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PCDHA1 protocadherin alpha 1 [ Homo sapiens (human) ]

Gene ID: 56147, updated on 11-Apr-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (140786136..141012347)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141311469..141537634)
105.20220307 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 uncharacterized LOC124901089 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
  • 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 (18) 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
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
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_2023_10

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

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