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Aliases for PCDH15 Gene

Aliases for PCDH15 Gene

  • Protocadherin-Related 15 2 3 5
  • Cadherin-Related Family Member 15 2 3
  • USH1F 3 4
  • Deafness, Autosomal Recessive 23 2
  • Protocadherin 15 2
  • CDHR15 3
  • DFNB23 3

External Ids for PCDH15 Gene

Previous HGNC Symbols for PCDH15 Gene

  • USH1F
  • DFNB23

Previous GeneCards Identifiers for PCDH15 Gene

  • GC10M054397
  • GC10M054586
  • GC10M055473
  • GC10M054925
  • GC10M055250
  • GC10M049544

Summaries for PCDH15 Gene

Entrez Gene Summary for PCDH15 Gene

  • This gene is a member of the cadherin superfamily. Family members encode integral membrane proteins that mediate calcium-dependent cell-cell adhesion. It plays an essential role in maintenance of normal retinal and cochlear function. Mutations in this gene result in hearing loss and Usher Syndrome Type IF (USH1F). Extensive alternative splicing resulting in multiple isoforms has been observed in the mouse ortholog. Similar alternatively spliced transcripts are inferred to occur in human, and additional variants are likely to occur. [provided by RefSeq, Dec 2008]

GeneCards Summary for PCDH15 Gene

PCDH15 (Protocadherin-Related 15) is a Protein Coding gene. Diseases associated with PCDH15 include Usher Syndrome, Type 1F and Deafness, Autosomal Recessive 23. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH20.

UniProtKB/Swiss-Prot for PCDH15 Gene

  • Calcium-dependent cell-adhesion protein. Essential for maintenance of normal retinal and cochlear function.

Gene Wiki entry for PCDH15 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDH15 Gene

Genomics for PCDH15 Gene

Regulatory Elements for PCDH15 Gene

Enhancers for PCDH15 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PCDH15 on UCSC Golden Path with GeneCards custom track

Genomic Location for PCDH15 Gene

53,802,771 bp from pter
55,627,942 bp from pter
1,825,172 bases
Minus strand

Genomic View for PCDH15 Gene

Genes around PCDH15 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDH15 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDH15 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDH15 Gene

Proteins for PCDH15 Gene

  • Protein details for PCDH15 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A6NL19
    • C6ZEF5
    • C6ZEF6
    • C6ZEF7
    • Q5VY38
    • Q5VY39
    • Q6TRH8
    • Q8NDB9
    • Q96QT8

    Protein attributes for PCDH15 Gene

    1955 amino acids
    Molecular mass:
    216069 Da
    Quaternary structure:
    • Interacts with MYO7A. antiparallel heterodimer with CDH23 (By similarity). Interacts with USH1G; this interaction may recruit USH1G to the plasma membrane (By similarity). Interacts with LHFPL5/TMHS; this interaction is required for efficient localization to hair bundles (By similarity).
    • Sequence=ACF76477.1; Type=Miscellaneous discrepancy; Note=Unlikely isoform. Probable cloning artifact.; Evidence={ECO:0000305};

    Alternative splice isoforms for PCDH15 Gene


neXtProt entry for PCDH15 Gene

Proteomics data for PCDH15 Gene at MOPED

Post-translational modifications for PCDH15 Gene

  • Glycosylation at Asn 52, Asn 97, Asn 201, Asn 419, Asn 559, Asn 662, Asn 724, Asn 768, Asn 821, Asn 851, Asn 1064, Asn 1084, and Asn 1175
  • Modification sites at PhosphoSitePlus

Antibody Products

  • R&D Systems Antibodies for PCDH15 (Protocadherin-15)

No data available for DME Specific Peptides for PCDH15 Gene

Domains & Families for PCDH15 Gene

Gene Families for PCDH15 Gene

Protein Domains for PCDH15 Gene

Graphical View of Domain Structure for InterPro Entry



  • Cadherin repeats 1 and 2 mediate calcium-dependent heterophilic interaction with CDH23.
  • Cadherin repeats 1 and 2 mediate calcium-dependent heterophilic interaction with CDH23.
  • Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections, imparting a strong curvature to the full-length ectodomain.
  • Contains 11 cadherin domains.
genes like me logo Genes that share domains with PCDH15: view

Function for PCDH15 Gene

Molecular function for PCDH15 Gene

UniProtKB/Swiss-Prot Function:
Calcium-dependent cell-adhesion protein. Essential for maintenance of normal retinal and cochlear function.
genes like me logo Genes that share phenotypes with PCDH15: view

Human Phenotype Ontology for PCDH15 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDH15 Gene

Localization for PCDH15 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDH15 Gene

Cell membrane; Single-pass type I membrane protein. Note=Efficient localization to the plasma membrane requires the presence of LHFPL5. {ECO:0000250}.
Isoform 3: Secreted.

Subcellular locations from

Jensen Localization Image for PCDH15 Gene COMPARTMENTS Subcellular localization image for PCDH15 gene
Compartment Confidence
extracellular 5
plasma membrane 5
cytoskeleton 2
endoplasmic reticulum 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for PCDH15 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0016021 integral component of membrane IEA --
GO:0032421 stereocilium bundle IEA --
genes like me logo Genes that share ontologies with PCDH15: view

Pathways & Interactions for PCDH15 Gene

SuperPathways for PCDH15 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDH15 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001964 startle response IEA --
GO:0002009 morphogenesis of an epithelium IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007628 adult walking behavior IEA --
GO:0035058 nonmotile primary cilium assembly IEA --
genes like me logo Genes that share ontologies with PCDH15: view

No data available for Pathways by source and SIGNOR curated interactions for PCDH15 Gene

Drugs & Compounds for PCDH15 Gene

(1) Drugs for PCDH15 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with PCDH15: view

Transcripts for PCDH15 Gene

mRNA/cDNA for PCDH15 Gene

Unigene Clusters for PCDH15 Gene

Protocadherin-related 15:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PCDH15 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^
SP1: -
SP2: -

ExUns: 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32
SP1: -

Relevant External Links for PCDH15 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDH15 Gene

mRNA expression in normal human tissues for PCDH15 Gene

mRNA differential expression in normal tissues according to GTEx for PCDH15 Gene

This gene is overexpressed in Brain - Amygdala (x6.1), Brain - Substantia nigra (x5.3), Brain - Hypothalamus (x4.9), Brain - Hippocampus (x4.8), and Brain - Anterior cingulate cortex (BA24) (x4.4).

Protein differential expression in normal tissues from HIPED for PCDH15 Gene

This gene is overexpressed in Fetal Brain (32.9), Blymphocyte (8.5), and Tlymphocyte (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PCDH15 Gene

SOURCE GeneReport for Unigene cluster for PCDH15 Gene Hs.280209

mRNA Expression by UniProt/SwissProt for PCDH15 Gene

Tissue specificity: Expressed in brain, lung, kidney, spleen and testis. Found also in the inner and outer synaptic layers, and the nerve fiber layer in adult and fetal retinas. Found in the supporting cells, outer sulcus cells and spiral ganglion of fetal cochlea. Expressed in cytotoxic tumor-derived T- and NK-cell lines as well as biopsies of nasal NK/T-cell lymphomas. Not detected in normal or in vitro activated peripheral blood cells, CD4 or CD8 lymphocytes or NK cells. Isoform 3 is expressed in brain, heart, cerebellum and kidney. CD1 isoforms, such as isoform 1, have a limited pattern of expression and is detected in testis, retina and cochlea. CD2 isoforms, such as isoforms 4 and 5, are expressed in heart, kidney, thymus, spleen, testis, retina and cochlea. CD3 isoforms, such as isoform 6, are widely expressed.
genes like me logo Genes that share expression patterns with PCDH15: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Protein tissue co-expression partners for PCDH15 Gene

Orthologs for PCDH15 Gene

This gene was present in the common ancestor of animals.

Orthologs for PCDH15 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia LOC100140108 35
  • 89.98 (n)
  • 93.96 (a)
PCDH15 36
  • 82 (a)
(Canis familiaris)
Mammalia PCDH15 35
  • 86.53 (n)
  • 92.94 (a)
PCDH15 36
  • 86 (a)
(Mus musculus)
Mammalia Pcdh15 35
  • 82.45 (n)
  • 90.37 (a)
Pcdh15 16
Pcdh15 36
  • 85 (a)
(Pan troglodytes)
Mammalia PCDH15 35
  • 97.29 (n)
  • 96.71 (a)
PCDH15 36
  • 13 (a)
(Rattus norvegicus)
Mammalia Pcdh15 35
  • 81.83 (n)
  • 90.42 (a)
(Monodelphis domestica)
Mammalia PCDH15 36
  • 89 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 51 (a)
-- 36
  • 86 (a)
-- 36
  • 71 (a)
(Gallus gallus)
Aves PCDH15 35
  • 74.72 (n)
  • 78.99 (a)
PCDH15 36
  • 69 (a)
(Anolis carolinensis)
Reptilia PCDH15 36
  • 77 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdh15 35
  • 69.75 (n)
  • 72.73 (a)
(Danio rerio)
Actinopterygii pcdh15b 35
  • 65.34 (n)
  • 67.2 (a)
pcdh15a 36
  • 58 (a)
pcdh15b 36
  • 57 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002310 35
  • 42.27 (n)
  • 34.05 (a)
fruit fly
(Drosophila melanogaster)
Insecta Cad99C 35
  • 42.17 (n)
  • 31.77 (a)
Cad99C 36
  • 23 (a)
(Caenorhabditis elegans)
Secernentea cdh-5 35
  • 42.04 (n)
  • 29.14 (a)
cdh-3 36
  • 10 (a)
Species with no ortholog for PCDH15:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 PCDH15 Gene

Gene Tree for PCDH15 (if available)
Gene Tree for PCDH15 (if available)

Paralogs for PCDH15 Gene

Paralogs for PCDH15 Gene

genes like me logo Genes that share paralogs with PCDH15: view

Variants for PCDH15 Gene

Sequence variations from dbSNP and Humsavar for PCDH15 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
VAR_024035 Deafness, autosomal recessive, 23 (DFNB23)
VAR_024036 Deafness, autosomal recessive, 23 (DFNB23)
rs61731387 Usher syndrome 1F (USH1F) 53,831,493(+) CGGCT(G/T)AAAGT reference, missense
rs11004439 - 54,664,208(+) GAGAG(A/C/T)GCCCA reference, missense
rs10825269 - 54,195,850(+) TAGAC(C/T)GGCAA reference, missense

Structural Variations from Database of Genomic Variants (DGV) for PCDH15 Gene

Variant ID Type Subtype PubMed ID
esv2750962 CNV Loss 17911159
dgv280e1 CNV Complex 17122850
nsv895410 CNV Loss 21882294
nsv895429 CNV Loss 21882294
esv2659575 CNV Deletion 23128226
nsv825390 CNV Gain 20364138
nsv895430 CNV Loss 21882294
nsv6687 CNV Insertion 18451855
nsv467213 CNV Loss 19166990
nsv825391 CNV Gain 20364138
esv2736995 CNV Deletion 23290073
esv2737006 CNV Deletion 23290073
esv2168362 CNV Deletion 18987734
esv2737017 CNV Deletion 23290073
dgv14e180 CNV Deletion 20482838
esv2737029 CNV Deletion 23290073
esv1589340 CNV Deletion 17803354
esv2676676 CNV Deletion 23128226
nsv825392 CNV Gain 20364138
nsv8667 CNV Loss 18304495
nsv527039 CNV Loss 19592680
esv268650 CNV Insertion 20981092
nsv467214 CNV Loss 19166990
esv2737040 CNV Deletion 23290073
esv9702 CNV Loss 19470904
esv2661074 CNV Deletion 23128226
nsv895431 CNV Loss 21882294
nsv895432 CNV Loss 21882294
esv1378415 CNV Insertion 17803354
esv29200 CNV Loss 19812545
nsv895433 CNV Loss 21882294
esv2654824 CNV Deletion 19546169
esv2034822 CNV Deletion 18987734
esv2737051 CNV Deletion 23290073
esv2662719 CNV Deletion 23128226
esv268804 CNV Insertion 20981092
nsv6698 CNV Loss 18451855
nsv831879 CNV Gain 17160897
esv2737062 CNV Deletion 23290073
esv2737073 CNV Deletion 23290073
nsv825393 CNV Loss 20364138
nsv467217 CNV Loss 19166990
dgv712n71 CNV Loss 21882294
dgv713n71 CNV Loss 21882294
nsv818762 CNV Loss 17921354
dgv93n27 CNV Loss 19166990
nsv25061 CNV Insertion 16902084
esv1228234 CNV Insertion 17803354
esv1014340 CNV Insertion 17803354
esv273645 CNV Insertion 20981092
esv269814 CNV Insertion 20981092
nsv516160 CNV Loss 19592680
esv270700 CNV Insertion 20981092
esv272658 CNV Insertion 20981092
esv1007583 CNV Insertion 20482838
esv2668457 CNV Deletion 23128226
dgv714n71 CNV Loss 21882294
esv268224 CNV Insertion 20981092
dgv94n27 CNV Loss 19166990
nsv467221 CNV Loss 19166990
nsv818763 CNV Loss 17921354
nsv895443 CNV Loss 21882294
dgv95n27 CNV Loss 19166990
nsv470942 CNV Gain 18288195
nsv520151 CNV Gain 19592680
nsv895444 CNV Loss 21882294
nsv470943 CNV Loss 18288195
dgv715n71 CNV Loss 21882294
nsv467226 CNV Loss 19166990
nsv6709 CNV Loss 18451855
nsv524035 CNV Loss 19592680
nsv467228 CNV Loss 19166990
nsv467229 CNV Loss 19166990
dgv281e1 CNV Complex 17122850
nsv895447 CNV Loss 21882294
dgv282e1 CNV Complex 17122850
nsv8668 CNV Loss 18304495
dgv152n67 CNV Loss 20364138
nsv820422 CNV Duplication 20802225
esv259883 OTHER Complex 20981092
nsv820195 CNV Loss 19587683
esv22182 CNV Loss 19812545
esv33398 CNV Gain 17666407
nsv442577 CNV CNV 18776908
nsv895448 CNV Gain 21882294
dgv283e1 CNV Complex 17122850
nsv514560 CNV Gain 21397061
nsv520863 CNV Gain 19592680
nsv526545 CNV Loss 19592680
esv29623 CNV Gain 19812545
esv1009504 CNV Gain 20482838
esv1006375 CNV Gain 20482838
dgv716n71 CNV Loss 21882294
nsv895452 CNV Gain 21882294
esv2737084 CNV Deletion 23290073
nsv525948 CNV Loss 19592680
nsv895453 CNV Loss 21882294
esv2561219 CNV Deletion 19546169
esv2321279 CNV Deletion 18987734
esv2676429 CNV Deletion 23128226
esv2737095 CNV Deletion 23290073
esv1246910 CNV Deletion 17803354
nsv24798 CNV Loss 16902084
nsv895454 CNV Loss 21882294
nsv471793 CNV Loss 16327809
dgv96n27 CNV Loss 19166990

Variation tolerance for PCDH15 Gene

Residual Variation Intolerance Score: 92.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 21.81; 99.34% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDH15 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDH15 Gene

Disorders for PCDH15 Gene

MalaCards: The human disease database

(15) MalaCards diseases for PCDH15 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
usher syndrome, type 1f
  • ush1f
deafness, autosomal recessive 23
  • deafness, autosomal recessive, 23
usher syndrome, type 1d
  • usher syndrome, type 1d/f digenic
usher syndrome, type 1g
  • usher syndrome type 1g
autosomal recessive non-syndromic sensorineural deafness type dfnb
  • autosomal recessive isolated neurosensory deafness type dfnb
- elite association - COSMIC cancer census association via MalaCards


  • Deafness, autosomal recessive, 23 (DFNB23) [MIM:609533]: A form of non-syndromic sensorineural hearing loss. 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:14570705, ECO:0000269 PubMed:18719945}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Usher syndrome 1D/F (USH1DF) [MIM:601067]: USH1DF patients are heterozygous for mutations in CDH23 and PCDH15, indicating a digenic inheritance pattern. {ECO:0000269 PubMed:15537665, ECO:0000269 PubMed:18719945}. Note=The disease is caused by mutations affecting distinct genetic loci, including the gene represented in this entry.
  • Usher syndrome 1F (USH1F) [MIM:602083]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH1 is characterized by profound congenital sensorineural deafness, absent vestibular function and prepubertal onset of progressive retinitis pigmentosa leading to blindness. {ECO:0000269 PubMed:15660226, ECO:0000269 PubMed:22815625}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PCDH15

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with PCDH15: view

No data available for Genatlas for PCDH15 Gene

Publications for PCDH15 Gene

  1. PCDH15 is expressed in the neurosensory epithelium of the eye and ear and mutant alleles are responsible for both USH1F and DFNB23. (PMID: 14570705) Ahmed Z.M. … Wilcox E.R. (Hum. Mol. Genet. 2003) 2 3 4 23 67
  2. Mutations of the protocadherin gene PCDH15 cause Usher syndrome type 1F. (PMID: 11398101) Ahmed Z.M. … Wilcox E.R. (Am. J. Hum. Genet. 2001) 2 3 23
  3. A nonsynonymous SNP within PCDH15 is associated with lipid traits in familial combined hyperlipidemia. (PMID: 19816713) Huertas-Vazquez A. … Pajukanta P. (Hum. Genet. 2010) 3 23
  4. Profound, prelingual nonsyndromic deafness maps to chromosome 10q21 and is caused by a novel missense mutation in the Usher syndrome type IF gene PCDH15. (PMID: 19107147) Doucette L. … Young T.L. (Eur. J. Hum. Genet. 2009) 3 23
  5. Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome. (PMID: 18719945) Ahmed Z.M. … Friedman T.B. (Hum. Genet. 2008) 3 23

Products for PCDH15 Gene

Sources for PCDH15 Gene