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PCDHGC4 protocadherin gamma subfamily C, 4 [ Homo sapiens (human) ]

Gene ID: 56098, updated on 2-May-2024

Summary

Official Symbol
PCDHGC4provided by HGNC
Official Full Name
protocadherin gamma subfamily C, 4provided by HGNC
Primary source
HGNC:HGNC:8717
See related
Ensembl:ENSG00000242419 MIM:606305; AllianceGenome:HGNC:8717
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
NEDGS; PCDH-GAMMA-C4
Summary
This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
Orthologs
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Genomic context

See PCDHGC4 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 (141485030..141512975)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (142011001..142038959)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140864597..140892542)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene protocadherin gamma subfamily A, 1 Neighboring gene protocadherin gamma cluster Neighboring gene protocadherin gamma subfamily A, 2 Neighboring gene protocadherin gamma subfamily A, 3 Neighboring gene protocadherin gamma subfamily B, 1 Neighboring gene protocadherin gamma subfamily A, 4 Neighboring gene protocadherin gamma subfamily B, 2 Neighboring gene protocadherin gamma subfamily A, 5 Neighboring gene protocadherin gamma subfamily B, 3 Neighboring gene protocadherin gamma subfamily A, 6 Neighboring gene protocadherin gamma subfamily A, 7 Neighboring gene protocadherin gamma subfamily B, 4 Neighboring gene protocadherin gamma subfamily A, 8 Neighboring gene protocadherin gamma subfamily B, 5 Neighboring gene protocadherin gamma subfamily A, 9 Neighboring gene protocadherin gamma subfamily B, 6 Neighboring gene protocadherin gamma subfamily A, 10 Neighboring gene protocadherin gamma subfamily B, 7 Neighboring gene protocadherin gamma subfamily A, 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140821493-140821993 Neighboring gene protocadherin gamma subfamily A, 12 Neighboring gene protocadherin gamma subfamily B, 9 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140855840-140856383 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23297 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:140864468-140864695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23299 Neighboring gene RNA, 7SL, cytoplasmic 68, pseudogene Neighboring gene protocadherin gamma subfamily C, 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23301 Neighboring gene protocadherin gamma subfamily C, 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140888408-140888908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23303 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140893101-140893726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140893727-140894352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140894353-140894978 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140895605-140896230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140896231-140896856 Neighboring gene uncharacterized LOC124901091 Neighboring gene Sharpr-MPRA regulatory region 13534 Neighboring gene diaphanous related formin 1 Neighboring gene MPRA-validated peak5501 silencer Neighboring gene Sharpr-MPRA regulatory region 13738 Neighboring gene DIAPH1 antisense RNA 1

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC24978, MGC119489

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 negative regulation of neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in synapse organization IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 

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_050746.1 RefSeqGene

    Range
    4857..32802
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
  2. NG_000012.2 

    Range
    195371..223176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001386884.1NP_001373813.1  protocadherin gamma-C4 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC008781
    Consensus CDS
    CCDS93796.1
    UniProtKB/TrEMBL
    A0A087WUC2
    Related
    ENSP00000478541.1, ENST00000618371.4
    Conserved Domains (1) summary
    pfam15974
    Location:7101
    Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
  2. NM_018928.3NP_061751.1  protocadherin gamma-C4 isoform 1 precursor

    See identical proteins and their annotated locations for NP_061751.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
    Source sequence(s)
    AC008781
    Consensus CDS
    CCDS4262.1
    UniProtKB/Swiss-Prot
    Q495T2, Q9Y5C3, Q9Y5F7
    UniProtKB/TrEMBL
    A4FU17
    Related
    ENSP00000306918.1, ENST00000306593.2
    Conserved Domains (3) summary
    cd11304
    Location:246346
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:30111
    Cadherin_2; Cadherin-like
    pfam15974
    Location:817911
    Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
  3. NM_032406.1NP_115782.1  protocadherin gamma-C4 isoform 2 precursor

    See identical proteins and their annotated locations for NP_115782.1

    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 the shorter isoform (2).
    Source sequence(s)
    AF152525
    Consensus CDS
    CCDS75349.1
    UniProtKB/TrEMBL
    A4FU17
    Related
    ENSP00000483845.1, ENST00000617094.1
    Conserved Domains (2) summary
    cd11304
    Location:246346
    Cadherin_repeat; Cadherin tandem repeat domain
    cl09101
    Location:30111
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

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
    141485030..141512975
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    142011001..142038959
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)