• Gene id: 1286

Gene Summary

• Gene Symbol: COL4A4   Gene   UCSC   Ensembl
• Aliases: ATS2, BFH, CA44
• Gene name: collagen type IV alpha 4 chain
• Alternate names: collagen alpha-4(IV) chain, Collagen IV, alpha-4 polypeptide, collagen of basement membrane, alpha-4 chain, collagen, type IV, alpha 4,
• Gene location: 2q36.3 (227164481: 226970292)     Exons: 54     NC_000002.12
• Gene summary(Entrez): This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. This particular collagen IV subunit, however, is only found in a subset of basement membranes. Like the other members of the type IV colla
• OMIM: 610519

SNPs

rs587777160

Strand:    Allele origin:   Allele change:   Mutation type: snv

NC_000020.11   g.440344C>T
NC_000020.10   g.420988C>T
NG_034082.1   g.27210G>A
NM_144628.3   c.672G>A
NM_144628.4   c.672G>A
NM_144628.2   c.672G>A
NR_111901.1   n.820G>A
XM_006723540.3   c.486G>A
XM_005260661.1   c.672G>A
XM_017027645.1   c.486G>A
NP_653229.1   p.Trp224T

rs587777159

Strand:    Allele origin:   Allele change:   Mutation type: delins

NC_000020.11   g.442029_442030del
NC_000020.10   g.422673_422674del
NG_034082.1   g.25525_25526del
NM_144628.3   c.352_353del
NM_144628.4   c.352_353del
NM_144628.2   c.352_353del
NR_111901.1   n.500_501del
XM_006723540.3   c.166_167del
XM_005260661.1   c.352_353del
X  

rs587777158

Strand:    Allele origin:   Allele change:   Mutation type: snv

NC_000020.11   g.445095G>A
NC_000020.10   g.425739G>A
NG_034082.1   g.22459C>T
NM_144628.3   c.292C>T
NM_144628.4   c.292C>T
NM_144628.2   c.292C>T
NR_111901.1   n.440C>T
XM_006723540.3   c.106C>T
XM_005260661.1   c.292C>T
XM_017027645.1   c.106C>T
NP_653229.1   p.Gln98Te

rs587777157

Strand:    Allele origin:   Allele change:   Mutation type: snv

NC_000020.11   g.447946G>A
NC_000020.10   g.428590G>A
NG_034082.1   g.19608C>T
NM_144628.3   c.199C>T
NM_144628.4   c.199C>T
NM_144628.2   c.199C>T
NR_111901.1   n.347C>T
XM_005260661.1   c.199C>T
NP_653229.1   p.Arg67Ter
XP_005260718.1   p.Arg67Ter|SEQ=[G/A]|GENE=TBC1D

Protein Summary

• Protein general information: P53420  
  • Name: Collagen alpha 4(IV) chain
  • Length: 1690  
  • Mass: 164038
  • Tissue specificity: Expressed in Bruch's membrane, outer plexiform layer, inner nuclear layer, inner plexiform layer, ganglion cell layer, inner limiting membrane and around the blood vessels of the retina (at protein level) (PubMed
• Sequence:

  MWSLHIVLMRCSFRLTKSLATGPWSLILILFSVQYVYGSGKKYIGPCGGRDCSVCHCVPEKGSRGPPGPPGPQGP
  IGPLGAPGPIGLSGEKGMRGDRGPPGAAGDKGDKGPTGVPGFPGLDGIPGHPGPPGPRGKPGMSGHNGSRGDPGF
  PGGRGALGPGGPLGHPGEKGEKGNSVFILGAVKGIQGDRGDPGLPGLPGSWGAGGPAGPTGYPGEPGLVGPPGQP
  GRPGLKGNPGVGVKGQMGDPGEVGQQGSPGPTLLVEPPDFCLYKGEKGIKGIPGMVGLPGPPGRKGESGIGAKGE
  KGIPGFPGPRGDPGSYGSPGFPGLKGELGLVGDPGLFGLIGPKGDPGNRGHPGPPGVLVTPPLPLKGPPGDPGFP
  GRYGETGDVGPPGPPGLLGRPGEACAGMIGPPGPQGFPGLPGLPGEAGIPGRPDSAPGKPGKPGSPGLPGAPGLQ
  GLPGSSVIYCSVGNPGPQGIKGKVGPPGGRGPKGEKGNEGLCACEPGPMGPPGPPGLPGRQGSKGDLGLPGWLGT
  KGDPGPPGAEGPPGLPGKHGASGPPGNKGAKGDMVVSRVKGHKGERGPDGPPGFPGQPGSHGRDGHAGEKGDPGP
  PGDHEDATPGGKGFPGPLGPPGKAGPVGPPGLGFPGPPGERGHPGVPGHPGVRGPDGLKGQKGDTISCNVTYPGR
  HGPPGFDGPPGPKGFPGPQGAPGLSGSDGHKGRPGTPGTAEIPGPPGFRGDMGDPGFGGEKGSSPVGPPGPPGSP
  GVNGQKGIPGDPAFGHLGPPGKRGLSGVPGIKGPRGDPGCPGAEGPAGIPGFLGLKGPKGREGHAGFPGVPGPPG
  HSCERGAPGIPGQPGLPGYPGSPGAPGGKGQPGDVGPPGPAGMKGLPGLPGRPGAHGPPGLPGIPGPFGDDGLPG
  PPGPKGPRGLPGFPGFPGERGKPGAEGCPGAKGEPGEKGMSGLPGDRGLRGAKGAIGPPGDEGEMAIISQKGTPG
  EPGPPGDDGFPGERGDKGTPGMQGRRGEPGRYGPPGFHRGEPGEKGQPGPPGPPGPPGSTGLRGFIGFPGLPGDQ
  GEPGSPGPPGFSGIDGARGPKGNKGDPASHFGPPGPKGEPGSPGCPGHFGASGEQGLPGIQGPRGSPGRPGPPGS
  SGPPGCPGDHGMPGLRGQPGEMGDPGPRGLQGDPGIPGPPGIKGPSGSPGLNGLHGLKGQKGTKGASGLHDVGPP
  GPVGIPGLKGERGDPGSPGISPPGPRGKKGPPGPPGSSGPPGPAGATGRAPKDIPDPGPPGDQGPPGPDGPRGAP
  GPPGLPGSVDLLRGEPGDCGLPGPPGPPGPPGPPGYKGFPGCDGKDGQKGPVGFPGPQGPHGFPGPPGEKGLPGP
  PGRKGPTGLPGPRGEPGPPADVDDCPRIPGLPGAPGMRGPEGAMGLPGMRGPSGPGCKGEPGLDGRRGVDGVPGS
  PGPPGRKGDTGEDGYPGGPGPPGPIGDPGPKGFGPGYLGGFLLVLHSQTDQEPTCPLGMPRLWTGYSLLYLEGQE
  KAHNQDLGLAGSCLPVFSTLPFAYCNIHQVCHYAQRNDRSYWLASAAPLPMMPLSEEAIRPYVSRCAVCEAPAQA
  VAVHSQDQSIPPCPQTWRSLWIGYSFLMHTGAGDQGGGQALMSPGSCLEDFRAAPFLECQGRQGTCHFFANKYSF
  WLTTVKADLQFSSAPAPDTLKESQAQRQKISRCQVCVKYS

• Structural information:
  • Protein Domains: (1465..169-)
    NC1 (/note="Collagen-IV)
    (/evidence="ECO:0000255|PROSITE-ProRule:PRU00736"-)
  • Interpro: IPR008160  IPR001442  IPR036954  IPR016187  
  • Prosite: PS51403
  • PDB: 5NB1
  • PDBsum: 5NB1
  • STRING: ENSP00000379866
• Other Databases: GeneCards:  COL4A4  Malacards:  COL4A4

Gene ontology

GO accession	Term name	Evidence code	Go category
GO:0005201	extracellular matrix structural constituent	IBA	molecular function
GO:0005615	extracellular space	IBA	cellular component
GO:0031012	extracellular matrix	IBA	cellular component
GO:0038063	collagen-activated tyrosine kinase receptor signaling pathway	IBA	biological process
GO:0005587	collagen type IV trimer	IBA	cellular component
GO:0030198	extracellular matrix organization	IBA	biological process
GO:0032836	glomerular basement membrane development	IBA	biological process
GO:0005201	extracellular matrix structural constituent	IEA	molecular function
GO:0005581	collagen trimer	IEA	cellular component
GO:0005576	extracellular region	IEA	cellular component
GO:0005604	basement membrane	IEA	cellular component
GO:0005581	collagen trimer	IEA	cellular component
GO:0030198	extracellular matrix organization	TAS	biological process
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005788	endoplasmic reticulum lumen	TAS	cellular component
GO:0005788	endoplasmic reticulum lumen	TAS	cellular component
GO:0005788	endoplasmic reticulum lumen	TAS	cellular component
GO:0005604	basement membrane	IEA	cellular component
GO:0005201	extracellular matrix structural constituent	IEA	molecular function
GO:0032836	glomerular basement membrane development	IEA	biological process
GO:0005587	collagen type IV trimer	IEA	cellular component
GO:0062023	collagen-containing extracellular matrix	HDA	cellular component
GO:0030020	extracellular matrix structural constituent conferring tensile strength	RCA	molecular function
GO:0005604	basement membrane	IEA	cellular component
GO:0005587	collagen type IV trimer	IDA	cellular component
GO:0005604	basement membrane	IDA	cellular component
GO:0005201	extracellular matrix structural constituent	IMP	molecular function
GO:0032836	glomerular basement membrane development	IMP	biological process
GO:0005201	extracellular matrix structural constituent	IMP	molecular function
GO:0032836	glomerular basement membrane development	IMP	biological process

KEGG pathways

Pathway id	Pathway name
hsa05200	Pathways in cancer
hsa04151	PI3K-Akt signaling pathway
hsa05165	Human papillomavirus infection
hsa04510	Focal adhesion
hsa04926	Relaxin signaling pathway
hsa04974	Protein digestion and absorption
hsa04512	ECM-receptor interaction
hsa05222	Small cell lung cancer
hsa04933	AGE-RAGE signaling pathway in diabetic complications
hsa05146	Amoebiasis

Diseases

Associated diseases	References
Alport syndrome	KEGG:H00581
Benign familial hematuria	KEGG:H00582
Alport syndrome	KEGG:H00581
Benign familial hematuria	KEGG:H00582
Benign familial hematuria	PMID:19357112
Cryptorchidism	MIK: 28606200

PubMed references

PMID	Condition	Mutation	Ethnicity	Population details	Infertility_type	Associated_genes
28606200	Cryptorchidism			Monozgotic twins (1 control, I cwith cryptorchidism)	Male infertility	MeDIP-Seq