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    PCDH19 protocadherin 19 [ Homo sapiens (human) ]

    Gene ID: 57526, updated on 28-Oct-2024

    Summary

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    Official Symbol
    PCDH19provided by HGNC
    Official Full Name
    protocadherin 19provided by HGNC
    Primary source
    HGNC:HGNC:14270
    See related
    Ensembl:ENSG00000165194 MIM:300460; AllianceGenome:HGNC:14270
    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
    DEE9; EFMR; EIEE9
    Summary
    The protein encoded by this gene is a member of the delta-2 protocadherin subclass of the cadherin superfamily. The encoded protein is thought to be a calcium-dependent cell-adhesion protein that is primarily expressed in the brain. Mutations in this gene on human chromosome X are associated with sporadic infantile epileptic encephalopathy and to a female-restricted form of epilepsy (EFMR; also known as PCDH19RE). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]
    Expression
    Biased expression in brain (RPKM 4.4), fat (RPKM 1.2) and 8 other tissues See more
    Orthologs
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    Genomic context

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    See PCDH19 in Genome Data Viewer
    Location:
    Xq22.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (100291644..100410273, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (98734021..98852681, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (99546642..99665271, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene CTDSPL2 pseudogene 1 Neighboring gene ribosomal protein SA pseudogene 8 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrX:99551001-99551552 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrX:99551553-99552102 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:99606908-99607128 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:99650039-99650643 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:99657381-99658580 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:99690569-99691186 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:99749275-99749776 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:99749777-99750276 Neighboring gene uncharacterized LOC105373298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20914 Neighboring gene tenomodulin

    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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    Related articles in PubMed

    1. PCDH19-related epilepsy in two mosaic male patients. Terracciano A, et al. Epilepsia, 2016 Mar. PMID 26765483
    2. Epilepsy and mental retardation restricted to females: X-linked epileptic infantile encephalopathy of unusual inheritance. Duszyc K, et al. J Appl Genet, 2015 Feb. PMID 25204757
    3. PCDH19 mutations in female patients from Southern Italy. Gagliardi M, et al. Seizure, 2015 Jan. PMID 25218114
    4. Identification of four novel PCDH19 Mutations and prediction of their functional impact. Leonardi E, et al. Ann Hum Genet, 2014 Nov. PMID 25227595
    5. Cognitive development in females with PCDH19 gene-related epilepsy. Cappelletti S, et al. Epilepsy Behav, 2015 Jan. PMID 25499160

    See all (86) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NGS-Based Identification of Two Novel PCDH19 Mutations in Female Patients with Early-Onset Epilepsy.
      Title: NGS-Based Identification of Two Novel PCDH19 Mutations in Female Patients with Early-Onset Epilepsy.
    2. Morphometric network-based abnormalities correlate with psychiatric comorbidities and gene expression in PCDH19-related developmental and epileptic encephalopathy.
      Title: Morphometric network-based abnormalities correlate with psychiatric comorbidities and gene expression in PCDH19-related developmental and epileptic encephalopathy.
    3. PCDH19 in Males: Are Hemizygous Variants Linked to Autism?
      Title: PCDH19 in Males: Are Hemizygous Variants Linked to Autism?
    4. Expanding the genetic and clinical characteristics of Protocadherin 19 gene mutations.
      Title: Expanding the genetic and clinical characteristics of Protocadherin 19 gene mutations.
    5. Cadherins and the pathogenesis of epilepsy.
      Title: Cadherins and the pathogenesis of epilepsy.
    6. The epilepsy-associated protein PCDH19 undergoes NMDA receptor-dependent proteolytic cleavage and regulates the expression of immediate-early genes.
      Title: The epilepsy-associated protein PCDH19 undergoes NMDA receptor-dependent proteolytic cleavage and regulates the expression of immediate-early genes.
    7. A complete Protocadherin-19 ectodomain model for evaluating epilepsy-causing mutations and potential protein interaction sites.
      Title: A complete Protocadherin-19 ectodomain model for evaluating epilepsy-causing mutations and potential protein interaction sites.
    8. Dravet syndrome and Dravet syndrome-like phenotype: a systematic review of the SCN1A and PCDH19 variants.
      Title: Dravet syndrome and Dravet syndrome-like phenotype: a systematic review of the SCN1A and PCDH19 variants.
    9. X-chromosome inactivation and PCDH19-associated epileptic encephalopathy: A novel PCDH19 variant in a Chinese family.
      Title: X-chromosome inactivation and PCDH19-associated epileptic encephalopathy: A novel PCDH19 variant in a Chinese family.
    10. Comparative characterization of PCDH19 missense and truncating variants in PCDH19-related epilepsy.
      Title: Comparative characterization of PCDH19 missense and truncating variants in PCDH19-related epilepsy.
    Submit: New GeneRIF Correction See all GeneRIFs (65)

    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

    Associated conditions

    Description Tests
    Developmental and epileptic encephalopathy, 9
    MedGen: C1848137 OMIM: 300088 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2023-02-14)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2023-02-14)

    ClinGen Genome Curation Page

    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

    Clone Names

    • KIAA1313, DKFZp686P1843

    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
    		  
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protocadherin-19

    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_021319.1 RefSeqGene

      Range
      5001..123630
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_843

    mRNA and Protein(s)

    1. NM_001105243.2 → NP_001098713.1  protocadherin-19 isoform a precursor

      See identical proteins and their annotated locations for NP_001098713.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) lacks an alternate in-frame exon compared to variant 3. The resulting isoform (a) has the same N- and C-termini but is shorter compared to isoform c.
      Source sequence(s)
      AB037734, AK096591, AL355593, BM975868, CR749278, DA500179
      Consensus CDS
      CCDS43976.1
      UniProtKB/Swiss-Prot
      Q8TAB3
      UniProtKB/TrEMBL
      B3KU71
      Related
      ENSP00000255531.7, ENST00000255531.8
      Conserved Domains (2) summary
      cd11304
      Location:242 → 342
      Cadherin_repeat; Cadherin tandem repeat domain
      cl09101
      Location:25 → 106
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    2. NM_001184880.2 → NP_001171809.1  protocadherin-19 isoform c precursor

      See identical proteins and their annotated locations for NP_001171809.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (c).
      Source sequence(s)
      AB037734, BM975868, EF676096
      Consensus CDS
      CCDS55462.1
      UniProtKB/Swiss-Prot
      B0LDS4, E9PAM6, Q5JTG1, Q5JTG2, Q68DT7, Q8TAB3, Q9P2N3
      Related
      ENSP00000362125.4, ENST00000373034.8
      Conserved Domains (2) summary
      cd11304
      Location:242 → 342
      Cadherin_repeat; Cadherin tandem repeat domain
      cl09101
      Location:25 → 106
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    3. NM_020766.3 → NP_065817.2  protocadherin-19 isoform b precursor

      See identical proteins and their annotated locations for NP_065817.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon and uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 3. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform c.
      Source sequence(s)
      AB037734, AK096591, AL355593, BM975868, CR749278, DA500179
      Consensus CDS
      CCDS48141.1
      UniProtKB/Swiss-Prot
      Q8TAB3
      UniProtKB/TrEMBL
      B3KU71
      Related
      ENSP00000400327.2, ENST00000420881.6
      Conserved Domains (2) summary
      cd11304
      Location:242 → 342
      Cadherin_repeat; Cadherin tandem repeat domain
      cl09101
      Location:25 → 106
      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_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      100291644..100410273 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      98734021..98852681 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TAB3.3 GenPept UniProtKB/Swiss-Prot:Q8TAB3

    Gene LinkOut

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

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