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

COL4A6 Gene(Protein Coding)

Collagen Type IV Alpha 6 Chain

GCID:
GC0XM108155
GIFtS:
60
Genes Participants
UDN Logo

Aliases for COL4A6 Gene

Aliases for COL4A6 Gene

  • Collagen Type IV Alpha 6 Chain 2 3 5
  • Collagen, Type IV, Alpha 6 2 3
  • 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
  • CXDELq22.3 3
  • EC 2.7.7.8 61
  • DELXq22.3 3
  • DFNX6 3

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 Chain) 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 Collagen chain trimerization and Phospholipase-C Pathway. GO annotations related to this gene include structural molecule activity and extracellular matrix structural constituent. An important paralog of this gene is COL4A2.

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 CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL4A6 Gene

Genomics for COL4A6 Gene

Products:

  1. Regulatory Element

Regulatory Elements for COL4A6 Gene

Enhancers for COL4A6 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XG108395 1.6 FANTOM5 Ensembl ENCODE dbSUPER 14.8 +41.0 40956 6.9 TBP NFIB ZBTB21 JUN TEAD4 MAX BRCA1 ZNF664 GATA3 GATA2 COL4A5 COL4A6 ENSG00000189372 GC0XP108425
GH0XG108353 0.5 ENCODE 11.9 +86.0 85968 0.7 GATA3 CTBP1 DPF2 ENSG00000189372 COL4A5 COL4A6 GC0XP108251
GH0XG108307 1.2 FANTOM5 ENCODE 2.5 +130.6 130634 3.1 ELF3 TBP FOXA2 ZSCAN4 FEZF1 BRCA1 RAD21 RFX5 YY1 GATA2 PSMD10 COL4A5 COL4A6 GC0XP108251 ENSG00000189372
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around COL4A6 on UCSC Golden Path with GeneCards custom track

Promoters for COL4A6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000247910 -504 4399 PKNOX1 ATF1 CREB3L1 SIN3A FEZF1 ZNF2 ZNF766 ZNF263 SP3 ZHX2

Transcription factor binding sites by QIAGEN in the COL4A6 gene promoter:

Genomic Location for COL4A6 Gene

Chromosome:
X
Start:
108,155,607 bp from pter
End:
108,439,497 bp from pter
Size:
283,891 bases
Orientation:
Minus strand

Genomic View for COL4A6 Gene

Genes around COL4A6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL4A6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL4A6 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for COL4A6 Gene

Proteins for COL4A6 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    Q14031-CO4A6_HUMAN
    Recommended name:
    Collagen alpha-6(IV) chain
    Protein Accession:
    Q14031
    Secondary Accessions:
    • Q12823
    • Q14053
    • Q5JYH6
    • Q5JYH8
    • Q9NQM5
    • Q9NTX3
    • Q9UJ76
    • Q9UMG6
    • Q9Y4L4

    Protein attributes for COL4A6 Gene

    Size:
    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

    UniProtKB/Swiss-Prot:

neXtProt entry for COL4A6 Gene

Protein Expression for COL4A6 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for COL4A6 Gene

Q14031:
  • LPGKDGL
  • LPGRDGL

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

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for COL4A6 Gene

Gene Families for COL4A6 Gene

HGNC:

Protein Domains for COL4A6 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for COL4A6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q14031

UniProtKB/Swiss-Prot:

CO4A6_HUMAN :
  • 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.
  • Belongs to the type IV collagen family.
Domain:
  • 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.
Family:
  • Belongs to the type IV collagen family.
genes like me logo Genes that share domains with COL4A6: view

Function for COL4A6 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

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: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
GenomeRNAi human phenotypes for COL4A6:
genes like me logo Genes that share phenotypes with COL4A6: view

Human Phenotype Ontology for COL4A6 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

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

Flow Cytometry Products

No data available for Transcription Factor Targets 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

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COL4A6 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
plasma membrane 2
mitochondrion 1
peroxisome 1
nucleus 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for COL4A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA,TAS --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005581 collagen trimer IEA --
GO:0005587 collagen type IV trimer IEA,NAS 8125972
GO:0005604 basement membrane IEA --
genes like me logo Genes that share ontologies with COL4A6: view

Pathways & Interactions 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:0030198 extracellular matrix organization TAS,IEA --
GO:0030574 collagen catabolic process TAS --
GO:0038063 collagen-activated tyrosine kinase receptor signaling pathway IEA --
GO:0071230 cellular response to amino acid stimulus IEA --
genes like me logo Genes that share ontologies with COL4A6: view

No data available for SIGNOR curated interactions for COL4A6 Gene

Drugs & Compounds for COL4A6 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for COL4A6 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for COL4A6 Gene

(9) REFSEQ mRNAs :
(13) Additional mRNA sequences :
(55) Selected AceView cDNA sequences:
(10) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for COL4A6 Gene

Collagen, type IV, alpha 6:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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
COL4A6
ECgene alternative splicing isoforms for
COL4A6

Expression for COL4A6 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COL4A6 Gene

mRNA expression in normal human tissues for COL4A6 Gene
mRNA expression by BioGPS for COL4A6 GenemRNA expression by GTEx 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 (x17.6) and Esophagus - Muscularis (x14.4).

Protein differential expression in normal tissues from HIPED for COL4A6 Gene

This gene is overexpressed in Gallbladder (32.5), Pancreas (15.3), and Heart (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for COL4A6 Gene



NURSA nuclear receptor signaling pathways regulating expression of COL4A6 Gene:

COL4A6

SOURCE GeneReport for Unigene cluster for COL4A6 Gene:

Hs.145586

Evidence on tissue expression from TISSUES for COL4A6 Gene

  • Kidney(4.3)
  • Eye(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for COL4A6 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • urinary
Organs:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • head
  • inner ear
  • mouth
  • pharynx
Thorax:
  • bronchus
  • esophagus
  • trachea
Abdomen:
  • intestine
  • kidney
  • large intestine
  • stomach
Pelvis:
  • rectum
  • ureter
  • urinary bladder
  • vagina
General:
  • blood
  • blood vessel
  • coagulation system
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with COL4A6: view

Primer Products

No data available for Protein tissue co-expression partners and 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
chimpanzee
(Pan troglodytes)
 Mammalia COL4A6 34 35
  • 99.04 (n)
cow
(Bos Taurus)
 Mammalia COL4A6 34 35
  • 86.25 (n)
dog
(Canis familiaris)
 Mammalia COL4A6 34 35
  • 86.09 (n)
mouse
(Mus musculus)
 Mammalia Col4a6 34 16 35
  • 81.99 (n)
rat
(Rattus norvegicus)
 Mammalia Col4a6 34
  • 80.99 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia COL4A6 35
  • 58 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves COL4A6 34 35
  • 65.69 (n)
lizard
(Anolis carolinensis)
 Reptilia COL4A6 35
  • 63 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia col4a6 34
  • 62.23 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.3640 34
zebrafish
(Danio rerio)
 Actinopterygii col4a6 34 35
  • 57.07 (n)
fruit fly
(Drosophila melanogaster)
 Insecta Cg25C 36
  • 39 (a)
vkg 36
  • 38 (a)
worm
(Caenorhabditis elegans)
 Secernentea let-2 36
  • 71 (a)
emb-9 36
  • 40 (a)
Species where no ortholog for COL4A6 was found in the sources mined by GeneCards:
  • 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

ENSEMBL:
Gene Tree for COL4A6 (if available)
TreeFam:
Gene Tree for COL4A6 (if available)

Paralogs for COL4A6 Gene

Paralogs for COL4A6 Gene

(9) SIMAP similar genes for COL4A6 Gene using alignment to 9 proteins:

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
rs779748859 Pathogenic, Deafness, X-linked, 6 (DFNX6) [MIM:300914] 108,187,279(+) ATCAC(C/T)CTAGA nc-transcript-variant, reference, missense
VAR_035748 A colorectal cancer sample
rs104886049 Pathogenic 108,440,138(+) TGCGT(G/T)GAGTC upstream-variant-2KB, reference, stop-gained
rs104886050 Pathogenic 108,440,126(+) GAAGA(A/G)TGAAA upstream-variant-2KB, reference, missense
rs104886376 Pathogenic 108,440,127(+) AAGAA(-/TG)AAACT upstream-variant-2KB, reference, frameshift-variant

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

Variant ID Type Subtype PubMed ID
dgv2361e212 CNV gain 25503493
esv9265 CNV gain 19470904
nsv1125117 CNV duplication 24896259
nsv476288 CNV novel sequence insertion 20440878

Variation tolerance for COL4A6 Gene

Residual Variation Intolerance Score: 94.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.02; 60.39% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL4A6 Gene

Human Gene Mutation Database (HGMD)
COL4A6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL4A6

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

Disorders for COL4A6 Gene

MalaCards: The human disease database

(9) MalaCards diseases for COL4A6 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
deafness, x-linked 6
  • dfnx6
x-linked non-syndromic sensorineural deafness type dfn
  • x-linked isolated neurosensory deafness type dfn
dfnx6 nonsyndromic hearing loss and deafness
  • deafness, x-linked 6
leiomyomatosis
  • leiomyomatosis, no icd-o subtype
alport syndrome
  • alport syndrome, x-linked
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CO4A6_HUMAN
  • 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.
  • 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).

Relevant External Links for COL4A6

Genetic Association Database (GAD)
COL4A6
Human Genome Epidemiology (HuGE) Navigator
COL4A6
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL4A6
genes like me logo Genes that share disorders with COL4A6: view

No data available for Genatlas for COL4A6 Gene

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 22 64
  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 22 64
  3. Novel form of X-linked nonsyndromic hearing loss with cochlear malformation caused by a mutation in the type IV collagen gene COL4A6. (PMID: 23714752) Rost S. … Kunstmann E. (Eur. J. Hum. Genet. 2014) 3 4 64
  4. Identification of fetal and maternal single nucleotide polymorphisms in candidate genes that predispose to spontaneous preterm labor with intact membranes. (PMID: 20452482) Romero R. … Menon R. (Am. J. Obstet. Gynecol. 2010) 3 46 64
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 64

Products for COL4A6 Gene

Sources for COL4A6 Gene

Content
Loading form....