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    PCDH15 protocadherin related 15 [ Homo sapiens (human) ]

    Gene ID: 65217, updated on 5-Nov-2017
    Official Symbol
    PCDH15provided by HGNC
    Official Full Name
    protocadherin related 15provided by HGNC
    Primary source
    HGNC:HGNC:14674
    See related
    Ensembl:ENSG00000150275 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
    Location:
    10q21.1
    Exon count:
    49
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 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

    • 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 Jun 15 11:32:44 2016

    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
    cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    cell-cell signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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
     
    nervous system development IBA
    Inferred from Biological aspect of Ancestor
    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 
    integral component of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 
    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_009191.3 RefSeqGene

      Range
      832892..1813083
      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
      ENSP00000363068.4, OTTHUMP00000275584, ENST00000373957.7, 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
      ENSP00000354950.3, OTTHUMP00000185547, ENST00000361849.7, 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
      ENSP00000412628.2, OTTHUMP00000275595, ENST00000437009.5, 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
      ENSP00000378818.1, OTTHUMP00000185548, ENST00000395430.5, 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
      ENSP00000378820.2, ENST00000395432.6
      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_001142769.2NP_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, OTTHUMP00000185545, ENST00000613657.4
      Conserved Domains (1) summary
      cd11304
      Location:633725
      Cadherin_repeat; Cadherin tandem repeat domain
    8. NM_001142770.2NP_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, OTTHUMP00000185553, ENST00000617271.4
      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
      ENSP00000484454.1, OTTHUMP00000275591, ENST00000621708.4, OTTHUMT00000476352
      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
      ENSP00000363076.3, OTTHUMP00000185546, ENST00000373965.6, 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
      ENSP00000378821.1, OTTHUMP00000185549, ENST00000395433.5, OTTHUMT00000291340
      Conserved Domains (1) summary
      cd11304
      Location:599691
      Cadherin_repeat; Cadherin tandem repeat domain
    12. NM_001354404.1NP_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, AW005431, AY029237
      Conserved Domains (1) summary
      cd11304
      Location:599691
      Cadherin_repeat; Cadherin tandem repeat domain
    13. NM_001354411.1NP_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)
      EU718480
      Conserved Domains (1) summary
      cd11304
      Location:628720
      Cadherin_repeat; Cadherin tandem repeat domain
    14. NM_001354420.1NP_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
      Conserved Domains (1) summary
      cd11304
      Location:621713
      Cadherin_repeat; Cadherin tandem repeat domain
    15. NM_001354429.1NP_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_001354430.1NP_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
      Conserved Domains (1) summary
      cd11304
      Location:621713
      Cadherin_repeat; Cadherin tandem repeat domain
    17. 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
      ENSP00000322604.6, OTTHUMP00000019623, ENST00000320301.10, OTTHUMT00000048121
      Conserved Domains (1) summary
      cd11304
      Location:621713
      Cadherin_repeat; Cadherin tandem repeat domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p7 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_017016572.1XP_016872061.1  protocadherin-15 isoform X2

      UniProtKB/Swiss-Prot
      Q96QU1
      Related
      ENSP00000483745.1, OTTHUMP00000275590, ENST00000616114.4, OTTHUMT00000476351
      Conserved Domains (1) summary
      cd11304
      Location:621713
      Cadherin_repeat; Cadherin tandem repeat domain
    2. XM_017016571.1XP_016872060.1  protocadherin-15 isoform X1

      Conserved Domains (1) summary
      cd11304
      Location:621713
      Cadherin_repeat; Cadherin tandem repeat domain
    3. XM_017016573.1XP_016872062.1  protocadherin-15 isoform X3

    RNA

    1. XR_001747192.1 RNA Sequence

    2. XR_001747193.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018921.2 Alternate CHM1_1.1

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