COL4A4

gene
On this page

Also known as CA44

Summary

COL4A4 (collagen type IV alpha 4 chain, HGNC:2206) is a protein-coding gene on chromosome 2q36.3, encoding Collagen alpha-4(IV) chain (P53420). 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.

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 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. Mutations in this gene are associated with type II autosomal recessive Alport syndrome (hereditary glomerulonephropathy) and with familial benign hematuria (thin basement membrane disease). Two transcripts, differing only in their transcription start sites, have been identified for this gene and, as is common for collagen genes, multiple polyadenylation sites are found in the 3’ UTR.

Source: NCBI Gene 1286 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Alport syndrome (Definitive, ClinGen) — +3 more curated relationships
  • GWAS associations: 13
  • Clinical variants (ClinVar): 3,774 total — 257 pathogenic, 517 likely-pathogenic
  • Phenotypes (HPO): 30
  • Druggable target: yes
  • MANE Select transcript: NM_000092

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2206
Approved symbolCOL4A4
Namecollagen type IV alpha 4 chain
Location2q36.3
Locus typegene with protein product
StatusApproved
AliasesCA44
Ensembl geneENSG00000081052
Ensembl biotypeprotein_coding
OMIM120131
Entrez1286

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000396625, ENST00000643379, ENST00000682098, ENST00000682248, ENST00000682548, ENST00000683508, ENST00000684257, ENST00000684524

RefSeq mRNA: 1 — MANE Select: NM_000092 NM_000092

CCDS: CCDS42828

Canonical transcript exons

ENST00000396625 — 48 exons

ExonStartEnd
ENSE00001071074227059405227059623
ENSE00001124594227022048227022173
ENSE00001124612227002714227007588
ENSE00001135763227012181227012297
ENSE00001135841227008018227008304
ENSE00001135926227094125227094289
ENSE00001135929227098694227098798
ENSE00001305015227057439227057600
ENSE00001311859227010313227010501
ENSE00001313262227032148227032276
ENSE00001315992227027902227028009
ENSE00001321359227031945227032055
ENSE00001326349227055945227056115
ENSE00001328587227030443227030598
ENSE00001331272227077894227078077
ENSE00001377510227050977227051158
ENSE00001385501227042148227042255
ENSE00001387144227054594227054737
ENSE00001387733227043077227043184
ENSE00001400869227033410227033481
ENSE00001403233227121014227121148
ENSE00001404531227052305227052412
ENSE00001414504227060136227060243
ENSE00001422171227080443227080549
ENSE00001431479227088653227088816
ENSE00001434411227118645227118761
ENSE00001461298227047475227047549
ENSE00001461299227050068227050131
ENSE00001461300227062530227062598
ENSE00001461302227082115227082187
ENSE00001461305227089868227089957
ENSE00001461306227099620227099689
ENSE00001461307227101504227101557
ENSE00001461308227101865227101909
ENSE00001461309227102789227102848
ENSE00001461310227103144227103197
ENSE00001461311227103972227104052
ENSE00001461312227108581227108622
ENSE00001461313227108833227108868
ENSE00001461314227109224227109286
ENSE00001461316227111678227111713
ENSE00001461317227114628227114696
ENSE00001461319227119895227119939
ENSE00001461320227140161227140238
ENSE00001461321227144516227144558
ENSE00001461322227147413227147584
ENSE00001831933227164007227164205
ENSE00002511083227025802227025810

Expression profiles

Bgee: expression breadth ubiquitous, 187 present calls, max score 87.51.

FANTOM5 (CAGE): breadth broad, TPM avg 2.8577 / max 134.8880, expressed in 516 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
343381.8190428
343390.7027294
343410.2233104
343370.090034
343400.02277

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
renal medullaUBERON:000036287.51gold quality
metanephros cortexUBERON:001053386.40gold quality
pigmented layer of retinaUBERON:000178281.91gold quality
cauda epididymisUBERON:000436081.77gold quality
right coronary arteryUBERON:000162580.26gold quality
coronary arteryUBERON:000162179.80gold quality
left coronary arteryUBERON:000162679.70gold quality
caput epididymisUBERON:000435879.48gold quality
visceral pleuraUBERON:000240179.45gold quality
ascending aortaUBERON:000149679.36gold quality
thoracic aortaUBERON:000151579.34gold quality
kidneyUBERON:000211379.20gold quality
right atrium auricular regionUBERON:000663179.15gold quality
adult mammalian kidneyUBERON:000008278.95gold quality
left lobe of thyroid glandUBERON:000112078.94gold quality
descending thoracic aortaUBERON:000234578.92gold quality
pituitary glandUBERON:000000778.86gold quality
cortex of kidneyUBERON:000122578.85gold quality
thyroid glandUBERON:000204678.77gold quality
cardiac atriumUBERON:000208178.70gold quality
biceps brachiiUBERON:000150778.08silver quality
mucosa of stomachUBERON:000119977.81gold quality
metanephrosUBERON:000008177.73gold quality
right lobe of thyroid glandUBERON:000111977.55gold quality
seminal vesicleUBERON:000099877.49gold quality
adenohypophysisUBERON:000219677.38gold quality
adrenal cortexUBERON:000123576.69gold quality
left adrenal glandUBERON:000123476.68gold quality
right adrenal gland cortexUBERON:003582776.53gold quality
left adrenal gland cortexUBERON:003582576.29gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.69

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): LMX1B

miRNA regulators (miRDB)

170 targeting COL4A4, 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-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-3646100.0073.565283
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-5692A100.0074.406850
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-366299.9973.825684
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-428299.9975.366408
HSA-MIR-548N99.9871.944170
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-314899.9775.066478
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-6793-5P99.9765.95758
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-590-3P99.9674.346478
HSA-MIR-767-5P99.9570.85993
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163

Literature-anchored findings (GeneRIF, showing 40)

  • COL4A4 mutation: from familial hematuria to autosomal-dominant or recessive Alport syndrome. (PMID:12028435)
  • No collagen alpha3(IV) or alpha4(IV) in lens capsules of 54-day human embryos, while collagen alpha3(IV) and alpha4(IV) were detected in adult humans. (PMID:12225806)
  • Six of seven (86%) individuals with autosomal recessive Alport syndrome who had 3 novel COL4A4 mutations in the compound heterozygous or homozygous forms developed renal failure in adulthood, as well as hearing loss and ocular abnormalities. (PMID:12325029)
  • Two stop codons (R1377X and 2788/91delG) and a glycine substitution (G960R) resulted in hematuria. S969X mutation. (PMID:12631110)
  • COL4A4 gene is associted with Alport’s syndrome in which males and females are severely affected. (PMID:12768082)
  • In kidney, when expressed onto Col4a3(-/-) background, human alpha3(IV) chain restored expression of and co-assembled with mouse alpha4 and alpha5(IV) chains at sites where human alpha3(IV) was expressed. All three chains required for network assembly. (PMID:14507670)
  • Mutations in COL4A3 and COL4A4 genes produce alteration to glomerular basement membrane(GBM). Phenotype may range from thinned GBM ro GBM thickening, lamellation and splitting. Review. (PMID:15280517)
  • 40% of families with TBMN have hematuria that segregates with the corresponding locus ( COL4A3/COL4A4 ), and identical mutations occur in both conditions. (PMID:15880327)
  • novel mutations identified during routine molecular diagnostics for Alport syndrome (PMID:15954103)
  • Persistent familial hematuria in children often occurs at the COLA4A locus for thin membrane nephropathy. (PMID:16235097)
  • The molecular analysis demonstrated that the probands were genetic compounds for two different mutations in the COL4A4 gene pinpointing to the correct diagnosis of autosomal recessive ATS. (PMID:16338941)
  • Possibly mutated in Alport syndrome (review) (PMID:16895672)
  • A clinical evaluation of probands and their relatives of the five families carrying mutations in either the COL4A3 or the COL4A4 gene was carried out to underline the natural history of the autosomal recessive ATS. (PMID:16970251)
  • Polymorphisms in thus genes is particularly important to enable diagnostic laboratories to distinguish mutations from uncommon normal variants. (PMID:17216251)
  • 16 novel mutations identified in COL4A3, COL4A4 & COL4A5 genes in Slovenian families with Alport syndrome & benign familial hematuria (BFH); 4 heterozygous mutations in COL4A4 (2 splice site, 1 in-frame deletion & 1 missense) identified in BFH (PMID:17396119)
  • COL4A3/COL4A4 mutations predispose some patients to FSGS and chronic renal failure. (PMID:17942953)
  • our data show many patients with collagen IV mutations may develop focal & segmental glomerulosclerosis, on top of thin basement membrane nephropathy & microscopic hematuria, which often progresses to chronic renal failure or end-stage renal disease (PMID:18661361)
  • analysis of noncollagenous sites encoding specific interactions and quaternary assembly of alpha 3 alpha 4 alpha 5(IV) collagen (PMID:18930919)
  • On the basis of linked-function analysis, we demonstrated that collagen binding domain of MMP2 tuned the cleavage of collagen IV by MMP9, presumably by inducing a ligand-linked structural change on the type IV collagen. (PMID:19109975)
  • It is difficult to make a differential diagnosis with a benign familial haematuria due to heterozygous mutations of COL4A4 and COL4A3, especially in young patients, and with a X-linked form of Alport syndrome in families where only females are affected. (PMID:19129241)
  • association of heterozygous COL4A3/COL4A4 mutations with familial microscopic haematuria, thin basement membrane nephropathy and the late development of familial proteinuria, CRF, and ESRD, due to FSGS (PMID:19357112)
  • Novel variants in the COL4A4 gene in Korean patients with thin basement membrane nephropathy. (PMID:19675380)
  • This is the first mutational screening of COL4A3 and COL4A4 genes in keratoconus patients to establish the status of these genes and compare them to a control population. (PMID:20029656)
  • The absence of pathogenic mutations in COL4A4 gene in our large number of unrelated keratoconus patients indicates that other genetic factors are involved in the development of this disorder (PMID:20664914)
  • Our findings suggest that variants in the COL4A4 gene may contribute to the development of lattice degeneration of the retina. (PMID:22723992)
  • The expression of collagen type IV and its alpha chains (alpha1-6) was investigated in different endothelial cell culture systems in vitro qualitatively and quantitatively. (PMID:23551189)
  • 9 mutation in COL4A4 associated with autosomal dominant Alport syndrome. (PMID:24033287)
  • Twenty mutation pairs (50%) affected COL4A3 and 20 pairs affected COL4A4 in Alport syndrome. (PMID:24052634)
  • COL4A4 related nephropathy caused by novel mutation in a large consanguineous Saudi family. (PMID:24398087)
  • We could hypothesize that mutations in COL4A3 and COL4A4 genes are not involved in keratoconus risk in Greek population. (PMID:25083577)
  • We found that 7 out of 70 families (10%) with familial focal segmental glomerulosclerosis in our cohort have rare variants in COL4A3 and COL4A4. (PMID:25229338)
  • New COL4A4 mutations among Portuguese patients with collagen IV-related nephropathies were identified in 8 unrelated families. (PMID:25307543)
  • COL4A4 missense variants [c.G2636A (p.Gly879Glu) and c.C4715T (p.Pro1572Leu)] in family 1. COL4A4 c.G2636A, a novel variant, co-segregated with renal disease among maternal relatives. (PMID:25381091)
  • we identified seven families with associated mutations in COL4A3 and COL4A4 genes and four families with associated mutations in COL4A4 and COL4A5. We did not find kindreds with digenic inheritance attributable to mutations in COL4A3 and COL4A5 (PMID:25575550)
  • COL4A4 rs2229813 AA and GA+AA genotypes as well as the A allele play roles as risk factors for developing Keratoconus in our population. (PMID:25651396)
  • Tetrastatin, the NC1 alpha 4 collagen IV domain level increases in pulmonary tumor extracts. (PMID:25935259)
  • we describe a novel splicing mutation in COL4A4 that results in TBMN. This analysis increases our understanding of TBMN phenotype-genotype correlations, which should facilitate more accurate diagnosis and prenatal diagnosis of TBMN. (PMID:26833262)
  • These findings indicate that the heterozygous mutations in COL4A3 or COL4A4 may cause ESRD on their own, although secondary factors, such as environmental factors or unknown genetic changes, might also contribute to the phenotype of kidney disease in patients with ADAS. (PMID:27281700)
  • This finding broadens mutation spectrum of the COL4A4 gene and extends the phenotypic spectrum of collagen IV nephropathies. (PMID:27469977)
  • Alport syndrome is the result of mutations in any of three type IV collagen genes, COL4A3, COL4A4, or COL4A5. Because the three collagen chains form heterotrimers, there is an absence of all three proteins in the basement membranes where they are expressed. (Review) (PMID:27576055)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriocol4a4ENSDARG00000002831
mus_musculusCol4a4ENSMUSG00000067158
rattus_norvegicusCol4a4ENSRNOG00000014851
drosophila_melanogastervkgFBGN0016075
caenorhabditis_elegansWBGENE00001263

Paralogs (37): COL9A2 (ENSG00000049089), COL23A1 (ENSG00000050767), COL11A1 (ENSG00000060718), COL17A1 (ENSG00000065618), COL5A3 (ENSG00000080573), 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), COL4A5 (ENSG00000188153), COL25A1 (ENSG00000188517), COL27A1 (ENSG00000196739), COL13A1 (ENSG00000197467), COL4A6 (ENSG00000197565), COL11A2 (ENSG00000204248), COL5A2 (ENSG00000204262), COL15A1 (ENSG00000204291), COLQ (ENSG00000206561), COL28A1 (ENSG00000215018)

Protein

Protein identifiers

Collagen alpha-4(IV) chainP53420 (reviewed: P53420)

All UniProt accessions (5): P53420, A0A2R8Y548, A0A804HI71, A0A804HI86, A0A804HLF6

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. The alpha 3(IV) chain forms a triple helical protomer with alpha 4(IV) and alpha 5(IV); this triple helical structure dimerizes through NC1-NC1 domain interactions such that the alpha 3(IV), alpha 4(IV) and alpha 5(IV) chains of one protomer connect with the alpha 5(IV), alpha 4(IV) and alpha 3(IV) chains of the opposite protomer, respectively. Associates with LAMB2 at the neuromuscular junction and in GBM.

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

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). 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 levels of expression of alpha 3 and alpha 4 type IV collagens in kidney, but PubMed:7523402 reports that in kidney levels of alpha 3 type IV collagen are significantly lower than those of alpha 4 type IV collagen. Highest levels of expression of alpha 4 type IV collagen are detected in kidney, calvaria, neuroretina and cardiac muscle. Lower levels of expression are observed in brain, lung and thymus, and no expression is detected in choroid plexus, liver, adrenal, pancreas, ileum or skin.

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 2, autosomal recessive (ATS2) [MIM:203780] A syndrome characterized by progressive glomerulonephritis, glomerular basement membrane defects, renal failure, sensorineural deafness and specific eye abnormalities (lenticonous and macular flecks). 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. Hematuria, benign familial, 1 (BFH1) [MIM:141200] An autosomal dominant condition characterized by non-progressive isolated microscopic hematuria that does not result in renal failure. It is characterized pathologically by thinning of the glomerular basement membrane. The disease is caused by variants affecting the gene represented in this entry.

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.

Similarity. Belongs to the type IV collagen family.

RefSeq proteins (1): NP_000083* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001442Collagen_IV_NCDomain
IPR008160CollagenRepeat
IPR016187CTDL_foldHomologous_superfamily
IPR036954Collagen_IV_NC_sfHomologous_superfamily
IPR050149Collagen_superfamilyFamily

Pfam: PF01391, PF01413

UniProt features (97 total): compositionally biased region 21, sequence variant 21, strand 18, short sequence motif 8, region of interest 7, disulfide bond 6, helix 6, glycosylation site 2, sequence conflict 2, turn 2, signal peptide 1, chain 1, domain 1, site 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
6WKUX-RAY DIFFRACTION1.76
5NB1X-RAY DIFFRACTION2.82

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P53420-F149.030.08

Functional residue map

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

Catalytic / active sites (1): 1206–1207 (cleavage; by collagenase)

Disulfide bonds (6): 1480–1569, 1513–1566, 1525–1531, 1588–1686, 1622–1683, 1634–1641

Glycosylation sites (2): 142, 669

Function

Pathways and Gene Ontology

Reactome pathways

14 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-9638630Attachment of bacteria to epithelial cells

MSigDB gene sets: 251 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, TGGTGCT_MIR29A_MIR29B_MIR29C, MYOGENIN_Q6, GOBP_COLLAGEN_FIBRIL_ORGANIZATION, MODULE_571, FISCHER_G1_S_CELL_CYCLE, GOCC_COLLAGEN_TRIMER, GCANCTGNY_MYOD_Q6, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, REACTOME_NCAM_SIGNALING_FOR_NEURITE_OUT_GROWTH, RIZKI_TUMOR_INVASIVENESS_3D_DN, LHX3_01, TTGGGAG_MIR150, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, CEBP_Q2

GO Biological Process (2): collagen fibril organization (GO:0030199), glomerular basement membrane development (GO:0032836)

GO Molecular Function (3): extracellular matrix structural constituent (GO:0005201), extracellular matrix structural constituent conferring tensile strength (GO:0030020), molecular adaptor activity (GO:0060090)

GO Cellular Component (6): extracellular region (GO:0005576), collagen type IV trimer (GO:0005587), basement membrane (GO:0005604), endoplasmic reticulum lumen (GO:0005788), extracellular matrix (GO:0031012), collagen trimer (GO:0005581)

Reactome top-level categories

Rollup of top-8 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
Biofilm formation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
extracellular matrix organization2
extracellular matrix2
glomerulus development1
anatomical structure development1
structural molecule activity1
extracellular matrix structural constituent1
molecular_function1
binding1
cellular anatomical structure1
network-forming collagen trimer1
chicken-wire-like collagen network1
endoplasmic reticulum1
intracellular organelle lumen1
external encapsulating structure1
protein-containing complex1

Protein interactions and networks

STRING

1224 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
COL4A4IGBP1P78318858
COL4A4NPHS1O60500768
COL4A4NPHS2Q9NP85763
COL4A4LMX1BO60663704
COL4A4MYH9P35579664
COL4A4CD151P48509604
COL4A4NID1P14543588
COL4A4COL4A3Q01955535
COL4A4RHBDD1Q8TEB9526
COL4A4VSX1Q9NZR4507
COL4A4INF2Q27J81476
COL4A4LMX1AQ8TE12470
COL4A4NKX2-2O95096470
COL4A4COL4A5P29400469
COL4A4LHX1P48742444

IntAct

10 interactions, top by confidence:

ABTypeScore
KLK6COL4A4psi-mi:“MI:0570”(protein cleavage)0.440
COL4A4HNRNPMpsi-mi:“MI:0915”(physical association)0.400
MecomESYT2psi-mi:“MI:0914”(association)0.350
FGD6COL4A4psi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
LAIR2PLOD3psi-mi:“MI:0914”(association)0.350
LAIR2AGRNpsi-mi:“MI:0914”(association)0.350
PLOD1PLOD2psi-mi:“MI:0914”(association)0.350

BioGRID (9): COL4A4 (Protein-RNA), COL4A4 (Proximity Label-MS), COL4A4 (Affinity Capture-MS), COL4A4 (Affinity Capture-MS), COL4A4 (Affinity Capture-MS), COL4A4 (Proximity Label-MS), COL4A4 (Affinity Capture-MS), ACAA2 (Cross-Linking-MS (XL-MS)), COL4A4 (Affinity Capture-MS)

ESM2 similar proteins: A0A060WQA3, A0MSJ1, A5PN28, A6NHN0, A8WR59, C0HLN2, C7DZK3, O35167, O35348, O76368, O88207, P08122, P08572, P12106, P12107, P12108, P13942, P20849, P20850, P20908, P20909, P25067, P25940, P53420, P83371, P98085, Q01955, Q03637, Q05722, Q07092, Q07643, Q0VF58, Q14031, Q14055, Q14993, Q17RW2, Q28083, Q30D77, Q32S24, Q4ZJM7

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

SIGNOR signaling

4 interactions.

AEffectBMechanism
COL4A4“up-regulates activity”“A2/b1 integrin”binding
COL4A4up-regulatesECM_synthesis
PXDN“up-regulates quantity by stabilization”COL4A4“catalytic activity”
COL4A4“up-regulates activity”“A1/b1 integrin”binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

3774 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic257
Likely pathogenic517
Uncertain significance966
Likely benign1369
Benign183

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1036012NM_000092.5(COL4A4):c.870G>A (p.Lys290=)Pathogenic
1068523NM_000092.5(COL4A4):c.118G>T (p.Gly40Ter)Pathogenic
1069400NM_000092.5(COL4A4):c.3319_3358del (p.Leu1107fs)Pathogenic
1070032NM_000092.5(COL4A4):c.1768G>T (p.Gly590Ter)Pathogenic
1070585NM_000092.5(COL4A4):c.4200dup (p.Gly1401fs)Pathogenic
1070939NM_000092.5(COL4A4):c.2219_2220del (p.Pro740fs)Pathogenic
1070978NM_000092.5(COL4A4):c.2906C>A (p.Ser969Ter)Pathogenic
1071074NM_000092.5(COL4A4):c.1696+1delPathogenic
1073049NM_000092.5(COL4A4):c.4962_4969dup (p.Ala1657delinsGlyTer)Pathogenic
1073470NM_000092.5(COL4A4):c.4444del (p.Leu1482fs)Pathogenic
1073781NM_000092.5(COL4A4):c.4449_4450dup (p.Met1484fs)Pathogenic
1073782NM_000092.5(COL4A4):c.2842G>T (p.Gly948Ter)Pathogenic
1073919NM_000092.5(COL4A4):c.156C>A (p.Cys52Ter)Pathogenic
1075869NM_000092.5(COL4A4):c.1862del (p.Pro621fs)Pathogenic
1076015NM_000092.5(COL4A4):c.794_804del (p.Asp264_Phe265insTer)Pathogenic
1284919NM_000092.5(COL4A4):c.2833G>T (p.Gly945Ter)Pathogenic
1298378NM_000092.5(COL4A4):c.2860+2T>GPathogenic
1342006NM_000092.5(COL4A4):c.4720C>T (p.Gln1574Ter)Pathogenic
1344700NM_000092.5(COL4A4):c.2383G>A (p.Gly795Arg)Pathogenic
1344701NM_000092.5(COL4A4):c.4503dup (p.Ala1502fs)Pathogenic
1344702NM_000092.5(COL4A4):c.1697-1G>CPathogenic
1350377NM_000092.5(COL4A4):c.4787G>A (p.Trp1596Ter)Pathogenic
1356715NM_000092.5(COL4A4):c.4849_4850del (p.Met1617fs)Pathogenic
1359803NM_000092.5(COL4A4):c.2531_2537del (p.Tyr844fs)Pathogenic
1366631NC_000002.11:g.(?227872031)(227985874_?)delPathogenic
1374552NM_000092.5(COL4A4):c.4473_4474dup (p.Ser1492fs)Pathogenic
1382507NM_000092.5(COL4A4):c.2196del (p.Phe732fs)Pathogenic
1385943NM_000092.5(COL4A4):c.1143_1144del (p.Asp383fs)Pathogenic
1386713NM_000092.5(COL4A4):c.1247del (p.Pro416fs)Pathogenic
1399009NM_000092.5(COL4A4):c.105T>G (p.Tyr35Ter)Pathogenic

SpliceAI

6201 predictions. Top by Δscore:

VariantEffectΔscore
2:227010273:A:ACdonor_gain1.0000
2:227010274:C:CCdonor_gain1.0000
2:227025861:G:Cacceptor_gain1.0000
2:227025880:T:Cacceptor_gain1.0000
2:227027896:GCTCA:Gdonor_loss1.0000
2:227027897:CTCAC:Cdonor_loss1.0000
2:227027898:TCACC:Tdonor_loss1.0000
2:227027899:CACCC:Cdonor_loss1.0000
2:227027900:A:ACdonor_gain1.0000
2:227027900:AC:Adonor_gain1.0000
2:227027900:ACCCG:Adonor_loss1.0000
2:227027901:C:Adonor_loss1.0000
2:227027901:C:CCdonor_gain1.0000
2:227027901:CC:Cdonor_gain1.0000
2:227027927:C:CAdonor_gain1.0000
2:227028009:CCT:Cacceptor_gain1.0000
2:227028010:C:CCacceptor_gain1.0000
2:227028011:T:Cacceptor_gain1.0000
2:227028011:T:TCacceptor_gain1.0000
2:227030438:CATA:Cdonor_loss1.0000
2:227030441:A:ACdonor_gain1.0000
2:227030441:A:Cdonor_loss1.0000
2:227030442:C:CCdonor_gain1.0000
2:227030442:C:CTdonor_loss1.0000
2:227030442:CCTTT:Cdonor_gain1.0000
2:227030468:T:TAdonor_gain1.0000
2:227030594:TGCTC:Tacceptor_gain1.0000
2:227030596:CTC:Cacceptor_gain1.0000
2:227030598:CCT:Cacceptor_loss1.0000
2:227030599:C:CCacceptor_gain1.0000

AlphaMissense

10580 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:227010359:A:CS1492R0.998
2:227010359:A:TS1492R0.998
2:227010361:T:GS1492R0.998
2:227007535:G:CS1621R0.997
2:227007535:G:TS1621R0.997
2:227007537:T:GS1621R0.997
2:227008135:G:CS1564R0.997
2:227008135:G:TS1564R0.997
2:227008137:T:GS1564R0.997
2:227007350:C:GC1683S0.996
2:227007351:A:TC1683S0.996
2:227007532:G:CC1622W0.996
2:227007497:C:GC1634S0.995
2:227007498:A:TC1634S0.995
2:227007445:C:AW1651C0.994
2:227007445:C:GW1651C0.994
2:227007533:C:GC1622S0.994
2:227007533:C:TC1622Y0.994
2:227007534:A:TC1622S0.994
2:227008130:C:GC1566S0.994
2:227008131:A:TC1566S0.994
2:227008201:C:AW1542C0.994
2:227008201:C:GW1542C0.994
2:227008288:G:CC1513W0.994
2:227007349:G:CC1683W0.993
2:227007351:A:GC1683R0.993
2:227007443:A:GL1652P0.993
2:227007447:A:GW1651R0.993
2:227007447:A:TW1651R0.993
2:227007534:A:GC1622R0.993

dbSNP variants (sampled 300 via entrez): RS1000026260 (2:227065328 G>C), RS1000029305 (2:227038752 A>G), RS1000038316 (2:227071486 G>A,C), RS1000058225 (2:227155486 G>C), RS1000067030 (2:226981305 T>G), RS1000088961 (2:227154972 T>C), RS1000093117 (2:227056206 T>C), RS1000094354 (2:227112850 T>G), RS1000106924 (2:227030004 T>C), RS1000109668 (2:227117803 A>C,G), RS1000121696 (2:226988117 A>T), RS1000123870 (2:227126177 A>G), RS1000137686 (2:227142600 CA>C,CAA), RS1000139419 (2:227030413 A>G,T), RS1000176849 (2:227055925 A>G)

Disease associations

OMIM: gene MIM:120131 | disease phenotypes: MIM:141200, MIM:203780, MIM:301050, MIM:104200, MIM:156000, MIM:173900, MIM:614483, MIM:160700, MIM:276900, MIM:615432

GenCC curated gene-disease

DiseaseClassificationInheritance
autosomal recessive Alport syndromeDefinitiveAutosomal recessive
Alport syndromeDefinitiveSemidominant
hematuria, benign familial, 1StrongAutosomal dominant
autosomal dominant Alport syndromeSupportiveAutosomal dominant

ClinGen Gene-Disease Validity (1)

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

DiseaseClassificationInheritance
Alport syndromeDefinitiveSD

Mondo (24): hematuria, benign familial, 1 (MONDO:0007709), autosomal recessive Alport syndrome (MONDO:0008762), Alport syndrome (MONDO:0018965), hematuria, benign familial (MONDO:0957317), autosomal dominant Alport syndrome (MONDO:0007086), Meniere disease (MONDO:0007972), hearing loss disorder (MONDO:0005365), kidney disorder (MONDO:0005240), focal segmental glomerulosclerosis (MONDO:0100313), polycystic kidney disease (MONDO:0020642), X-linked Alport syndrome (MONDO:0010520), brain small vessel disease 2A, autosomal dominant (MONDO:0013773), myopia (MONDO:0001384), proteinuria (MONDO:0003634), hypertensive disorder (MONDO:0005044)

Orphanet (10): Alport syndrome (Orphanet:63), Autosomal recessive Alport syndrome (Orphanet:88919), Autosomal dominant Alport syndrome (Orphanet:88918), X-linked Alport syndrome (Orphanet:88917), Porencephaly (Orphanet:2940), Familial porencephaly (Orphanet:99810), Usher syndrome (Orphanet:886), Atypical hemolytic uremic syndrome (Orphanet:2134), NON RARE IN EUROPE: Benign familial hematuria (Orphanet:97562), NON RARE IN EUROPE: Menière disease (Orphanet:45360)

HPO phenotypes

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

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000083Renal insufficiency
HP:0000093Proteinuria
HP:0000100Nephrotic syndrome
HP:0000123Nephritis
HP:0000365Hearing impairment
HP:0000407Sensorineural hearing impairment
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:0001873Thrombocytopenia
HP:0002907Microscopic hematuria
HP:0003676Progressive
HP:0003680Nonprogressive
HP:0003774Stage 5 chronic kidney disease
HP:0004722Thickened glomerular basement membrane
HP:0006756Diffuse leiomyomatosis
HP:0008064Ichthyosis
HP:0011501Anterior lenticonus
HP:0012577Thin glomerular basement membrane
HP:0030034Glomerular basement membrane lamellation
HP:0200020Corneal erosion
HP:6001026Reduced epidermal collagen IV alpha 5 chain staining

GWAS associations

13 associations (top):

StudyTraitp-value
GCST001538_19Immune reponse to smallpox (secreted IFN-alpha)3.000000e-09
GCST002783_270Body mass index5.000000e-06
GCST002783_625Body mass index6.000000e-06
GCST004208_2Body mass index4.000000e-08
GCST005196_217Coronary artery disease7.000000e-06
GCST006463_6Urinary albumin excretion (no hypertensive medication)2.000000e-08
GCST006586_22Urinary albumin excretion5.000000e-09
GCST006976_39Macular thickness2.000000e-16
GCST007267_82Systolic blood pressure5.000000e-10
GCST008362_206Birth weight2.000000e-12
GCST008790_14Urinary albumin-to-creatinine ratio9.000000e-11
GCST008794_27Urinary albumin-to-creatinine ratio2.000000e-11
GCST009640_39Urinary albumin-to-creatinine ratio3.000000e-11

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0004645response to vaccine
EFO:0004873cytokine measurement
EFO:0004340body mass index
EFO:0004285albuminuria
EFO:0006335systolic blood pressure
EFO:0004344birth weight
EFO:0007778urinary albumin to creatinine ratio

MeSH disease descriptors (15)

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
D005921GlomerulonephritisC12.050.351.968.419.570.363; C12.200.777.419.570.363; C12.950.419.570.363
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
D008575Meniere DiseaseC09.218.568.217.500
D009216MyopiaC11.744.636
D009404Nephrotic SyndromeC12.050.351.968.419.630.643; C12.200.777.419.630.643; C12.950.419.630.643
D007690Polycystic Kidney DiseasesC12.050.351.968.419.403.875; C12.200.777.419.403.875; C12.950.419.403.875; C16.131.077.717; C16.320.184.625
D011507ProteinuriaC12.050.351.968.934.734; C12.200.777.934.734; C12.950.934.734; C23.888.942.750
D013921ThrombocytopeniaC15.378.140.855; C15.378.243.937
D052245Usher SyndromesC09.218.458.341.186.500.500; C09.218.458.341.887.886; C10.597.751.418.341.186.500.500; C10.597.751.418.341.887.886; C10.597.751.941.162.625.500; C11.768.585.658.500.813; C11.966.075.375.500; C16.131.077.299.500; C16.320.290.684.500; C23.888.592.763.393.341.887.886
C562476Hematuria, Benign Familial (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL2364188 (PROTEIN COMPLEX GROUP), CHEMBL3988505 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Vorinostataffects cotreatment, increases expression2
Doxorubicindecreases expression, increases expression2
triphenyl phosphateaffects expression1
bisphenol Adecreases methylation1
trichostatin Aincreases expression1
sodium arsenitedecreases expression1
butyraldehydedecreases expression1
evodiaminedecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, increases expression1
Irinotecandecreases expression1
Resveratroldecreases expression, affects cotreatment1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Chelating Agentsaffects binding, increases expression1
Copperaffects binding, increases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Methotrexateincreases expression1
Nickelincreases expression1
Phenobarbitaldecreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Smokedecreases expression1
Tetrachlorodibenzodioxinincreases expression1
Tobacco Smoke Pollutiondecreases expression1
Triclosanincreases expression1
Valproic Acidincreases expression1
Vitalliumincreases expression1
8-Bromo Cyclic Adenosine Monophosphatedecreases expression1

Cellosaurus cell lines

7 cell lines: 5 induced pluripotent stem cell, 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_B1NXAbcam HeLa COL4A4 KOCancer cell lineFemale
CVCL_B5IVNCKDi005-AInduced pluripotent stem cellMale
CVCL_E0AMUbigene HeLa COL4A4 KOCancer cell lineFemale
CVCL_IX43HPSI0416i-sevr_1Induced pluripotent stem cellFemale
CVCL_IX44HPSI0416i-sevr_2Induced pluripotent stem cellFemale
CVCL_LF15HPSI0516i-yist_1Induced pluripotent stem cellMale
CVCL_LF16HPSI0516i-yist_3Induced pluripotent stem cellMale

Clinical trials (associated diseases)

300 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)
NCT01574313PHASE4COMPLETEDEffect of Stellate Ganglion Block on Meniere’s Disease
NCT02529475PHASE4TERMINATEDEvaluation of Inner Ear and Brain Structures With Contrast-enhanced MRI in Healthy Subjects (HYDROPS)
NCT04815187PHASE4ACTIVE_NOT_RECRUITINGRepurposed Use of Allergic Rhinitis and Allergic Asthma Drug to Reduce Vertigo and Hearing Loss in Meniere’s Disease
NCT00205881PHASE4COMPLETEDBilateral Benefit in Adult Users of the HiRes 90K Bionic Ear System
NCT00331539PHASE4UNKNOWNRelationship Between Auto NRT and Behavioural T & C Levels With the Nucleus Freedom Cochlear Implant
NCT00424307PHASE4UNKNOWNBilateral Cochlear Implant Benefit in Young Children
NCT00765635PHASE4COMPLETEDChlorobutanol, Potassium Carbonate, and Irrigation in Cerumen Removal
NCT03321006PHASE4COMPLETEDTreating Hearing Loss to Improve Mood and Cognition in Older Adults
NCT03749447PHASE3TERMINATEDAn Extended Access Program for Bardoxolone Methyl in Patients With CKD (EAGLE)
NCT03664674PHASE3COMPLETEDPhase 3 Study of OTO-104 in Subjects With Unilateral Meniere’s Disease
NCT04677972PHASE3COMPLETEDSPI-1005 for the Treatment of Meniere’s Disease
NCT05851508PHASE3RECRUITINGThe Effecttiveness of Intratympanic Methylprednisolon Injections Compared to Placebo in the Treatment of Vertigo Attacks in Meniere’s Disease
NCT01499901PHASE3WITHDRAWNComparison of the Bilateral Sequential and Simultaneous Cochlear Implantation in the Deaf Children
NCT02561091PHASE3COMPLETEDAM-111 in the Treatment of Acute Inner Ear Hearing Loss
NCT03331627PHASE3COMPLETEDSafety and Efficacy of STR001-IT and STR001-ER in Patients With SSHL
NCT05532657PHASE3ACTIVE_NOT_RECRUITINGACHIEVE Brain Health Follow-Up Study
NCT07523581PHASE2NOT_YET_RECRUITINGEXACT Study: A Blinded Study in Patients With Alport Syndrome to Evaluate Exaluren Efficacy and Safety
NCT00309257PHASE2COMPLETEDEffects of an Intensified Treatment With ACE-I,ATA II and Statins in Alport Syndrome
NCT02855268PHASE2TERMINATEDStudy of Lademirsen (SAR339375) in Patients With Alport Syndrome
NCT04573920PHASE2ACTIVE_NOT_RECRUITINGAtrasentan in Patients With Proteinuric Glomerular Diseases
NCT05003986PHASE2RECRUITINGStudy of Sparsentan Treatment in Pediatrics With Proteinuric Glomerular Diseases
NCT05267262PHASE2COMPLETEDStudy to Evaluate R3R01 in Patients With Alport Syndrome and Patients With Focal Segmental Glomerulosclerosis
NCT05448755PHASE2COMPLETEDA Study of ELX-02 in Patients With Alport Syndrome
NCT06425055PHASE2COMPLETEDVonafexor ALPort Syndrome Efficacy & Safety TRIAl-1 (ALPESTRIA-1)
NCT07211685PHASE2RECRUITINGBAY3401016; Biomarker Study Alport
NCT05420350PHASE2UNKNOWNLamotrigine and Bupropion for Meniere’s Disease
NCT06544434PHASE2RECRUITINGLaser Acupuncture for Meniere Disease
NCT00013455PHASE2COMPLETEDQuantifying Auditory Perceptual Learning Following Hearing Aid Fitting
NCT00323427PHASE2COMPLETEDClinical Trial of the Living Well With Hearing Loss Workshop
NCT00552786PHASE2COMPLETEDAntioxidation Medication for Noise-induced Hearing Loss
NCT00802425PHASE2COMPLETEDEfficacy of AM-111 in Patients With Acute Sensorineural Hearing Loss
NCT01139281PHASE2COMPLETEDThe Protective Effect of Ginkgo Biloba Extract on Cisplatin-induced Ototoxicity in Humans
NCT01451853PHASE2UNKNOWNSPI-1005 for Prevention and Treatment of Chemotherapy Induced Hearing Loss
NCT01588925PHASE2COMPLETEDHearing Preservation Using Dexamethasone and Hyaluronic Acid for Cochlear Implantation
NCT01773278PHASE2RECRUITINGCholesterol and Antioxidant Treatment in Patients With Smith-Lemli-Opitz Syndrome (SLOS)
NCT02832128PHASE2COMPLETEDEvaluating Possible Improvement in Speech and Hearing Tests After 28 Days of Dosing of the Study Drug AUT00063 Compared to Placebo (QuicKfire)
NCT04915183PHASE2RECRUITINGAtorvastatin to Reduce Cisplatin-Induced Hearing Loss Among Individuals With Head and Neck Cancer
NCT05258773PHASE2COMPLETEDEvaluation of the Presence of SENS-401 in the Perilymph