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Aliases for PCDH15 Gene

Aliases for PCDH15 Gene

  • Protocadherin-Related 15 2 3
  • USH1F 3 4 6
  • Cadherin-Related Family Member 15 2 3
  • DFNB23 3 6
  • Deafness, Autosomal Recessive 23 2
  • Protocadherin 15 2
  • Protocadherin-15 3
  • CDHR15 3

External Ids for PCDH15 Gene

Previous Symbols for PCDH15 Gene

  • USH1F
  • DFNB23

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 deafness, autosomal recessive 23 and usher syndrome, type 1f. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is FAT4.

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

Genomic Location for PCDH15 Gene

Start:
53,802,771 bp from pter
End:
55,627,942 bp from pter
Size:
1,825,172 bases
Orientation:
Minus strand

Genomic View for PCDH15 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PCDH15 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDH15 Gene

Regulatory Elements for PCDH15 Gene

Proteins for PCDH15 Gene

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

    Protein Symbol:
    Q96QU1-PCD15_HUMAN
    Recommended name:
    Protocadherin-15
    Protein Accession:
    Q96QU1
    Secondary Accessions:
    • A6NL19
    • C6ZEF5
    • C6ZEF6
    • C6ZEF7
    • Q5VY38
    • Q5VY39
    • Q6TRH8
    • Q8NDB9
    • Q96QT8

    Protein attributes for PCDH15 Gene

    Size:
    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).
    SequenceCaution:
    • Sequence=ACF76477.1; Type=Miscellaneous discrepancy; Note=Unlikely isoform. Probable cloning artifact.; Evidence={ECO:0000305};

    Alternative splice isoforms for PCDH15 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDH15 Gene

Proteomics data for PCDH15 Gene at MOPED

Post-translational modifications for PCDH15 Gene

  • Modification sites at PhosphoSitePlus
  • Glycosylation at Asn52, Asn97, Asn201, Asn419, Asn559, Asn662, Asn724, Asn768, Asn821, Asn851, Asn1064, Asn1084, and Asn1175

No data available for DME Specific Peptides for PCDH15 Gene

Domains for PCDH15 Gene

Gene Families for PCDH15 Gene

HGNC:
  • CDHR :Cadherins / Cadherin-related

Protein Domains for PCDH15 Gene

UniProtKB/Swiss-Prot:

PCD15_HUMAN
Domain:
  • Cadherin repeats 1 and 2 mediate calcium-dependent heterophilic interaction with CDH23.:
    • Q96QU1
  • 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.:
    • Q96QU1
  • Contains 11 cadherin domains.:
    • Q96QU1
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

Gene Ontology (GO) - Molecular Function for PCDH15 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding --
genes like me logo Genes that share ontologies with PCDH15: view
genes like me logo Genes that share phenotypes with PCDH15: view

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targeting 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

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

Gene Ontology (GO) - Cellular Components for PCDH15 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001750 photoreceptor outer segment IDA 14570705
GO:0005615 extracellular space IDA 16369489
GO:0005737 cytoplasm --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane --
genes like me logo Genes that share ontologies with PCDH15: view

Pathways 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 --
GO:0002009 morphogenesis of an epithelium --
GO:0007015 actin filament organization --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007601 visual perception --
genes like me logo Genes that share ontologies with PCDH15: view

No data available for Pathways by source for PCDH15 Gene

Compounds for PCDH15 Gene

(1) HMDB Compounds for PCDH15 Gene

Compound Synonyms Cas Number PubMed IDs
Calcium
  • Ca
7440-70-2
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: -
SP3:

ExUns: 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32
SP1: -
SP2:
SP3:

Relevant External Links for PCDH15 Gene

GeneLoc Exon Structure for
PCDH15
ECgene alternative splicing isoforms for
PCDH15

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 (6.1), Brain - Substantia nigra (5.3), Brain - Hypothalamus (4.9), Brain - Hippocampus (4.8), and Brain - Anterior cingulate cortex (BA24) (4.4).

Integrated Proteomics: protein expression 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

Q96QU1-PCD15_HUMAN
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 expressions with PCDH15: view

Orthologs for PCDH15 Gene

This gene was present in the common ancestor of animals.

Orthologs for PCDH15 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDH15 36
  • 97.29 (n)
  • 96.71 (a)
PCDH15 37
  • 13 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LOC100140108 36
  • 89.98 (n)
  • 93.96 (a)
PCDH15 37
  • 82 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PCDH15 36
  • 86.53 (n)
  • 92.94 (a)
PCDH15 37
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pcdh15 36
  • 82.45 (n)
  • 90.37 (a)
Pcdh15 16
Pcdh15 37
  • 85 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PCDH15 37
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 37
  • 51 (a)
OneToMany
-- 37
  • 86 (a)
OneToMany
-- 37
  • 71 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Pcdh15 36
  • 81.83 (n)
  • 90.42 (a)
chicken
(Gallus gallus)
Aves PCDH15 36
  • 74.72 (n)
  • 78.99 (a)
PCDH15 37
  • 69 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PCDH15 37
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdh15 36
  • 69.75 (n)
  • 72.73 (a)
zebrafish
(Danio rerio)
Actinopterygii pcdh15a 37
  • 58 (a)
OneToMany
pcdh15b 36
  • 65.34 (n)
  • 67.2 (a)
pcdh15b 37
  • 57 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002310 36
  • 42.27 (n)
  • 34.05 (a)
fruit fly
(Drosophila melanogaster)
Insecta Cad99C 36
  • 42.17 (n)
  • 31.77 (a)
Cad99C 37
  • 23 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea cdh-3 37
  • 10 (a)
OneToOne
cdh-5 36
  • 42.04 (n)
  • 29.14 (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

ENSEMBL:
Gene Tree for PCDH15 (if available)
TreeFam:
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 MAF
rs713272 -- 54,225,303(+) ATCTG(C/T)TATTT intron-variant
rs713273 -- 54,225,291(+) TGATA(C/T)GTTCA intron-variant
rs713274 -- 54,225,428(+) ACATT(C/T)TCCAA intron-variant
rs718308 -- 54,021,455(-) AAATT(C/G)AATTA intron-variant
rs718309 -- 54,021,421(-) AAAAA(C/T)CACAT intron-variant

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

Relevant External Links for PCDH15 Gene

HapMap Linkage Disequilibrium report
PCDH15
Human Gene Mutation Database (HGMD)
PCDH15
Locus Specific Mutation Databases (LSDB)
PCDH15

Disorders for PCDH15 Gene

(3) OMIM Diseases for PCDH15 Gene (605514)

UniProtKB/Swiss-Prot

PCD15_HUMAN
  • 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.
  • 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.
  • 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.

(3) University of Copenhagen DISEASES for PCDH15 Gene

(3) Novoseek inferred disease relationships for PCDH15 Gene

Disease -log(P) Hits PubMed IDs
usher syndrome 96.2 14
retinitis pigmentosa 77 3
blindness 49.7 1

Relevant External Links for PCDH15

GeneTests
PCDH15
GeneReviews
PCDH15
Genetic Association Database (GAD)
PCDH15
Human Genome Epidemiology (HuGE) Navigator
PCDH15
genes like me logo Genes that share disorders with PCDH15: view

Publications for PCDH15 Gene

  1. 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 4 23
  2. 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
  3. Characterization of Usher syndrome type I gene mutations in an Usher syndrome patient population. (PMID: 15660226) Ouyang X.M. … Liu X.Z. (Hum. Genet. 2005) 3 4 23 49
  4. The R245X mutation of PCDH15 in Ashkenazi Jewish children diagnosed with nonsyndromic hearing loss foreshadows retinitis pigmentosa. (PMID: 15028842) Brownstein Z. … Avraham K.B. (Pediatr. Res. 2004) 3 23 49
  5. Protocadherin 15 (PCDH15): a new secreted isoform and a potential marker for NK/T cell lymphomas. (PMID: 16369489) Rouget-Quermalet V. … Schmitt C. (Oncogene 2006) 3 4 23

Products for PCDH15 Gene

  • antibodies-online peptides for PCDH15
  • antibodies-online antibodies for PCDH15
  • antibodies-online kits for PCDH15

Sources for PCDH15 Gene

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