COL4A5

gene
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Summary

COL4A5 (collagen type IV alpha 5 chain, HGNC:2207) is a protein-coding gene on chromosome Xq22.3, encoding Collagen alpha-5(IV) chain (P29400). 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. It is haploinsufficient (ClinGen: sufficient evidence).

This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. Mutations in this gene are associated with X-linked Alport syndrome, also known as hereditary nephritis. 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. Alternatively spliced transcript variants have been identified for this gene.

Source: NCBI Gene 1287 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Alport syndrome (Definitive, ClinGen) — +1 more curated relationship
  • Clinical variants (ClinVar): 3,508 total — 625 pathogenic, 658 likely-pathogenic
  • Phenotypes (HPO): 56
  • Druggable target: yes
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_033380

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2207
Approved symbolCOL4A5
Namecollagen type IV alpha 5 chain
LocationXq22.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000188153
Ensembl biotypeprotein_coding
OMIM303630
Entrez1287

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 9 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000328300, ENST00000361603, ENST00000470339, ENST00000477429, ENST00000483338, ENST00000489230, ENST00000504541, ENST00000505728, ENST00000510690, ENST00000515658, ENST00000642185, ENST00000644079, ENST00000949141, ENST00000949142, ENST00000949143

RefSeq mRNA: 2 — MANE Select: NM_033380 NM_000495, NM_033380

CCDS: CCDS14543, CCDS35366

Canonical transcript exons

ENST00000328300 — 53 exons

ExonStartEnd
ENSE00001152517108626210108626349
ENSE00001262874108695267108695439
ENSE00001262884108694807108694921
ENSE00001262981108655331108655457
ENSE00001340002108665507108665587
ENSE00001340048108668319108668504
ENSE00001340050108667133108667183
ENSE00001362206108692748108692925
ENSE00001362209108687482108687694
ENSE00001434905108578291108578383
ENSE00001435010108582884108582937
ENSE00001435129108578078108578119
ENSE00001435244108577952108577987
ENSE00001435302108568759108568821
ENSE00001435451108580983108581027
ENSE00001435485108575910108575972
ENSE00001436068108571811108571837
ENSE00001436285108580682108580738
ENSE00001436434108573574108573654
ENSE00001436548108580533108580586
ENSE00001436663108666496108666594
ENSE00001436779108571413108571466
ENSE00001600586108670228108670236
ENSE00001860956108439838108440206
ENSE00003465267108680885108680956
ENSE00003471758108595509108595601
ENSE00003482829108602964108603061
ENSE00003486836108559064108559153
ENSE00003489323108563882108563926
ENSE00003493604108620259108620426
ENSE00003497266108686031108686129
ENSE00003502643108622676108622825
ENSE00003538467108606742108606892
ENSE00003550123108539746108539805
ENSE00003555831108586615108586747
ENSE00003558371108596998108597068
ENSE00003575967108680679108680751
ENSE00003583814108591058108591231
ENSE00003588347108677500108677633
ENSE00003596104108625705108625794
ENSE00003598869108681760108681888
ENSE00003627141108598702108598870
ENSE00003634688108568629108568673
ENSE00003636495108614911108615024
ENSE00003644068108591561108591644
ENSE00003644175108601393108601485
ENSE00003661167108601885108601989
ENSE00003667613108674745108674753
ENSE00003669472108624236108624334
ENSE00003670092108621803108621892
ENSE00003670660108597377108597568
ENSE00003683504108584484108584525
ENSE00003899112108696297108697545

Expression profiles

Bgee: expression breadth ubiquitous, 267 present calls, max score 99.06.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.5852 / max 868.3864, expressed in 1106 samples.

FANTOM5 promoters (13 alternative TSS)

Promoter IDTPM avgSamples expressed
1972115.44431053
1972161.177076
1972120.8712352
1972200.578473
1972180.572673
1972130.4231230
1972140.165578
1972100.096534
1972190.079648
1972090.061714

Top tissues by expression

290 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
mucosa of stomachUBERON:000119999.06gold quality
ventricular zoneUBERON:000305398.01gold quality
lower esophagus muscularis layerUBERON:003583397.95gold quality
lower esophagusUBERON:001347397.89gold quality
esophagogastric junction muscularis propriaUBERON:003584197.79gold quality
seminal vesicleUBERON:000099897.58gold quality
corpus callosumUBERON:000233696.88gold quality
body of uterusUBERON:000985396.73gold quality
urethraUBERON:000005796.64gold quality
cauda epididymisUBERON:000436096.49gold quality
right uterine tubeUBERON:000130296.16gold quality
inferior vagus X ganglionUBERON:000536396.08gold quality
left uterine tubeUBERON:000130396.02gold quality
urinary bladderUBERON:000125595.46gold quality
hair follicleUBERON:000207395.46gold quality
C1 segment of cervical spinal cordUBERON:000646995.39gold quality
blood vessel layerUBERON:000479795.03gold quality
spinal cordUBERON:000224094.97gold quality
myometriumUBERON:000129694.94gold quality
endocervixUBERON:000045894.84gold quality
dorsal motor nucleus of vagus nerveUBERON:000287094.84gold quality
inferior olivary complexUBERON:000212794.61gold quality
caput epididymisUBERON:000435894.02gold quality
popliteal arteryUBERON:000225094.01gold quality
tibial arteryUBERON:000761094.01gold quality
mucosa of paranasal sinusUBERON:000503094.00gold quality
subthalamic nucleusUBERON:000190693.91gold quality
mucosa of urinary bladderUBERON:000125993.80gold quality
fundus of stomachUBERON:000116093.70gold quality
germinal epithelium of ovaryUBERON:000130493.39gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-HCAD-35yes75.14
E-HCAD-25yes52.01
E-CURD-119yes24.11
E-ANND-3yes11.54
E-MTAB-7249yes2.97
E-CURD-10no222.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

93 targeting COL4A5, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-3163100.0077.238605
HSA-MIR-5692A100.0074.406850
HSA-MIR-453199.9969.703181
HSA-MIR-428299.9975.366408
HSA-MIR-186-5P99.9970.833707
HSA-MIR-450099.9972.722367
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-767-5P99.9570.85993
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-311999.9271.342390
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-368699.9070.532432
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-568299.8972.561005

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • SSCP analysis in X-linked Alport syndrome (PMID:11462238)
  • new point mutation in a Spanish family with X-linked Alport syndrome (PMID:11961405)
  • an imbalance of glomerular alpha2(IV) and alpha5(IV) chain expression occurred in IgA nephropathy (PMID:12021518)
  • thin basement membrane disease might be caused by an abnormality of the alpha5(IV) antigen along the glomerular basement membrane (PMID:12218303)
  • human CA54 protein has a natural tendency towards variants (PMID:12732331)
  • This study showed abnormal composition of alpha(IV) chains in the anterior lens capsule of a patient with anterior lenticonus caused by a nonsense mutation in the COL4A5 gene. (PMID:12796257)
  • absence of genotype-phenotype correlation and the large intrafamilial phenotypic heterogeneity (PMID:14514738)
  • there is no correlation between the severity of the glomerular involvement (expressed by proteinuria) and the staining of the alpha 5 chain in the EBM in females with X-linked Alport syndrome. (PMID:14531812)
  • We provide a first indication that highly specialized patterns characteristic of COL4A5-COL4A6 expression in vivo arise from effects of distributed cis-acting regulatory elements on a bidirectional proximal promoter, itself transcriptionally competent. (PMID:14592452)
  • critical role of COL4A5 gene mutations in the pathogenesis of Alport’s syndrome. (PMID:14993485)
  • Alport syndrome in French Polynesia is due to a founder mutation, a tandem duplication of 35 exons, that occurred onto a common haplotype (PMID:15149316)
  • Collagen chains alpha5(IV) and alpha6(IV) were frequently absent in basement membrane from pancreatic adenocarcinoma, and their absence might be related to the invasion of cancer cells. (PMID:15211113)
  • The predicted rates of AA substitutions for glycine were compared with missense mutations that have been observed to cause disease. Any Gly replacement will cause disease & the level of triple-helix destabilization determines clinical outcome. (PMID:15365990)
  • distinctive patterns of expression of the alpha1 (IV) and alpha5 (IV) collagen chains may be related to the histogenic sudoral origin of cyli (PMID:15583824)
  • COL4A5 mutations observed in evident X-linked Alport syndrome using genomic DNA. (PMID:15780079)
  • novel mutations identified during routine molecular diagnostics for Alport syndrome (PMID:15954103)
  • both COL12A1 and COL4A5 constitute good candidate target genes in the pathogenesis of subungual exostosis (PMID:16284948)
  • The expression of the alpha5(IV)/alpha6(IV) chains was down-regulated in colorectal cancer, and the loss of expression of the alpha5(IV)/alpha6(IV) chains was associated with the hypermethylation of their promoter region. (PMID:16507901)
  • analysis of conformational features of a natural break in the type IV collagen Gly-X-Y repeat (PMID:16613845)
  • Immunolocalization of alpha5 type (IV)-chain collagen in the kidney may correspond to the severity of the clinical phenotype. (PMID:16940319)
  • Twenty-one mutations in COL4A5 gene were identified in patients with Alport syndrome and they include four gross deletions, two deep intronic mutations, three frameshifts, three splice site mutations, eight missense mutations and one inframe deletion. (PMID:16941480)
  • The cysteine to tyrosine substitution in the NC1 domain of the alpha5(IV) collagen chain in this family leads to a mild form of Alport syndrome, including absence of extra-renal features. (PMID:17277342)
  • Ultrastructure of COL4A5 immunofluorescence staining of the glomerular basement membrane and Bowman capsule was demonstrated. In conrast, this protein was absent in the basement membrane of skin cells. (PMID:17294221)
  • 16 novel mutations identified in COL4A3, COL4A4 & COL4A5 genes in Slovenian families with Alport syndrome(ATS)& benign familial hematuria; 12 mutations found in COL4A5 gene in ATS patients (9 missense, 1 splice site, 1 frameshift & 1 nonsense mutation) (PMID:17396119)
  • Comparison of alpha5(IV) with alpha2(IV) expression in Alport patients is simple and eliminates technical artifacts. (PMID:17554254)
  • These findings indicate that a defect in heterotrimer formation is the main molecular mechanism underlying the pathogenesis of AS caused by mutation in the NC1 domain. (PMID:18083113)
  • combination of cDNA and MLPA analysis improves the mutation detection rate in COL4A5 and that MLPA should be the first step in genetic testing for X-linked AS (PMID:18616531)
  • The co-detection of alpha5 and alpha2 chains of collagen IV in frozen skin biopsies is therefore proposed as a simple technique to diagnose Alport syndrome. (PMID:18706356)
  • analysis of noncollagenous sites encoding specific interactions and quaternary assembly of alpha 3 alpha 4 alpha 5(IV) collagen (PMID:18930919)
  • a novel splicing mutation of c.1517-1G to T in the COL4A5 gene causing Alport syndrome in a Chinese family (PMID:19065523)
  • study reports on a family with atypical Alport disease initially presenting as hereditary focal and segmental glomerulosclerosis; a previously undescribed COL4A5 mutation was identified as cause of the disease (PMID:19281745)
  • Aromatic residues greatly accelerate the kinetics of self-association in a typical sequence from the alpha5 chain of type IV collagen, decreasing lag time and leading to insoluble, well-defined linear fibrils as well as small soluble aggregates. (PMID:19610672)
  • underlying COL4A5 (collagen type IV alpha 5) mutation, truncating or non-truncating, can significantly predict the age at End stage renal disease in male patients (PMID:19728970)
  • An assay useful for mutations responsible for the most adult type Alport syndrome in the U.S. is recommended for testing individuals from families carrying one of the COL4A5 mutations tested: Cys1564Ser, Leu1649Arg or Arg1677Gln. (PMID:19919694)
  • Severe mutations in male individuals with X-linked Alport syndrome are associated with the perimacular dot-and-fleck retinopathy. Furthermore, the retinopathy indicates that male individuals are at increased risk for renal failure before the age of 30 (PMID:19965530)
  • younger age at onset of ESRD associated with mutations at the 5’ end of the gene (PMID:20378821)
  • A curated disease-specific database containing reported sequence variants in COL4A5, was developed. (PMID:20574986)
  • A novel COL4A5 mutation causes rapid progression to end-stage renal disease in males, despite the absence of clinical and biopsy findings associated with Alport syndrome. (PMID:20881942)
  • expression of collagen type IV alpha5 chain in the smooth muscle BM of the gastrointestinal tract is restricted to the esophagus in humans (PMID:20951201)
  • Identified mutations of the COL4A5 and COL4A3 gene in five Chinese Alport syndrome families. (PMID:21143337)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusCol4a5ENSMUSG00000031274
rattus_norvegicusCol4a5ENSRNOG00000018951

Paralogs (37): COL9A2 (ENSG00000049089), COL23A1 (ENSG00000050767), COL11A1 (ENSG00000060718), COL17A1 (ENSG00000065618), COL5A3 (ENSG00000080573), COL4A4 (ENSG00000081052), COL16A1 (ENSG00000084636), COL9A3 (ENSG00000092758), COL20A1 (ENSG00000101203), COL1A1 (ENSG00000108821), COL9A1 (ENSG00000112280), COL7A1 (ENSG00000114270), COL21A1 (ENSG00000124749), COL5A1 (ENSG00000130635), COL4A2 (ENSG00000134871), COL2A1 (ENSG00000139219), COL6A1 (ENSG00000142156), COL6A2 (ENSG00000142173), EDA (ENSG00000158813), COL26A1 (ENSG00000160963), COL1A2 (ENSG00000164692), COL3A1 (ENSG00000168542), COL4A3 (ENSG00000169031), COL22A1 (ENSG00000169436), COL24A1 (ENSG00000171502), COL18A1 (ENSG00000182871), EMID1 (ENSG00000186998), COL4A1 (ENSG00000187498), COL25A1 (ENSG00000188517), COL27A1 (ENSG00000196739), COL13A1 (ENSG00000197467), COL4A6 (ENSG00000197565), COL11A2 (ENSG00000204248), COL5A2 (ENSG00000204262), COL15A1 (ENSG00000204291), COLQ (ENSG00000206561), COL28A1 (ENSG00000215018)

Protein

Protein identifiers

Collagen alpha-5(IV) chainP29400 (reviewed: P29400)

All UniProt accessions (6): A0A2R8Y5W0, P29400, H0Y998, H0Y9H0, H0Y9R8, Q49AM6

UniProt curated annotations — full annotation on UniProt →

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.

Subunit / interactions. There are six type IV collagen isoforms, alpha 1(IV)-alpha 6(IV), each of which can form a triple helix structure with 2 other chains to generate type IV collagen network.

Subcellular location. Secreted. Extracellular space. Extracellular matrix. Basement membrane.

Tissue specificity. Isoform 2 is found in kidney.

Post-translational modifications. Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains. Type IV collagens contain numerous cysteine residues which are involved in inter- and intramolecular disulfide bonding. 12 of these, located in the NC1 domain, are conserved in all known type IV collagens. The trimeric structure of the NC1 domains is stabilized by covalent bonds between Lys and Met residues.

Disease relevance. Alport syndrome 1, X-linked (ATS1) [MIM:301050] A syndrome that is characterized by progressive glomerulonephritis, renal failure, sensorineural deafness, specific eye abnormalities (lenticonous and macular flecks), and glomerular basement membrane defects. The disorder shows considerable heterogeneity in that families differ in the age of end-stage renal disease and the occurrence of deafness. The disease is caused by variants affecting the gene represented in this entry. Deletions covering the N-terminal regions of COL4A5 and COL4A6, which are localized in a head-to-head manner, are found in the chromosome Xq22.3 centromeric deletion syndrome. This results in a phenotype with features of diffuse leiomyomatosis and Alport syndrome (DL-ATS).

Domain organisation. Alpha chains of type IV collagen have a non-collagenous domain (NC1) at their C-terminus, frequent interruptions of the G-X-Y repeats in the long central triple-helical domain (which may cause flexibility in the triple helix), and a short N-terminal triple-helical 7S domain.

Miscellaneous. Contains 2 extra G-X-X repeats into the triple-helix domain.

Similarity. Belongs to the type IV collagen family.

Isoforms (2)

UniProt IDNamesCanonical?
P29400-11yes
P29400-22

RefSeq proteins (2): NP_000486, NP_203699* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001442Collagen_IV_NCDomain
IPR008160CollagenRepeat
IPR016187CTDL_foldHomologous_superfamily
IPR036954Collagen_IV_NC_sfHomologous_superfamily
IPR050149Collagen_superfamilyFamily

Pfam: PF01391, PF01413

UniProt features (244 total): sequence variant 165, compositionally biased region 28, strand 20, disulfide bond 9, helix 7, sequence conflict 4, region of interest 3, cross-link 2, signal peptide 1, chain 1, domain 1, turn 1, glycosylation site 1, splice variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
6WKUX-RAY DIFFRACTION1.76
5NAZX-RAY DIFFRACTION1.85

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P29400-F149.040.15

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 1549, 1667

Disulfide bonds (9): 451, 481, 484, 1476–1567, 1509–1564, 1521–1527, 1586–1681, 1620–1678, 1632–1638

Glycosylation sites (1): 125

Function

Pathways and Gene Ontology

Reactome pathways

15 pathways

IDPathway
R-HSA-1442490Collagen degradation
R-HSA-1566977Fibronectin matrix formation
R-HSA-1650814Collagen biosynthesis and modifying enzymes
R-HSA-186797Signaling by PDGF
R-HSA-2022090Assembly of collagen fibrils and other multimeric structures
R-HSA-216083Integrin cell surface interactions
R-HSA-2214320Anchoring fibril formation
R-HSA-2243919Crosslinking of collagen fibrils
R-HSA-3000157Laminin interactions
R-HSA-3000171Non-integrin membrane-ECM interactions
R-HSA-3000178ECM proteoglycans
R-HSA-419037NCAM1 interactions
R-HSA-8948216Collagen chain trimerization
R-HSA-9010553Regulation of expression of SLITs and ROBOs
R-HSA-9638630Attachment of bacteria to epithelial cells

MSigDB gene sets: 364 (showing top): VALK_AML_WITH_FLT3_ITD, GOBP_NEUROMUSCULAR_JUNCTION_DEVELOPMENT, TGGTGCT_MIR29A_MIR29B_MIR29C, LEE_NEURAL_CREST_STEM_CELL_DN, MULLIGHAN_NPM1_SIGNATURE_3_UP, BENPORATH_ES_WITH_H3K27ME3, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN, GOBP_COLLAGEN_FIBRIL_ORGANIZATION, GOCC_COLLAGEN_TRIMER, GOZGIT_ESR1_TARGETS_DN, ASTON_MAJOR_DEPRESSIVE_DISORDER_DN, REACTOME_NCAM_SIGNALING_FOR_NEURITE_OUT_GROWTH, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, HNF1_Q6, AAAYRNCTG_UNKNOWN

GO Biological Process (3): neuromuscular junction development (GO:0007528), collagen fibril organization (GO:0030199), collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)

GO Molecular Function (3): extracellular matrix structural constituent conferring tensile strength (GO:0030020), extracellular matrix structural constituent (GO:0005201), protein binding (GO:0005515)

GO Cellular Component (7): extracellular region (GO:0005576), collagen type IV trimer (GO:0005587), endoplasmic reticulum lumen (GO:0005788), extracellular matrix (GO:0031012), neuromuscular junction (GO:0031594), collagen trimer (GO:0005581), basement membrane (GO:0005604)

Reactome top-level categories

Rollup of top-9 pathways:

CategoryPathways
Extracellular matrix organization5
Collagen formation2
Assembly of collagen fibrils and other multimeric structures2
Degradation of the extracellular matrix1
Signaling by Receptor Tyrosine Kinases1
NCAM signaling for neurite out-growth1
Collagen biosynthesis and modifying enzymes1
Signaling by ROBO receptors1
Biofilm formation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
extracellular matrix2
synapse organization1
extracellular matrix organization1
cell surface receptor protein tyrosine kinase signaling pathway1
collagen-activated signaling pathway1
extracellular matrix structural constituent1
structural molecule activity1
binding1
cellular anatomical structure1
network-forming collagen trimer1
chicken-wire-like collagen network1
endoplasmic reticulum1
intracellular organelle lumen1
external encapsulating structure1
synapse1
protein-containing complex1

Protein interactions and networks

STRING

1650 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
COL4A5BECN1Q14457944
COL4A5AMMECR1Q9Y4X0849
COL4A5ATG14Q6ZNE5811
COL4A5ACSL4O60488806
COL4A5IGBP1P78318796
COL4A5KCNE5Q9UJ90700
COL4A5NPHS1O60500652
COL4A5LAMA5O15230646
COL4A5COL1A1P02452641
COL4A5NID1P14543641
COL4A5COL3A1P02461639
COL4A5COL1A2P02464612
COL4A5CD151P48509577
COL4A5NPHS2Q9NP85577
COL4A5COL6A3P12111534

IntAct

26 interactions, top by confidence:

ABTypeScore
STRN3STRNpsi-mi:“MI:0914”(association)0.880
COLGALT2COL1A1psi-mi:“MI:0914”(association)0.530
COL4A5KLK6psi-mi:“MI:0570”(protein cleavage)0.440
COL4A5ANXA7psi-mi:“MI:0915”(physical association)0.370
COL4A5CDKN1Apsi-mi:“MI:0915”(physical association)0.370
COL4A5DAZAP2psi-mi:“MI:0915”(physical association)0.370
COL4A5NR1H2psi-mi:“MI:0915”(physical association)0.370
COL4A5SMN1psi-mi:“MI:0915”(physical association)0.370
TK1COL4A5psi-mi:“MI:0915”(physical association)0.370
CEP170P1PCYT1Apsi-mi:“MI:0914”(association)0.350
KIF21Bpsi-mi:“MI:0914”(association)0.350
Lgals3bpCSpsi-mi:“MI:0914”(association)0.350
DAP3MBNL1psi-mi:“MI:0914”(association)0.350
Washc1COX7A2psi-mi:“MI:0914”(association)0.350
VPS26BKIF1Bpsi-mi:“MI:0914”(association)0.350
EsrrbWASLpsi-mi:“MI:0914”(association)0.350
PDK1VWA8psi-mi:“MI:0914”(association)0.350
KNL1SPC24psi-mi:“MI:0914”(association)0.350
SGK3AIPpsi-mi:“MI:0914”(association)0.350
P4HA1POLRMTpsi-mi:“MI:0914”(association)0.350
PLOD1PLK4psi-mi:“MI:0914”(association)0.350
COL8A2P4HA2psi-mi:“MI:0914”(association)0.350
KLHL22TRAV18psi-mi:“MI:0914”(association)0.350
FMR1COL4A5psi-mi:“MI:0915”(physical association)0.000
RNF10COL4A5psi-mi:“MI:0915”(physical association)0.000

BioGRID (62): COL4A5 (Affinity Capture-MS), COL4A5 (Affinity Capture-MS), COL4A5 (Affinity Capture-MS), COL4A5 (Affinity Capture-MS), COL4A5 (Affinity Capture-MS), COL4A5 (Affinity Capture-MS), COL4A5 (Affinity Capture-MS), COL4A5 (Affinity Capture-MS), COL4A5 (Affinity Capture-MS), COL4A5 (Affinity Capture-MS), COL4A5 (Affinity Capture-MS), COL4A5 (Affinity Capture-MS), COL4A5 (Affinity Capture-MS), COL4A5 (Affinity Capture-RNA), COL4A5 (Two-hybrid)

ESM2 similar proteins: A0MSJ1, A8WR59, B8V7R6, C0HLN2, O76368, O88207, P02462, P02463, P08120, P08122, P08125, P08572, P12106, P12107, P12108, P13942, P20849, P20850, P20908, P20909, P23206, P25067, P25318, P25940, P29400, P32017, P53420, P55787, Q01955, Q03692, Q05306, Q05722, Q07643, Q0VF58, Q14031, Q14050, Q14055, Q14993, Q28083, Q28247

Diamond homologs: P02462, P02463, P08120, P08122, P08572, P17139, P17140, P27393, P29400, P53420, P55787, Q01955, Q14031, Q28084, Q28247, Q29442, Q7SIB2, Q7SIB3, Q9QZR9, Q9QZS0

SIGNOR signaling

2 interactions.

AEffectBMechanism
COL4A5up-regulatesECM_synthesis
COL4A5“up-regulates activity”“A1/b1 integrin”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 40 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Collagen biosynthesis and modifying enzymes637.9×2e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

3508 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic625
Likely pathogenic658
Uncertain significance599
Likely benign876
Benign130

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
10453NG_011977.2:g.(239831_242576)_(252772_257824)delPathogenic
10455COL4A5, 10-15-KB INS, 40-KB DELPathogenic
10456NG_011977.2:g.(246966_251107)_?delPathogenic
10457NG_011977.2:g.?_(146097_162513)delPathogenic
10458NM_033380.3(COL4A5):c.3428G>A (p.Gly1143Asp)Pathogenic
10462NM_033380.3(COL4A5):c.1561G>T (p.Gly521Cys)Pathogenic
10463NM_033380.3(COL4A5):c.974G>A (p.Gly325Glu)Pathogenic
10465NM_033380.3(COL4A5):c.161G>A (p.Gly54Asp)Pathogenic
1053313NM_033380.3(COL4A5):c.4632G>C (p.Trp1544Cys)Pathogenic
1066187NM_033380.3(COL4A5):c.4015+2T>CPathogenic
1066898NM_033380.3(COL4A5):c.3827G>A (p.Gly1276Asp)Pathogenic
1069146NM_033380.3(COL4A5):c.3373G>C (p.Gly1125Arg)Pathogenic
1069768NM_033380.3(COL4A5):c.2786del (p.Gly929fs)Pathogenic
1069897NM_033380.3(COL4A5):c.136G>T (p.Glu46Ter)Pathogenic
1070099NM_033380.3(COL4A5):c.2262del (p.Leu755fs)Pathogenic
1070103NM_033380.3(COL4A5):c.5023G>T (p.Gly1675Ter)Pathogenic
1070190NM_033380.3(COL4A5):c.3491G>A (p.Gly1164Asp)Pathogenic
1070191NM_033380.3(COL4A5):c.3922C>T (p.Gln1308Ter)Pathogenic
1070192NM_033380.3(COL4A5):c.4462C>T (p.Gln1488Ter)Pathogenic
1070457NM_033380.3(COL4A5):c.994C>T (p.Gln332Ter)Pathogenic
1071493NM_033380.3(COL4A5):c.2042-1G>APathogenic
1072212NM_033380.3(COL4A5):c.781-2A>GPathogenic
1072610NM_033380.3(COL4A5):c.834+1G>CPathogenic
1072617NM_033380.3(COL4A5):c.3932del (p.Pro1311fs)Pathogenic
1072947NM_033380.3(COL4A5):c.4079G>A (p.Gly1360Asp)Pathogenic
1073029NM_033380.3(COL4A5):c.67_81+1delPathogenic
1073034NM_033380.3(COL4A5):c.1940G>T (p.Gly647Val)Pathogenic
1073265NM_033380.3(COL4A5):c.4706+2T>CPathogenic
1073728NM_033380.3(COL4A5):c.1033-1_1033insAAATTCCCAGPathogenic
1073886NM_033380.3(COL4A5):c.1633G>A (p.Gly545Ser)Pathogenic

SpliceAI

6714 predictions. Top by Δscore:

VariantEffectΔscore
X:108440202:CTGCG:Cdonor_gain1.0000
X:108440204:GCG:Gdonor_gain1.0000
X:108440204:GCGGT:Gdonor_loss1.0000
X:108440206:GGTAA:Gdonor_loss1.0000
X:108440207:G:GAdonor_loss1.0000
X:108440207:G:GGdonor_gain1.0000
X:108440208:TAAG:Tdonor_loss1.0000
X:108559058:TTGCA:Tacceptor_loss1.0000
X:108559059:TGCAG:Tacceptor_loss1.0000
X:108559060:GCAGG:Gacceptor_loss1.0000
X:108559062:AG:Aacceptor_gain1.0000
X:108559063:G:Aacceptor_loss1.0000
X:108559063:GG:Gacceptor_gain1.0000
X:108559063:GGGA:Gacceptor_gain1.0000
X:108559154:G:GAdonor_loss1.0000
X:108563927:G:GGdonor_gain1.0000
X:108568623:TTATA:Tacceptor_loss1.0000
X:108568625:ATAG:Aacceptor_gain1.0000
X:108568626:TA:Tacceptor_loss1.0000
X:108568627:A:AGacceptor_gain1.0000
X:108568627:A:ATacceptor_loss1.0000
X:108568627:AG:Aacceptor_gain1.0000
X:108568628:G:GGacceptor_gain1.0000
X:108568628:GG:Gacceptor_gain1.0000
X:108568672:CT:Cdonor_gain1.0000
X:108568672:CTGT:Cdonor_loss1.0000
X:108568673:TGTA:Tdonor_loss1.0000
X:108568674:G:Adonor_loss1.0000
X:108568674:G:GGdonor_gain1.0000
X:108568675:T:Adonor_loss1.0000

AlphaMissense

10607 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:108692851:G:CW1538C1.000
X:108692851:G:TW1538C1.000
X:108694900:G:CW1594C1.000
X:108694900:G:TW1594C1.000
X:108696352:T:AC1678S1.000
X:108696353:G:CC1678S1.000
X:108696354:T:GC1678W1.000
X:108692759:A:CS1508R0.999
X:108692761:C:AS1508R0.999
X:108692761:C:GS1508R0.999
X:108692816:T:AC1527S0.999
X:108692817:G:CC1527S0.999
X:108692849:T:AW1538R0.999
X:108692849:T:CW1538R0.999
X:108692853:T:CL1539P0.999
X:108692921:A:CS1562R0.999
X:108692923:T:AS1562R0.999
X:108692923:T:GS1562R0.999
X:108694810:T:GC1564W0.999
X:108694817:T:AC1567S0.999
X:108694818:G:CC1567S0.999
X:108694874:T:AC1586S0.999
X:108694874:T:CC1586R0.999
X:108694875:G:CC1586S0.999
X:108694888:G:CW1590C0.999
X:108694888:G:TW1590C0.999
X:108694905:G:AG1596D0.999
X:108694911:C:TS1598F0.999
X:108695321:T:AC1620S0.999
X:108695321:T:CC1620R0.999

dbSNP variants (sampled 300 via entrez): RS1000000615 (X:108483806 G>A), RS1000058920 (X:108632566 G>A,C,T), RS1000063262 (X:108552613 A>G), RS1000064411 (X:108620696 C>G,T), RS1000087575 (X:108619427 C>G), RS1000089031 (X:108468972 C>G), RS1000109709 (X:108554797 G>A), RS1000136763 (X:108543584 G>A,T), RS1000151638 (X:108493198 A>T), RS1000170968 (X:108587819 G>A,C), RS1000172362 (X:108664401 A>G), RS1000180264 (X:108511849 A>G), RS1000212766 (X:108512425 T>G), RS1000213158 (X:108519501 A>G), RS1000244684 (X:108459558 A>G)

Disease associations

OMIM: gene MIM:303630 | disease phenotypes: MIM:301050, MIM:104200, MIM:606232, MIM:125000

GenCC curated gene-disease

DiseaseClassificationInheritance
Alport syndromeDefinitiveX-linked
X-linked Alport syndromeDefinitiveX-linked

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
Alport syndromeDefinitiveXL

Mondo (17): X-linked Alport syndrome (MONDO:0010520), Alport syndrome (MONDO:0018965), kidney disorder (MONDO:0005240), nonsyndromic genetic hearing loss (MONDO:0019497), autosomal dominant Alport syndrome (MONDO:0007086), Phelan-McDermid syndrome (MONDO:0011652), focal segmental glomerulosclerosis (MONDO:0100313), hypertensive disorder (MONDO:0005044), glomerular disorder (MONDO:0019722), atypical hemolytic-uremic syndrome (MONDO:0016244), nephrotic syndrome (MONDO:0005377), hearing loss disorder (MONDO:0005365), proteinuria (MONDO:0003634), deafness, unilateral (MONDO:0007426), chronic kidney disease (MONDO:0005300)

Orphanet (10): Alport syndrome (Orphanet:63), X-linked Alport syndrome (Orphanet:88917), Rare non-syndromic genetic deafness (Orphanet:87884), Autosomal dominant Alport syndrome (Orphanet:88918), Phelan-McDermid syndrome (Orphanet:48652), Glomerular disease (Orphanet:93548), Atypical hemolytic uremic syndrome (Orphanet:2134), Rare genetic deafness (Orphanet:96210), OBSOLETE: Isolated macular dystrophy (Orphanet:519302), Rare disease with thoracic aortic aneurysm and aortic dissection (Orphanet:285014)

HPO phenotypes

56 total (30 of 56 shown, HPO-id order):

HPOTerm
HP:0000083Renal insufficiency
HP:0000093Proteinuria
HP:0000100Nephrotic syndrome
HP:0000112Nephropathy
HP:0000123Nephritis
HP:0000407Sensorineural hearing impairment
HP:0000478Abnormality of the eye
HP:0000491Keratitis
HP:0000518Cataract
HP:0000519Developmental cataract
HP:0000545Myopia
HP:0000790Hematuria
HP:0000822Hypertension
HP:0000829Hypoparathyroidism
HP:0001142Lenticonus
HP:0001417X-linked inheritance
HP:0001423X-linked dominant inheritance
HP:0001508Failure to thrive
HP:0001824Weight loss
HP:0001873Thrombocytopenia
HP:0002013Vomiting
HP:0002015Dysphagia
HP:0002020Gastroesophageal reflux
HP:0002031Abnormal esophagus morphology
HP:0002094Dyspnea
HP:0002205Recurrent respiratory infections
HP:0002571Achalasia
HP:0002907Microscopic hematuria
HP:0003262Anti-smooth muscle antibody positivity
HP:0003676Progressive

GWAS associations

0 associations (top):

MeSH disease descriptors (10)

DescriptorNameTree numbers
D065766Atypical Hemolytic Uremic SyndromeC12.050.351.968.419.936.463.500; C12.200.777.419.936.463.500; C12.950.419.936.463.500; C15.378.050.141.610.500; C15.378.140.855.925.500.500; C15.378.243.937.925.500.500
D005923Glomerulosclerosis, Focal SegmentalC12.050.351.968.419.570.363.640; C12.200.777.419.570.363.660; C12.950.419.570.363.640
D034381Hearing LossC09.218.458.341; C10.597.751.418.341; C23.888.592.763.393.341
D006973HypertensionC14.907.489
D007674Kidney DiseasesC12.050.351.968.419; C12.200.777.419; C12.950.419
D007676Kidney Failure, ChronicC12.050.351.968.419.780.750.500; C12.200.777.419.780.750.500; C12.950.419.780.750.500; C23.550.291.500.906.500
D009404Nephrotic SyndromeC12.050.351.968.419.630.643; C12.200.777.419.630.643; C12.950.419.630.643
D011507ProteinuriaC12.050.351.968.934.734; C12.200.777.934.734; C12.950.934.734; C23.888.942.750
C580334Nonsyndromic Deafness (supp.)
C536801Telomeric 22q13 Monosomy Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2364188 (PROTEIN COMPLEX GROUP)

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

44 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance3
Benzo(a)pyreneaffects methylation2
Nickeldecreases expression2
Tobacco Smoke Pollutiondecreases expression2
Cyclosporinedecreases expression2
aristolochic acid Idecreases expression1
selenomethylselenocysteineincreases expression1
pirinixic acidaffects binding, decreases expression, increases activity1
bisphenol Aaffects methylation1
tris(2-butoxyethyl) phosphateaffects expression1
sulforaphanedecreases expression, increases methylation1
butyraldehydedecreases expression1
benzo(e)pyreneaffects methylation1
potassium chromate(VI)decreases expression1
aflatoxin B2affects methylation1
methacrylaldehydeaffects cotreatment, increases expression1
perfluorooctane sulfonic aciddecreases expression1
Sunitinibdecreases expression1
Zoledronic Aciddecreases expression1
Acetaminophendecreases expression1
Acroleinaffects cotreatment, increases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Calcitriolincreases expression1
Cisplatinaffects response to substance1
Curcumindecreases expression1
Doxorubicinincreases expression1
Methapyrileneaffects methylation1
Ozoneaffects cotreatment, increases expression1
Parabensaffects cotreatment, increases expression1

Cellosaurus cell lines

22 cell lines: 14 induced pluripotent stem cell, 4 cancer cell line, 2 conditionally immortalized cell line, 1 embryonic stem cell, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_A1WMNCKDi001-AInduced pluripotent stem cellMale
CVCL_A1XTWMUi015-AInduced pluripotent stem cellMale
CVCL_A4VCGWCMCi002-AInduced pluripotent stem cellMale
CVCL_A7GESDUBMSi007-AInduced pluripotent stem cellMale
CVCL_A7GFSDUBMSi008-AInduced pluripotent stem cellMale
CVCL_A7NCWAe009-A-58Embryonic stem cellFemale
CVCL_B1NYAbcam HeLa COL4A5 KOCancer cell lineFemale
CVCL_C3G4ASP2-UPICConditionally immortalized cell lineFemale
CVCL_C3G5ASP3-UPICConditionally immortalized cell lineMale
CVCL_D9C9Ubigene HEK293 COL4A5 KOTransformed cell lineFemale

Clinical trials (associated diseases)

299 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT05655728PHASE4UNKNOWNTreatment With Metformin in Chinese Children With Alport Syndrome
NCT06499948PHASE4ACTIVE_NOT_RECRUITINGAlbuminuria Lowering Effect of Dapagliflozin, Spironolactone and Their Combination in Adult Patients With Alport Syndrome (COMBINE-ALPORT)
NCT00067990PHASE4COMPLETEDAngiotensin II Blockade for Chronic Allograft Nephropathy
NCT00117078PHASE4COMPLETEDAranesp® Monthly Preference Study - 2
NCT00117130PHASE4COMPLETEDStudy to Evaluate Effectiveness of Aranesp®
NCT00132431PHASE4COMPLETEDSTART: Sensipar Treatment Algorithm to Reach K/DOQI Targets in Chronic Kidney Disease Subjects With Secondary Hyperparathyroidism
NCT00140985PHASE4COMPLETEDAntiproteinuric Efficacy of Losartan Potassium in Patients With Non-Diabetic Proteinuric Renal Diseases (0954-213)
NCT00246129PHASE4COMPLETEDCamTac Trial:Campath-Tacrolimus vs IL2R MoAb/Tacrolimus/MMF in Renal Transplantation
NCT00275535PHASE4COMPLETEDThe Comparison of Tacrolimus and Sirolimus Immunosuppression Based Drug Regimens in Kidney Transplant Recipients
NCT00282217PHASE4COMPLETEDStudy Evaluating Sirolimus in the Treatment of Kidney Transplant
NCT00289614PHASE4COMPLETEDPatients With Renal Impairment and Diabetes Undergoing Computed Tomography (CT)
NCT00290069PHASE4UNKNOWNRenal Function Optimization With Mycophenolate Mofetil (MMF) Immunosuppressor Regimes (ALHAMBRA)
NCT00338468PHASE4TERMINATEDA Study to Assess Disability in Anemic Elderly Patients With Kidney Disease Receiving PROCRIT (Epoetin Alfa)
NCT00368901PHASE4COMPLETEDSTAAR-2 Clinical Study
NCT00369733PHASE4COMPLETEDSTAAR-3 Clinical Study
NCT00369772PHASE4COMPLETEDSTAAR-1 Clinical Study
NCT00379899PHASE4COMPLETEDADVANCE: Study to Evaluate Cinacalcet Plus Low Dose Vitamin D on Vascular Calcification in Subjects With Chronic Kidney Disease Receiving Hemodialysis
NCT00443508PHASE4UNKNOWNReduction or Discontinuation of CNI’s With Conversion to Everolimus-Based Immunosuppresion
NCT00452478PHASE4TERMINATEDConversion From Standard Phosphate Binder Therapy to Fosrenol® (Lanthanum Carbonate) in Chronic Kidney Disease Stage 5
NCT00492518PHASE4COMPLETEDAcetylcysteine, Theophylline, and a Combination of Both in the Prophylaxis of Contrast-Induced Nephropathy
NCT00505102PHASE4UNKNOWNSafe Renal Function In Long Term Heart Transplanted Patients
NCT00526331PHASE4COMPLETEDEvaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00688480PHASE4COMPLETEDDo Xanthine Oxidase Inhibitors Reduce Both Left Ventricular Hypertrophy and Endothelial Dysfunction in Cardiovascular Patients With Renal Dysfunction?
NCT00863707PHASE4COMPLETEDA Study of the Safety and Tolerance of Regadenoson in Subjects With Renal Impairment
NCT01101698PHASE4UNKNOWNVitamin K2 and Vessel Calcification in Chronic Kidney Disease Patients
NCT01150201PHASE4COMPLETEDAliskiren Combined With Losartan in Proteinuric, Non-diabetic Chronic Kidney Disease
NCT01155141PHASE4COMPLETEDIdiopathic Focal Segmental Glomerulosclerosis (FSGS) and Treatment With ACTH
NCT01228279PHASE4COMPLETEDSympathetic Activity in Patients With End-stage Renal Disease on Peritoneal Dialysis
NCT01334333PHASE4COMPLETEDComparison of Medication Adherence Between Once and Twice Daily Tacrolimus in Stable Renal Transplant Recipients
NCT01437943PHASE4TERMINATEDEffect of Short Term Aliskiren Treatment in Kidney Transplant Patients
NCT01545479PHASE4COMPLETEDIncreased Renal Oxygenation and Angiotensin Converting Enzyme Inhibition
NCT01614431PHASE4COMPLETEDN Acetyl Cysteine for Cystinosis Patients
NCT01631149PHASE4COMPLETEDEffect of Deep BLock on Intraoperative Surgical Conditions
NCT01722513PHASE4UNKNOWNEfficacy and Safety of Alprostadil Prevent Contrast Induced Nephropathy
NCT01985360PHASE4COMPLETEDISCHEMIA-Chronic Kidney Disease Trial
NCT02311010PHASE4UNKNOWNPractical Use of Advagraf de Novo After Kidney Transplantation According to Recipient Genetic Polymorphism
NCT02413073PHASE4COMPLETEDWhole Body Vibration in Kidney Disease
NCT02444013PHASE4UNKNOWNFolic Acid for Prevention of Contrast Induced Nephropathy
NCT02663713PHASE4COMPLETEDA Randomized, Pharmacodynamic Comparison of Low Dose Ticagrelor to Clopidogrel in Patients With Prior Myocardial Infarction
NCT02707809PHASE4COMPLETEDEffects of Dexmedetomidine on Microcirculation of Kidney Transplant Recipient