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

    Gene ID: 5098, updated on 10-Dec-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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Protocadherin Gamma C3 (PCDHGC3) Is Strongly Expressed in Glioblastoma and Its High Expression Is Associated with Longer Progression-Free Survival of Patients. Feldheim J, et al. Int J Mol Sci, 2022 Jul 22. PMID 35897674, Free PMC Article
    2. Epigenetic Deregulation of Protocadherin PCDHGC3 in Pheochromocytomas/Paragangliomas Associated With SDHB Mutations. Bernardo-Castiñeira C, et al. J Clin Endocrinol Metab, 2019 Nov 1. PMID 31216007
    3. Long-range epigenetic silencing of chromosome 5q31 protocadherins is involved in early and late stages of colorectal tumorigenesis through modulation of oncogenic pathways. Dallosso AR, et al. Oncogene, 2012 Oct 4. PMID 22249255, Free PMC Article
    4. Protocadherin Pcdh2 shows properties similar to, but distinct from, those of classical cadherins. Obata S, et al. J Cell Sci, 1995 Dec. PMID 8719883
    5. A common protocadherin tail: multiple protocadherins share the same sequence in their cytoplasmic domains and are expressed in different regions of brain. Obata S, et al. Cell Adhes Commun, 1998. PMID 9865466

    See all (30) citations in PubMed

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

    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

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

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