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PCDH15 protocadherin related 15 [ Homo sapiens (human) ]

Gene ID: 65217, updated on 25-Aug-2020

Summary

Official Symbol
PCDH15provided by HGNC
Official Full Name
protocadherin related 15provided by HGNC
Primary source
HGNC:HGNC:14674
See related
Ensembl:ENSG00000150275 MIM:605514
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]
Expression
Biased expression in brain (RPKM 1.2), adrenal (RPKM 0.8) and 5 other tissues See more
Orthologs

Genomic context

See PCDH15 in Genome Data Viewer
Location:
10q21.1
Exon count:
48
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (53802771..55629182, 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 RNA, U6 small nuclear 687, pseudogene Neighboring gene microRNA 548f-1 Neighboring gene neurofilament medium pseudogene 1 Neighboring gene zinc finger MYM-type containing 4 pseudogene Neighboring gene MT-RNR2 like 5 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 21

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients.
GeneReviews: Not available
Deafness, autosomal recessive 23 Compare labs
Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
GeneReviews: Not available
Genome-wide association study identifies two novel genomic regions in irritable bowel syndrome.
GeneReviews: Not available
Genome-wide association study of anthropometric traits and evidence of interactions with age and study year in Filipino women.
GeneReviews: Not available
Genome-wide association study of antibody response to smallpox vaccine.
GeneReviews: Not available
Genome-wide association study of lung function decline in adults with and without asthma.
GeneReviews: Not available
Usher syndrome type 1D
MedGen: C1832845 OMIM: 601067 GeneReviews: Usher Syndrome Type I
Compare labs
Usher syndrome type 1F
MedGen: C1865885 OMIM: 602083 GeneReviews: Usher Syndrome Type I
Compare labs

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 region IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
photoreceptor outer segment IDA
Inferred from Direct Assay
more info
PubMed 
stereocilium ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
synapse IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
protocadherin-15
Names
cadherin-related family member 15

NCBI Reference Sequences (RefSeq)

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_009191.3 RefSeqGene

    Range
    832952..1813084
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001142763.2NP_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
    ENSP00000363068.4, ENST00000373957.7
    Conserved Domains (1) summary
    cd11304
    Location:626718
    Cadherin_repeat; Cadherin tandem repeat domain
  2. NM_001142764.2NP_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
    ENSP00000354950.3, ENST00000361849.7
    Conserved Domains (1) summary
    cd11304
    Location:621713
    Cadherin_repeat; Cadherin tandem repeat domain
  3. NM_001142765.2NP_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
    ENSP00000412628.2, ENST00000437009.5
    Conserved Domains (1) summary
    cd11304
    Location:651744
    Cadherin_repeat; Cadherin tandem repeat domain
  4. NM_001142766.2NP_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
    ENSP00000378818.1, ENST00000395430.5
    Conserved Domains (1) summary
    cd11304
    Location:621713
    Cadherin_repeat; Cadherin tandem repeat domain
  5. NM_001142767.2NP_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
    ENSP00000378820.2, ENST00000395432.6
    Conserved Domains (1) summary
    cd11304
    Location:584676
    Cadherin_repeat; Cadherin tandem repeat domain
  6. NM_001142768.2NP_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_001142769.3NP_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, EU718480
    Consensus CDS
    CCDS73138.1
    UniProtKB/TrEMBL
    A0A087WZN9
    Related
    ENSP00000482794.1, ENST00000613657.4
    Conserved Domains (1) summary
    cd11304
    Location:633725
    Cadherin_repeat; Cadherin tandem repeat domain
  8. NM_001142770.3NP_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, EU718480
    Consensus CDS
    CCDS44400.1
    UniProtKB/TrEMBL
    A0A087WTR6
    Related
    ENSP00000478076.1, ENST00000617271.4
    Conserved Domains (1) summary
    cd11304
    Location:621713
    Cadherin_repeat; Cadherin tandem repeat domain
  9. NM_001142771.2NP_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
    ENSP00000484454.1, ENST00000621708.4
    Conserved Domains (1) summary
    cd11304
    Location:626718
    Cadherin_repeat; Cadherin tandem repeat domain
  10. NM_001142772.2NP_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
    ENSP00000363076.3, ENST00000373965.6
    Conserved Domains (1) summary
    cd11304
    Location:621713
    Cadherin_repeat; Cadherin tandem repeat domain
  11. NM_001142773.2NP_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
    ENSP00000378821.1, ENST00000395433.5
    Conserved Domains (1) summary
    cd11304
    Location:599691
    Cadherin_repeat; Cadherin tandem repeat domain
  12. NM_001354404.2NP_001341333.1  protocadherin-15 isoform CD1-a precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (M) is derived from an alternate upstream promoter and it thus differs in the 5' UTR, and it also lacks an alternate in-frame segment in both the 5' and 3' coding regions, compared to variant A. The encoded isoform (CD1-a) is shorter than isoform CD1-1.
    Source sequence(s)
    AK126923, AL365496, AW005431, AY029237
    Conserved Domains (1) summary
    cd11304
    Location:599691
    Cadherin_repeat; Cadherin tandem repeat domain
  13. NM_001354411.2NP_001341340.1  protocadherin-15 isoform CD2-a precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (N) lacks an alternate in-frame exon in the 5' coding region and has a distinct 3' splice pattern, compared to variant A. The encoded isoform (CD2-a, also known as CD2 isoform 1) lacks a 5-aa segment in the N-terminal region, has a distinct C-terminus, and is shorter than isoform CD1-1.
    Source sequence(s)
    AL365496, EU718480
    Consensus CDS
    CCDS86095.1
    Related
    ENSP00000378832.2, ENST00000395445.5
    Conserved Domains (1) summary
    cd11304
    Location:628720
    Cadherin_repeat; Cadherin tandem repeat domain
  14. NM_001354420.2NP_001341349.1  protocadherin-15 isoform CD3-a precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (O) lacks an alternate in-frame exon in the 5' coding region and has a distinct 3' splice pattern, compared to variant A. The encoded isoform (CD3-a, also known as CD3 isoform 1) lacks a 5-aa segment in the N-terminal region, has a distinct C-terminus, and is shorter than isoform CD1-1.
    Source sequence(s)
    AL365496, BM675194, EU718482
    Consensus CDS
    CCDS86094.1
    Related
    ENSP00000483745.1, ENST00000616114.4
    Conserved Domains (1) summary
    cd11304
    Location:621713
    Cadherin_repeat; Cadherin tandem repeat domain
  15. NM_001354429.2NP_001341358.1  protocadherin-15 isoform CD3-b precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (P) lacks an alternate in-frame exon in the 5' coding region and has a distinct 3' splice pattern, compared to variant A. The encoded isoform (CD3-b) lacks a 5-aa segment in the N-terminal region, has a distinct C-terminus, and is shorter than isoform CD1-1.
    Source sequence(s)
    AC013737, AC016817, AC024073, AC027671, AC051618, AL353784, AL356114, AL360214, AL365496, AY029237, BM675194
    Conserved Domains (1) summary
    cd11304
    Location:621713
    Cadherin_repeat; Cadherin tandem repeat domain
  16. NM_001354430.2NP_001341359.1  protocadherin-15 isoform CD-Sa precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (Q) lacks an alternate in-frame exon in the 5' coding region, lacks several 3' exons but instead contains a distinct 3' end, compared to variant A. The encoded isoform (CD-Sa) lacks a 5-aa segment in the N-terminal region, and has a distinct and significantly shorter C-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AC024073, AC027671, AL834134, AY029237
    Consensus CDS
    CCDS86093.1
    Related
    ENSP00000363066.1, ENST00000373955.5
    Conserved Domains (1) summary
    cd11304
    Location:621713
    Cadherin_repeat; Cadherin tandem repeat domain
  17. NM_001384140.1NP_001371069.1  protocadherin-15 soform CD3-c precursor

    Status: REVIEWED

    Source sequence(s)
    AC013737, AC016817, AC024073, AC027671, AC051618, AL353784, AL356114, AL360214, AL365496
    Related
    ENSP00000495195.1, ENST00000644397.1
  18. NM_033056.4NP_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
    ENSP00000322604.6, ENST00000320301.10
    Conserved Domains (1) summary
    cd11304
    Location:621713
    Cadherin_repeat; Cadherin tandem repeat domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

    Range
    53802771..55629182 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017016573.2XP_016872062.1  protocadherin-15 isoform X1

RNA

  1. XR_001747193.2 RNA Sequence

  2. XR_001747192.2 RNA Sequence

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