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PCDH19 protocadherin 19 [ Homo sapiens (human) ]

Gene ID: 57526, updated on 11-Apr-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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Location:
Xq22.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (100291644..100410273, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (98734021..98852681, complement)
105.20220307 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
  • 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 in Males: Are Hemizygous Variants Linked to Autism? Chouery E, et al. Genes (Basel), 2023 Feb 27. PMID 36980870, Free PMC Article
  2. PCDH19-related epilepsy in mosaic males: The phenotypic implication of genotype and variant allele frequency. Chen Y, et al. Front Neurol, 2022. PMID 36408521, Free PMC Article
  3. Expanding the genetic and clinical characteristics of Protocadherin 19 gene mutations. Dell'Isola GB, et al. BMC Med Genomics, 2022 Aug 17. PMID 35978409, Free PMC Article
  4. The epilepsy-associated protein PCDH19 undergoes NMDA receptor-dependent proteolytic cleavage and regulates the expression of immediate-early genes. Gerosa L, et al. Cell Rep, 2022 May 24. PMID 35613587, Free PMC Article
  5. X-chromosome inactivation and PCDH19-associated epileptic encephalopathy: A novel PCDH19 variant in a Chinese family. Hung LY, et al. Clin Chim Acta, 2021 Oct. PMID 34331950

See all (83) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. PCDH19 in Males: Are Hemizygous Variants Linked to Autism?
    Title: PCDH19 in Males: Are Hemizygous Variants Linked to Autism?
  3. Expanding the genetic and clinical characteristics of Protocadherin 19 gene mutations.
    Title: Expanding the genetic and clinical characteristics of Protocadherin 19 gene mutations.
  4. Cadherins and the pathogenesis of epilepsy.
    Title: Cadherins and the pathogenesis of epilepsy.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. A standardized patient-centered characterization of the phenotypic spectrum of PCDH19 girls clustering epilepsy.
    Title: A standardized patient-centered characterization of the phenotypic spectrum of PCDH19 girls clustering epilepsy.
Submit: New GeneRIF Correction See all GeneRIFs (64)

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
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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
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
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_2023_10

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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