGDRGPKGPKGDPGFPG
  APGTVGAPGIAGIPQKIAVQPGTVGPQGRRGPPGAPGEMGPQGPPGEPGFRGAPGKAGPQ
  GRGGVSAVPGFRGDEGPIGHQGPIGQEGAPGRPGSPGLPGMPGRSVSIGYLLVKHSQTDQ
  EPMCPVGMNKLWSGYSLLYFEGQEKAHNQDLGLAGSCLARFSTMPFLYCNPGDVCYYASR
  NDKSYWLSTTAPLPMMPVAEDEIKPYISRCSVCEAPAIAIAVHSQDVSIPHCPAGWRSLW
  IGYSFLMHTAAGDEGGGQSLVSPGSCLEDFRATPFIECNGGRGTCHYYANKYSFWLTTIP
  EQSFQGSPSADTLKAGLIRTHISRCQVCMKNL

• Sequence length: 1712