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PCDH19 protocadherin 19 [ Homo sapiens (human) ]

Gene ID: 57526, updated on 17-Jan-2022

Summary

Official Symbol
PCDH19provided by HGNC
Official Full Name
protocadherin 19provided by HGNC
Primary source
HGNC:HGNC:14270
See related
Ensembl:ENSG00000165194 MIM:300460
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

See PCDH19 in Genome Data Viewer
Location:
Xq22.1
Exon count:
6
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (100291644..100410273, complement)
105.20201022 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 uncharacterized LOC105373298 Neighboring gene tenomodulin

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Early infantile epileptic encephalopathy 9
MedGen: C1848137 OMIM: 300088 GeneReviews: Not available
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2013-06-06)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2013-06-06)

ClinGen Genome Curation PagePubMed

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 brain development IEA
Inferred from Electronic Annotation
more info
 
involved_in cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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_001105243.2NP_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:242342
    Cadherin_repeat; Cadherin tandem repeat domain
    cl09101
    Location:25106
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  2. NM_001184880.2NP_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
    Q8TAB3
    Related
    ENSP00000362125.4, ENST00000373034.8
    Conserved Domains (2) summary
    cd11304
    Location:242342
    Cadherin_repeat; Cadherin tandem repeat domain
    cl09101
    Location:25106
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  3. NM_020766.3NP_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:242342
    Cadherin_repeat; Cadherin tandem repeat domain
    cl09101
    Location:25106
    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: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011530997.2XP_011529299.1  protocadherin-19 isoform X1

    See identical proteins and their annotated locations for XP_011529299.1

    Conserved Domains (2) summary
    cd11304
    Location:242342
    Cadherin_repeat; Cadherin tandem repeat domain
    cl09101
    Location:25106
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
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