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    PCDHA1 protocadherin alpha 1 [ Homo sapiens (human) ]

    Gene ID: 56147, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PCDHA1provided by HGNC
    Official Full Name
    protocadherin alpha 1provided by HGNC
    Primary source
    HGNC:HGNC:8663
    See related
    Ensembl:ENSG00000204970 MIM:606307; AllianceGenome:HGNC:8663
    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
    PCDH-ALPHA1
    Summary
    This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]
    Orthologs
    mouse all
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    Genomic context

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    See PCDHA1 in Genome Data Viewer
    Location:
    5q31.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (140786136..141012347)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141311469..141537634)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140165721..140391932)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378198 Neighboring gene Sharpr-MPRA regulatory region 6103 Neighboring gene vault RNA 1-3 Neighboring gene ZFP14 zinc finger protein pseudogene Neighboring gene protocadherin alpha cluster, complex locus Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140215147-140215794 Neighboring gene protocadherin alpha 2 Neighboring gene protocadherin alpha 3 Neighboring gene protocadherin alpha 4 Neighboring gene protocadherin alpha 5 Neighboring gene uncharacterized LOC112267934 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140249655-140250330 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140250331-140251004 Neighboring gene protocadherin alpha 6 Neighboring gene protocadherin alpha 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140263344-140263928 Neighboring gene protocadherin alpha 8 Neighboring gene protocadherin alpha 9 Neighboring gene protocadherin alpha 10 Neighboring gene protocadherin alpha 14 (pseudogene) Neighboring gene protocadherin alpha 11 Neighboring gene protocadherin alpha 12 Neighboring gene protocadherin alpha 13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140306467-140307024 Neighboring gene NANOG hESC enhancer GRCh37_chr5:140307586-140308097 Neighboring gene protocadherin alpha subfamily C, 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140380918-140381512 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140381513-140382106 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140382107-140382700 Neighboring gene protocadherin alpha subfamily C, 2 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:140383889-140384481 Neighboring gene protocadherin alpha constant Neighboring gene uncharacterized LOC124901090 Neighboring gene VISTA enhancer hs2610 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:140430540-140431368 Neighboring gene PCDHB1 antisense RNA 1 Neighboring gene protocadherin beta 1 Neighboring gene protocadherin beta cluster

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. PCDHA1 High Expression is Associated With Poor Prognosis and Correlated With Immune Cell Infiltration in Breast Cancer. Du J, et al. Clin Breast Cancer, 2023 Jun. PMID 36858841
    2. Analysis of protocadherin alpha gene deletion variant in bipolar disorder and schizophrenia. Lachman HM, et al. Psychiatr Genet, 2008 Jun. PMID 18496207
    3. CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice. Guo Y, et al. Proc Natl Acad Sci U S A, 2012 Dec 18. PMID 23204437, Free PMC Article
    4. Genomic organization of the family of CNR cadherin genes in mice and humans. Sugino H, et al. Genomics, 2000 Jan 1. PMID 10662547
    5. The DNA sequence and comparative analysis of human chromosome 5. Schmutz J, et al. Nature, 2004 Sep 16. PMID 15372022

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PCDHA1 High Expression is Associated With Poor Prognosis and Correlated With Immune Cell Infiltration in Breast Cancer.
      Title: PCDHA1 High Expression is Associated With Poor Prognosis and Correlated With Immune Cell Infiltration in Breast Cancer.
    2. CTCF/cohesin-mediated DNA looping is required for protocadherin alpha promoter choice
      Title: CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice.
    3. A polymorphic copy number variation in this locus, a 16.7-kb deletion affecting PCDH-alpha exons 8-10 (alpha 8-alpha 10 Delta), was analyzed in this study as a potential candidate variant in schizophrenia and bipolar disorder.
      Title: Analysis of protocadherin alpha gene deletion variant in bipolar disorder and schizophrenia.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Analysis of protocadherin alpha gene deletion variant in bipolar disorder and schizophrenia.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protocadherin alpha-1
    Names
    KIAA0345-like 13
    PCDH-alpha-1

    NCBI Reference Sequences (RefSeq)

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    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_000016.2 

      Range
      52009..278218
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_018900.4 → NP_061723.1  protocadherin alpha-1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_061723.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
      Source sequence(s)
      AC005609, AC010223
      Consensus CDS
      CCDS54913.1
      UniProtKB/Swiss-Prot
      O75288, Q9NRT7, Q9Y5I3
      Related
      ENSP00000420840.3, ENST00000504120.4
      Conserved Domains (3) summary
      cd11304
      Location:246 → 346
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:30 → 111
      Cadherin_2; Cadherin-like
      pfam15974
      Location:799 → 942
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    2. NM_031410.2 → NP_113598.1  protocadherin alpha-1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_113598.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) utilizes the large, first exon then continues into the downstream intron 1 sequence before terminating. This one-exon transcript encodes a shorter isoform (2), compared to isoform 1. This short variant is represented based on data in PMID:10380929.
      Source sequence(s)
      AC005609, AF152479, BF089693, DA330326
      UniProtKB/Swiss-Prot
      Q9Y5I3
      Related
      ENSP00000367373.3, ENST00000378133.4
      Conserved Domains (2) summary
      cd11304
      Location:246 → 346
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:30 → 111
      Cadherin_2; Cadherin-like

    3. NM_031411.3 → NP_113599.1  protocadherin alpha-1 isoform 3 precursor

      See identical proteins and their annotated locations for NP_113599.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) utilizes an alternative splice donor site that truncates exon 1. This shortest isoform (3) lacks the transmembrane region and has four complete and one partial cadherin domain.
      Source sequence(s)
      AC005609, AC010223
      Consensus CDS
      CCDS54912.1
      UniProtKB/Swiss-Prot
      Q9Y5I3
      Related
      ENSP00000378129.3, ENST00000394633.7
      Conserved Domains (3) summary
      cd11304
      Location:246 → 346
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:30 → 111
      Cadherin_2; Cadherin-like
      pfam15974
      Location:535 → 678
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      140786136..141012347
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791778.1 Reference GRCh38.p14 PATCHES

      Range
      21312..247523
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      141311469..141537634
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y5I3.1 GenPept UniProtKB/Swiss-Prot:Q9Y5I3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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