Free for academic non-profit institutions. Other users need a Commercial license

Aliases for COL4A6 Gene

Aliases for COL4A6 Gene

  • Collagen, Type IV, Alpha 6 2 3
  • CXDELq22.3 3 6
  • DELXq22.3 3 6
  • DFNX6 3 6
  • Collagen Of Basement Membrane, Alpha-6 3
  • DJ889N15.4 (Collagen Alpha 6(IV)) 3
  • Collagen IV, Alpha-6 Polypeptide 3
  • Collagen Alpha-6(IV) Chain 3
  • EC 63

External Ids for COL4A6 Gene

Previous GeneCards Identifiers for COL4A6 Gene

  • GC0XM102806
  • GC0XM104474
  • GC0XM105431
  • GC0XM106170
  • GC0XM107204
  • GC0XM107285
  • GC0XM107386
  • GC0XM097021

Summaries for COL4A6 Gene

Entrez Gene Summary for COL4A6 Gene

  • This gene encodes one of the six subunits of type IV collagen, the major structural component 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, alpha 5 type IV collagen, so that the gene pair shares a common promoter. Deletions in the alpha 5 gene that extend into the alpha 6 gene result in diffuse leiomyomatosis accompanying the X-linked Alport syndrome caused by the deletion in the alpha 5 gene. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2013]

GeneCards Summary for COL4A6 Gene

COL4A6 (Collagen, Type IV, Alpha 6) is a Protein Coding gene. Diseases associated with COL4A6 include deafness, x-linked 6 and x-linked non-syndromic sensorineural deafness type dfn. Among its related pathways are PI3K-Akt signaling pathway and Pathways in cancer. GO annotations related to this gene include extracellular matrix structural constituent. An important paralog of this gene is COL3A1.

UniProtKB/Swiss-Prot for COL4A6 Gene

  • 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

Gene Wiki entry for COL4A6 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL4A6 Gene

Genomics for COL4A6 Gene

Regulatory Elements for COL4A6 Gene

Genomic Location for COL4A6 Gene

108,155,607 bp from pter
108,439,497 bp from pter
283,891 bases
Minus strand

Genomic View for COL4A6 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for COL4A6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL4A6 Gene

Proteins for COL4A6 Gene

  • Protein details for COL4A6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Collagen alpha-6(IV) chain
    Protein Accession:
    Secondary Accessions:
    • Q12823
    • Q14053
    • Q5JYH6
    • Q5JYH8
    • Q9NQM5
    • Q9NTX3
    • Q9UJ76
    • Q9UMG6
    • Q9Y4L4

    Protein attributes for COL4A6 Gene

    1691 amino acids
    Molecular mass:
    163807 Da
    Quaternary structure:
    • 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

    Alternative splice isoforms for COL4A6 Gene


neXtProt entry for COL4A6 Gene

Proteomics data for COL4A6 Gene at MOPED

Selected DME Specific Peptides for COL4A6 Gene

Post-translational modifications for COL4A6 Gene

  • Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains
  • The trimeric structure of the NC1 domains is stabilized by covalent bonds between Lys and Met residues.
  • 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
  • Glycosylation at Asn127
  • Modification sites at PhosphoSitePlus

Other Protein References for COL4A6 Gene

Domains for COL4A6 Gene

Gene Families for COL4A6 Gene


Graphical View of Domain Structure for InterPro Entry



  • Q14031
  • 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
  • Contains 1 collagen IV NC1 (C-terminal non-collagenous) domain.
  • Belongs to the type IV collagen family.
genes like me logo Genes that share domains with COL4A6: view

Function for COL4A6 Gene

Molecular function for COL4A6 Gene

GENATLAS Biochemistry: collagen type IV,alpha 6,basement membrane,expressed in kidney renal tubules,not located in glomerular BM,also expressed in esophagus and lung and in the dermoepidermal junction during fetal skin development
UniProtKB/Swiss-Prot 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

Enzyme Numbers (IUBMB) for COL4A6 Gene

Gene Ontology (GO) - Molecular Function for COL4A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005198 structural molecule activity --
GO:0005201 extracellular matrix structural constituent IEA --
genes like me logo Genes that share ontologies with COL4A6: view

Phenotypes for COL4A6 Gene

MGI mutant phenotypes for COL4A6:
inferred from 1 alleles
genes like me logo Genes that share phenotypes with COL4A6: view

Animal Models for COL4A6 Gene

MGI Knock Outs for COL4A6:

Animal Model Products

CRISPR Products

miRNA for COL4A6 Gene

miRTarBase miRNAs that target COL4A6

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for COL4A6

In Situ Assay Products

Flow Cytometry Products

No data available for Transcription Factor Targeting and HOMER Transcription for COL4A6 Gene

Localization for COL4A6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL4A6 Gene

Secreted, extracellular space, extracellular matrix, basement membrane.

Subcellular locations from

Jensen Localization Image for COL4A6 Gene COMPARTMENTS Subcellular localization image for COL4A6 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
plasma membrane 2
cytosol 1
lysosome 1
mitochondrion 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for COL4A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005581 collagen trimer --
GO:0005587 collagen type IV trimer NAS 8125972
GO:0005604 basement membrane --
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL4A6: view

Pathways for COL4A6 Gene

genes like me logo Genes that share pathways with COL4A6: view

Gene Ontology (GO) - Biological Process for COL4A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0022617 extracellular matrix disassembly TAS --
GO:0030198 extracellular matrix organization TAS --
GO:0030574 collagen catabolic process TAS --
GO:0071230 cellular response to amino acid stimulus --
genes like me logo Genes that share ontologies with COL4A6: view

Transcripts for COL4A6 Gene

Unigene Clusters for COL4A6 Gene

Collagen, type IV, alpha 6:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for COL4A6

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for COL4A6
  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL4A6 Gene

No ASD Table

Relevant External Links for COL4A6 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for COL4A6 Gene

mRNA expression in normal human tissues for COL4A6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL4A6 Gene

This gene is overexpressed in Esophagus - Gastroesophageal Junction (17.6) and Esophagus - Muscularis (14.4).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for COL4A6 Gene

SOURCE GeneReport for Unigene cluster for COL4A6 Gene Hs.145586

genes like me logo Genes that share expressions with COL4A6: view

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for COL4A6 Gene

Orthologs for COL4A6 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL4A6 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia COL4A6 35
  • 99.04 (n)
  • 98.74 (a)
COL4A6 36
  • 99 (a)
(Bos Taurus)
Mammalia COL4A6 35
  • 86.25 (n)
  • 84.92 (a)
COL4A6 36
  • 85 (a)
(Canis familiaris)
Mammalia COL4A6 35
  • 86.09 (n)
  • 84.71 (a)
COL4A6 36
  • 84 (a)
(Mus musculus)
Mammalia Col4a6 35
  • 81.99 (n)
  • 80.19 (a)
Col4a6 16
Col4a6 36
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia COL4A6 36
  • 58 (a)
(Rattus norvegicus)
Mammalia Col4a6 35
  • 80.99 (n)
  • 77.7 (a)
(Gallus gallus)
Aves COL4A6 35
  • 65.69 (n)
  • 65.31 (a)
COL4A6 36
  • 64 (a)
(Anolis carolinensis)
Reptilia COL4A6 36
  • 63 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.3640 35
tropical clawed frog
(Silurana tropicalis)
Amphibia col4a6 35
  • 62.23 (n)
  • 60.87 (a)
(Danio rerio)
Actinopterygii col4a6 35
  • 57.07 (n)
  • 54.62 (a)
col4a6 36
  • 54 (a)
fruit fly
(Drosophila melanogaster)
Insecta vkg 37
  • 38 (a)
Cg25C 37
  • 39 (a)
(Caenorhabditis elegans)
Secernentea emb-9 37
  • 40 (a)
let-2 37
  • 71 (a)
Species with no ortholog for COL4A6:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for COL4A6 Gene

Gene Tree for COL4A6 (if available)
Gene Tree for COL4A6 (if available)

Paralogs for COL4A6 Gene

genes like me logo Genes that share paralogs with COL4A6: view

Variants for COL4A6 Gene

Sequence variations from dbSNP and Humsavar for COL4A6 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs714707 -- 108,412,429(-) GCACA(A/G)TAAGT intron-variant
rs719116 -- 108,254,805(-) CCATT(A/C)CACAC intron-variant
rs744425 -- 108,173,461(+) CTTCA(A/G)gtgtg intron-variant
rs748280 -- 108,230,217(+) accac(C/T)atatc intron-variant
rs750756 -- 108,173,973(-) AGCCT(C/G)GCACA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for COL4A6 Gene

Variant ID Type Subtype PubMed ID
esv9265 CNV Gain 19470904

Relevant External Links for COL4A6 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL4A6 Gene

Disorders for COL4A6 Gene

(1) OMIM Diseases for COL4A6 Gene (303631)


  • Note=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).
  • Deafness, X-linked, 6 (DFNX6) [MIM:300914]: A non-syndromic form of sensorineural hearing loss with prelingual onset. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269 PubMed:23714752}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for COL4A6 Gene

(7) Novoseek inferred disease relationships for COL4A6 Gene

Disease -log(P) Hits PubMed IDs
leiomyomatosis 94.6 15
alport syndrome, x-linked 94.5 3
alports syndrome 93.7 17
leiomyoma 45.6 1
renal failure 25.8 2

Relevant External Links for COL4A6

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with COL4A6: view

Publications for COL4A6 Gene

  1. Deletion of the paired alpha 5(IV) and alpha 6(IV) collagen genes in inherited smooth muscle tumors. (PMID: 8356449) Zhou J. … Reeders S.T. (Science 1993) 2 3 4 23
  2. Structure of the human type IV collagen COL4A6 gene, which is mutated in Alport syndrome-associated leiomyomatosis. (PMID: 8661006) Zhang X. … Tryggvason K. (Genomics 1996) 3 4 23
  3. Isolation and structure of the COL4A6 gene encoding the human alpha 6(IV) collagen chain and comparison with other type IV collagen genes. (PMID: 7592929) Oohashi T. … Ninomiya Y. (J. Biol. Chem. 1995) 3 23
  4. The expression of type IV collagen alpha6 chain is related to the prognosis in patients with esophageal squamous cell carcinoma. (PMID: 17955302) Baba Y. … Baba H. (Ann. Surg. Oncol. 2008) 3 23
  5. Type IV collagen alpha6 chain-derived noncollagenous domain 1 (alpha6(IV)NC1) inhibits angiogenesis and tumor growth. (PMID: 18074349) Mundel T.M. … Kalluri R. (Int. J. Cancer 2008) 3 23

Products for COL4A6 Gene

Sources for COL4A6 Gene

Back to Top