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PCDH15 protocadherin-related 15 [ Homo sapiens (human) ]

Gene ID: 65217, updated on 24-Aug-2015
Official Symbol
PCDH15provided by HGNC
Official Full Name
protocadherin-related 15provided by HGNC
Primary source
HGNC:HGNC:14674
See related
Ensembl:ENSG00000150275; HPRD:05698; MIM:605514; Vega:OTTHUMG00000018259
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
USH1F; CDHR15; DFNB23
Summary
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]
Orthologs
See PCDH15 in Epigenomics, MapViewer
Location:
10q21.1
Exon count:
40
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 10 NC_000010.11 (53802771..54801291, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (55562531..56561051, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378310 Neighboring gene RNA, 5S ribosomal pseudogene 318 Neighboring gene uncharacterized LOC105378311 Neighboring gene microRNA 548f-1 Neighboring gene neurofilament, medium polypeptide pseudogene 1 Neighboring gene MT-RNR2-like 5 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 21

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

Description
A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients.
NHGRI GWA Catalog
Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
NHGRI GWA Catalog
Genome-wide association study identifies two novel genomic regions in irritable bowel syndrome.
NHGRI GWA Catalog
Genome-wide association study of anthropometric traits and evidence of interactions with age and study year in Filipino women.
NHGRI GWA Catalog
Genome-wide association study of antibody response to smallpox vaccine.
NHGRI GWA Catalog
Genome-wide association study of lung function decline in adults with and without asthma.
NHGRI GWA Catalog

Protein interactions

Protein Gene Interaction Pubs
Tat tat Microarray analysis indicates HIV-1 Tat-induced upregulation of protocadherin-related 15 (PCDH15) in primary human brain microvascular endothelial cells PubMed

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • DKFZp667A1711

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
equilibrioception IMP
Inferred from Mutant Phenotype
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
 
inner ear development IEA
Inferred from Electronic Annotation
more info
 
photoreceptor cell maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
sensory perception of light stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
photoreceptor outer segment IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
stereocilium ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
synapse IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
protocadherin-15
Names
cadherin-related family member 15

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009191.2 RefSeqGene

    Range
    5001..1003521
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001142763.1NP_001136235.1  protocadherin-15 isoform CD1-1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (A) encodes isoform CD1-1.
    Source sequence(s)
    AC013737, AC016817, AC024073, AC027671, AC051618, AL353784, AL356114, AL360214, AL365496
    Consensus CDS
    CCDS73137.1
    UniProtKB/TrEMBL
    A2A3D8
    Related
    ENSP00000363068, OTTHUMP00000275584, ENST00000373957, OTTHUMT00000476339
    Conserved Domains (1) summary
    cd11304
    Location:626718
    Cadherin_repeat; Cadherin tandem repeat domain
  2. NM_001142764.1NP_001136236.1  protocadherin-15 isoform CD1-2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (B) lacks an alternate in-frame exon in the 5' coding region, compared to variant A. The resulting isoform (CD1-2) lacks a 5-aa segment near the N-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AC013737, AC016817, AC024073, AC027671, AC051618, AL353784, AL356114, AL360214, AL365496
    Consensus CDS
    CCDS44404.1
    UniProtKB/TrEMBL
    A2A3E7
    Related
    ENSP00000354950, OTTHUMP00000185547, ENST00000361849, OTTHUMT00000291338
    Conserved Domains (1) summary
    cd11304
    Location:621713
    Cadherin_repeat; Cadherin tandem repeat domain
  3. NM_001142765.1NP_001136237.1  protocadherin-15 isoform CD1-6 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (D) lacks an alternate in-frame exon in the 5' coding region and two alternate in-frame exons in the central coding region, compared to variant A. The resulting isoform (CD1-6) lacks a 5-aa segment near the N-terminus and a 71-aa segment in the central protein, compared to isoform CD1-1.
    Source sequence(s)
    AC013737, AC016817, AC024073, AC027671, AC051618, AL353784, AL356114, AL360214, AL365496
    Consensus CDS
    CCDS73134.1
    UniProtKB/TrEMBL
    E7EM53
    Related
    ENSP00000412628, OTTHUMP00000275595, ENST00000437009, OTTHUMT00000476356
    Conserved Domains (1) summary
    cd11304
    Location:651744
    Cadherin_repeat; Cadherin tandem repeat domain
  4. NM_001142766.1NP_001136238.1  protocadherin-15 isoform CD1-7 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (E) lacks three alternate in-frame exons, compared to variant A. The resulting isoform (CD1-7) has the same N- and C-termini but lacks three internal segments, compared to isoform CD1-1.
    Source sequence(s)
    AC013737, AC016817, AC024073, AC027671, AC051618, AL353784, AL356114, AL360214, AL365496
    Consensus CDS
    CCDS44403.1
    UniProtKB/TrEMBL
    A2A3E6
    Related
    ENSP00000378818, OTTHUMP00000185548, ENST00000395430, OTTHUMT00000291339
    Conserved Domains (1) summary
    cd11304
    Location:621713
    Cadherin_repeat; Cadherin tandem repeat domain
  5. NM_001142767.1NP_001136239.1  protocadherin-15 isoform CD1-8 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (F) lacks 4 alternate in-frame exons, compared to variant A. The resulting isoform (CD1-8) has the same N- and C-termini but lacks four internal segments, compared to isoform CD1-1.
    Source sequence(s)
    AC013737, AC016817, AC024073, AC027671, AC051618, AL353784, AL356114, AL360214, AL365496
    UniProtKB/TrEMBL
    E7EMG0
    Related
    ENSP00000378820, ENST00000395432
    Conserved Domains (1) summary
    cd11304
    Location:584676
    Cadherin_repeat; Cadherin tandem repeat domain
  6. NM_001142768.1NP_001136240.1  protocadherin-15 isoform CD1-9 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (G) lacks two alternate in-frame exons in the 5' coding region, compared to variant A. The resulting isoform (CD1-9) lacks a 27-aa segment near the N-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AC013737, AC016817, AC024073, AC027671, AC051618, AL356114, AL360214, AL365496
    Conserved Domains (1) summary
    cd11304
    Location:599691
    Cadherin_repeat; Cadherin tandem repeat domain
  7. NM_001142769.1NP_001136241.1  protocadherin-15 isoform CD2-1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (I) includes an alternate in-frame exon in the central coding region and has a distinct 3' splice pattern, compared to variant A. The resulting isoform (CD2-1) includes an alternate 7-aa segment in the central coding region and has a distinct and longer C-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AC013737, AC016817, AC024073, AC027671, AC051618, AL353784, AL356114, AL360214, AL365496
    Consensus CDS
    CCDS73138.1
    UniProtKB/TrEMBL
    A0A087WZN9
    Related
    ENSP00000482794, OTTHUMP00000185545, ENST00000613657, OTTHUMT00000291335
    Conserved Domains (1) summary
    cd11304
    Location:633725
    Cadherin_repeat; Cadherin tandem repeat domain
  8. NM_001142770.1NP_001136242.1  protocadherin-15 isoform CD2-2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (J) lacks an alternate in-frame exon in the 5' coding region and has a distinct 3' splice pattern, compared to variant A. The resulting isoform (CD2-2) lacks a 5-aa segment in the 5' coding region and has a distinct and longer C-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AC013737, AC016817, AC024073, AC027671, AC051618, AL353784, AL356114, AL360214, AL365496
    Consensus CDS
    CCDS44400.1
    UniProtKB/TrEMBL
    A0A087WTR6
    Related
    ENSP00000478076, OTTHUMP00000185553, ENST00000617271, OTTHUMT00000291344
    Conserved Domains (1) summary
    cd11304
    Location:621713
    Cadherin_repeat; Cadherin tandem repeat domain
  9. NM_001142771.1NP_001136243.1  protocadherin-15 isoform CD3-1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (K) has a distinct 3' splice pattern, compared to variant A. The resulting isoform (CD3-1) has a distinct and longer C-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AC013737, AC016817, AC024073, AC027671, AC051618, AL353784, AL356114, AL360214, AL365496
    Consensus CDS
    CCDS73136.1
    UniProtKB/TrEMBL
    A0A087X1T6
    Related
    ENSP00000478512, ENST00000614895
    Conserved Domains (1) summary
    cd11304
    Location:626718
    Cadherin_repeat; Cadherin tandem repeat domain
  10. NM_001142772.1NP_001136244.1  protocadherin-15 isoform CD3-2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (L) lacks an alternate in-frame exon in the 5' coding region and has a distinct 3' splice pattern, compared to variant A. The resulting isoform (CD3-2) lacks a 5-aa segment near the N-terminus and has a distinct and longer C-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AC013737, AC016817, AC024073, AC027671, AC051618, AL353784, AL356114, AL360214, AL365496
    Consensus CDS
    CCDS73135.1
    UniProtKB/TrEMBL
    A9Z1W1
    Related
    ENSP00000363076, OTTHUMP00000185546, ENST00000373965, OTTHUMT00000291336
    Conserved Domains (1) summary
    cd11304
    Location:621713
    Cadherin_repeat; Cadherin tandem repeat domain
  11. NM_001142773.1NP_001136245.1  protocadherin-15 isoform CD1-10 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (H) lacks three alternate in-frame exons, compared to variant A. The resulting isoform (CD1-10) has the same N- and C-termini but lacks two internal segments, compared to isoform CD1-10.
    Source sequence(s)
    AC013737, AC016817, AC024073, AC027671, AC051618, AL356114, AL360214, AL365496
    Consensus CDS
    CCDS44401.1
    UniProtKB/TrEMBL
    A2A3E8
    Related
    ENSP00000378821, OTTHUMP00000185549, ENST00000395433, OTTHUMT00000291340
    Conserved Domains (1) summary
    cd11304
    Location:599691
    Cadherin_repeat; Cadherin tandem repeat domain
  12. NM_033056.3NP_149045.3  protocadherin-15 isoform CD1-4 precursor

    See identical proteins and their annotated locations for NP_149045.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (C) lacks two alternate in-frame exons in the 5' and 3' coding region, compared to variant A. The resulting isoform (CD1-4) lacks a 5-aa segment near the N-terminus and a 2-aa segment near the C-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AC013737, AC016817, AC024073, AC027671, AC051618, AL353784, AL356114, AL360214, AL365496
    Consensus CDS
    CCDS7248.1
    UniProtKB/Swiss-Prot
    Q96QU1
    Related
    ENSP00000322604, OTTHUMP00000019623, ENST00000320301, OTTHUMT00000048121
    Conserved Domains (1) summary
    cd11304
    Location:621713
    Cadherin_repeat; Cadherin tandem repeat domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p2 Primary Assembly

    Range
    53802771..54801291
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018921.2 Alternate CHM1_1.1

    Range
    55844015..56842749
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)