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PCDHGC3 protocadherin gamma subfamily C, 3 [ Homo sapiens (human) ]

Gene ID: 5098, updated on 2-Nov-2024

Summary

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Official Symbol
PCDHGC3provided by HGNC
Official Full Name
protocadherin gamma subfamily C, 3provided by HGNC
Primary source
HGNC:HGNC:8716
See related
Ensembl:ENSG00000240184 MIM:603627; AllianceGenome:HGNC:8716
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
PC43; PCDH2; PCDH-GAMMA-C3
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

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See PCDHGC3 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 (141475966..141512975)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (142001773..142038959)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140855533..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 ATAC-STARR-seq lymphoblastoid active region 23296 Neighboring gene protocadherin gamma subfamily B, 7 Neighboring gene protocadherin gamma subfamily A, 11 Neighboring gene protocadherin gamma subfamily B, 8 pseudogene 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 ATAC-STARR-seq lymphoblastoid active region 23297 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140855840-140856383 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 active region 23299 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16454 Neighboring gene RNA, 7SL, cytoplasmic 68, pseudogene Neighboring gene protocadherin gamma subfamily C, 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23301 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140888408-140888908 Neighboring gene protocadherin gamma subfamily C, 5 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_chr5:140894353-140894978 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140893727-140894352 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

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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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Protocadherin Gamma C3 (PCDHGC3) Is Strongly Expressed in Glioblastoma and Its High Expression Is Associated with Longer Progression-Free Survival of Patients.
    Title: Protocadherin Gamma C3 (PCDHGC3) Is Strongly Expressed in Glioblastoma and Its High Expression Is Associated with Longer Progression-Free Survival of Patients.
  2. Our data provide a map of the DNA methylome episignature specific to an SDHB-mutated cancer and establish PCDHGC3 as a putative suppressor gene
    Title: Epigenetic Deregulation of Protocadherin PCDHGC3 in Pheochromocytomas/Paragangliomas Associated With SDHB Mutations.
  3. our data suggest that the PCDH LRES is an important tumour suppressor locus in colorectal cancer, and that PCDHGC3 may be a strong marker and driver for the adenoma-carcinoma transition.
    Title: Long-range epigenetic silencing of chromosome 5q31 protocadherins is involved in early and late stages of colorectal tumorigenesis through modulation of oncogenic pathways.
  4. ADAM10 is the protease responsible for constitutive and regulated Pcdh gamma shedding events that modulate the cell adhesion role of Pcdh gamma.
    Title: Regulated ADAM10-dependent ectodomain shedding of gamma-protocadherin C3 modulates cell-cell adhesion.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules NAS
Non-traceable Author Statement
more info
 PubMed 
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
located_in membrane NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protocadherin gamma-C3
Names
cadherin-like 2
protocadherin 43
protocadherin-2

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_000012.2 

    Range
    186199..223176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002588.4 → NP_002579.2  protocadherin gamma-C3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_002579.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
    Source sequence(s)
    AC008781, BC006439, BC019299
    Consensus CDS
    CCDS4261.1
    UniProtKB/Swiss-Prot
    O60622, Q08192, Q9UN70, Q9Y5C4
    Related
    ENSP00000312070.3, ENST00000308177.5
    Conserved Domains (4) summary
    cd11304
    Location:249 → 348
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:33 → 114
    Cadherin_2; Cadherin-like
    pfam15974
    Location:813 → 907
    Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
    pfam16492
    Location:689 → 770
    Cadherin_C_2; Cadherin cytoplasmic C-terminal

  2. NM_032402.2 → NP_115778.1  protocadherin gamma-C3 isoform 2 precursor

    See identical proteins and their annotated locations for NP_115778.1

    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)
    AC008781, AF152524, BC006439, L11371
    Consensus CDS
    CCDS75348.1
    UniProtKB/Swiss-Prot
    Q9UN70
    UniProtKB/TrEMBL
    Q9BR81
    Related
    ENSP00000481219.1, ENST00000611950.1
    Conserved Domains (3) summary
    cd11304
    Location:249 → 348
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:33 → 114
    Cadherin_2; Cadherin-like
    pfam16492
    Location:689 → 775
    Cadherin_C_2; Cadherin cytoplasmic C-terminal

  3. NM_032403.3 → NP_115779.1  protocadherin gamma-C3 isoform 3

    See identical proteins and their annotated locations for NP_115779.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) utilizes an alternative splice donor site that truncates exon 1. This shortest isoform (3) contains no cadherin domains and lacks a signal sequence and transmembrane region. The functional significance of this isoform is unknown but the transcript is well represented in the EST database.
    Source sequence(s)
    AC008781, BC006439
    Consensus CDS
    CCDS75347.1
    UniProtKB/TrEMBL
    Q9BR81
    Related
    ENSP00000483383.1, ENST00000617641.4
    Conserved Domains (1) summary
    pfam15974
    Location:13 → 107
    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
    141475966..141512975
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    142001773..142038959
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UN70.1 GenPept UniProtKB/Swiss-Prot:Q9UN70

Gene LinkOut

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