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    PCDH10 protocadherin 10 [ Homo sapiens (human) ]

    Gene ID: 57575, updated on 3-Nov-2024

    Summary

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    Official Symbol
    PCDH10provided by HGNC
    Official Full Name
    protocadherin 10provided by HGNC
    Primary source
    HGNC:HGNC:13404
    See related
    Ensembl:ENSG00000138650 MIM:608286; AllianceGenome:HGNC:13404
    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
    PCDH19; OL-PCDH
    Summary
    This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. This family member contains 6 extracellular cadherin domains, a transmembrane domain and a cytoplasmic tail differing from those of the classical cadherins. The encoded protein is a cadherin-related neuronal receptor thought to function in the establishment of specific cell-cell connections in the brain. This gene plays a role in inhibiting cancer cell motility and cell migration. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2015]
    Expression
    Biased expression in brain (RPKM 21.3), placenta (RPKM 10.2) and 4 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PCDH10 in Genome Data Viewer
    Location:
    4q28.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (133149294..133208606)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (136472535..136531845)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (134070449..134115855)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377431 Neighboring gene PCDH10 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21907 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15691 Neighboring gene R3H domain containing 2 pseudogene 1 Neighboring gene uncharacterized LOC124900863 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:134184427-134185124 Neighboring gene Sharpr-MPRA regulatory region 13606 Neighboring gene MPRA-validated peak5117 silencer Neighboring gene MPRA-validated peak5118 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:134882009-134882508 Neighboring gene Sharpr-MPRA regulatory region 7344 Neighboring gene NANOG hESC enhancer GRCh37_chr4:134933235-134933765 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:134935198-134935698 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:134935699-134936199 Neighboring gene poly(A) binding protein cytoplasmic 4 like Neighboring gene ReSE screen-validated silencer GRCh37_chr4:134981541-134981750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:134991841-134992529

    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. Shifts in receptors during submergence of an encephalitic arbovirus.
      Title: Shifts in receptors during submergence of an encephalitic arbovirus.
    2. The role of Pcdh10 in neurological disease and cancer.
      Title: The role of Pcdh10 in neurological disease and cancer.
    3. E3 ubiquitin ligase RNF180 prevents excessive PCDH10 methylation to suppress the proliferation and metastasis of gastric cancer cells by promoting ubiquitination of DNMT1.
      Title: E3 ubiquitin ligase RNF180 prevents excessive PCDH10 methylation to suppress the proliferation and metastasis of gastric cancer cells by promoting ubiquitination of DNMT1.
    4. Miz1 promotes KRAS-driven lung tumorigenesis by repressing the protocadherin Pcdh10.
      Title: Miz1 promotes KRAS-driven lung tumorigenesis by repressing the protocadherin Pcdh10.
    5. PCDH10 exerts tumor-suppressor functions through modulation of EGFR/AKT axis in colorectal cancer.
      Title: PCDH10 exerts tumor-suppressor functions through modulation of EGFR/AKT axis in colorectal cancer.
    6. HOTAIR Induces Methylation of PCDH10, a Tumor Suppressor Gene, by Regulating DNMT1 and Sponging with miR-148b in Gastric Adenocarcinoma.
      Title: HOTAIR Induces Methylation of PCDH10, a Tumor Suppressor Gene, by Regulating DNMT1 and Sponging with miR-148b in Gastric Adenocarcinoma.
    7. PCDH10 inhibits invasion of lymphoma cells by regulating beta-catenin.
      Title: PCDH10 inhibits invasion of lymphoma cells by regulating β-catenin.
    8. Disruption of PCDH10 and TNRC18 Genes due to a Balanced Translocation.
      Title: Disruption of PCDH10 and TNRC18 Genes due to a Balanced Translocation.
    9. Quantitation Analysis of PCDH10 Methylation in Adolescent Idiopathic Scoliosis Using Pyrosequencing Study.
      Title: Quantitation Analysis of PCDH10 Methylation in Adolescent Idiopathic Scoliosis Using Pyrosequencing Study.
    10. Study found elevated promoter methylation and decreased expression of PCDH10 and PCDH17 in advanced gastric lesions, suggesting that elevated PCDH10 and PCDH17 methylation may be an early event in gastric carcinogenesis.
      Title: Methylation and Expression of Nonclustered Protocadherins Encoding Genes and Risk of Precancerous Gastric Lesions in a High-Risk Population.
    Submit: New GeneRIF Correction See all GeneRIFs (52)

    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

    Clone Names

    • KIAA1400, MGC133344, DKFZp761O2023

    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 glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protocadherin-10

    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.

    mRNA and Protein(s)

    1. NM_020815.3 → NP_065866.1  protocadherin-10 isoform 2 precursor

      See identical proteins and their annotated locations for NP_065866.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is intronless, and its 3' terminal end extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 2 which is shorter, and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC105383, AI479918, AW007480, AY013874, CX760781, DA318338
      Consensus CDS
      CCDS75192.1
      UniProtKB/TrEMBL
      Q14DV7
      Related
      ENSP00000480512.1, ENST00000618019.1
      Conserved Domains (3) summary
      cd11304
      Location:254 → 354
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:19 → 101
      Cadherin_2; Cadherin-like
      pfam16492
      Location:713 → 838
      Cadherin_C_2; Cadherin cytoplasmic C-terminal

    2. NM_032961.3 → NP_116586.1  protocadherin-10 isoform 1 precursor

      See identical proteins and their annotated locations for NP_116586.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB037821, AC105383, AL157470, BC039411, CB052787, DA318338
      Consensus CDS
      CCDS34063.1
      UniProtKB/Swiss-Prot
      Q4W5F6, Q96SF0, Q9P2E7
      UniProtKB/TrEMBL
      Q14DV7, X5D999
      Related
      ENSP00000264360.4, ENST00000264360.7
      Conserved Domains (3) summary
      cd11304
      Location:254 → 354
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:19 → 101
      Cadherin_2; Cadherin-like
      pfam16492
      Location:713 → 838
      Cadherin_C_2; Cadherin cytoplasmic C-terminal

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      133149294..133208606
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011532150.2 → XP_011530452.1  protocadherin-10 isoform X1

      UniProtKB/TrEMBL
      Q14DV7
      Conserved Domains (3) summary
      cd11304
      Location:254 → 354
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:19 → 101
      Cadherin_2; Cadherin-like
      pfam16492
      Location:713 → 838
      Cadherin_C_2; Cadherin cytoplasmic C-terminal

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      136472535..136531845
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350597.1 → XP_054206572.1  protocadherin-10 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P2E7.2 GenPept UniProtKB/Swiss-Prot:Q9P2E7

    Gene LinkOut

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

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