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Aliases for PCDH19 Gene

Aliases for PCDH19 Gene

  • Protocadherin 19 2 3
  • KIAA1313 4 6
  • EIEE9 3 6
  • EFMR 3 6
  • Epilepsy, Female Restricted, With Mental Retardation (Juberg-Hellman Syndrome) 2
  • Protocadherin-19 3

External Ids for PCDH19 Gene

Previous HGNC Symbols for PCDH19 Gene

  • EFMR

Previous GeneCards Identifiers for PCDH19 Gene

  • GC0XM094828
  • GC0XM096507
  • GC0XM097582
  • GC0XM098318
  • GC0XM099352
  • GC0XM099433
  • GC0XM099546
  • GC0XM089347

Summaries for PCDH19 Gene

Entrez Gene Summary for PCDH19 Gene

  • 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. Defects in this gene are a cause of epilepsy female-restricted with mental retardation (EFMR). Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]

GeneCards Summary for PCDH19 Gene

PCDH19 (Protocadherin 19) is a Protein Coding gene. Diseases associated with PCDH19 include epileptic encephalopathy, early infantile, 9 and pcdh19-related female-limited epilepsy. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH7.

UniProtKB/Swiss-Prot for PCDH19 Gene

  • Potential calcium-dependent cell-adhesion protein

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDH19 Gene

Genomics for PCDH19 Gene

Regulatory Elements for PCDH19 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for PCDH19 Gene

100,291,644 bp from pter
100,410,273 bp from pter
118,630 bases
Minus strand

Genomic View for PCDH19 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PCDH19 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDH19 Gene

Proteins for PCDH19 Gene

  • Protein details for PCDH19 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B0LDS4
    • E9PAM6
    • Q5JTG1
    • Q5JTG2
    • Q68DT7
    • Q9P2N3

    Protein attributes for PCDH19 Gene

    1148 amino acids
    Molecular mass:
    126253 Da
    Quaternary structure:
    No Data Available
    • Sequence=CAH18133.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAI41393.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAI41394.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for PCDH19 Gene


neXtProt entry for PCDH19 Gene

Proteomics data for PCDH19 Gene at MOPED

Post-translational modifications for PCDH19 Gene

  • Glycosylation at Asn261, Asn420, Asn485, Asn546, Asn570, and Asn676
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDH19 Gene

No data available for DME Specific Peptides for PCDH19 Gene

Domains for PCDH19 Gene

Gene Families for PCDH19 Gene

Protein Domains for PCDH19 Gene

Suggested Antigen Peptide Sequences for PCDH19 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 6 cadherin domains.
  • Contains 6 cadherin domains.
genes like me logo Genes that share domains with PCDH19: view

Function for PCDH19 Gene

Molecular function for PCDH19 Gene

UniProtKB/Swiss-Prot Function:
Potential calcium-dependent cell-adhesion protein

Gene Ontology (GO) - Molecular Function for PCDH19 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDH19: view

Animal Model Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PCDH19

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDH19 Gene

Localization for PCDH19 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDH19 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

Jensen Localization Image for PCDH19 Gene COMPARTMENTS Subcellular localization image for PCDH19 gene
Compartment Confidence
plasma membrane 5
extracellular 2
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for PCDH19 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDH19: view

Pathways for PCDH19 Gene

SuperPathways for PCDH19 Gene

No Data Available

Interacting Proteins for PCDH19 Gene

Gene Ontology (GO) - Biological Process for PCDH19 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
genes like me logo Genes that share ontologies with PCDH19: view

No data available for Pathways by source for PCDH19 Gene

Drugs for PCDH19 Gene

(1) HMDB Compounds for PCDH19 Gene

Compound Synonyms Cas Number PubMed IDs
  • Ca
genes like me logo Genes that share compounds with PCDH19: view

Transcripts for PCDH19 Gene

Unigene Clusters for PCDH19 Gene

Protocadherin 19:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PCDH19

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDH19 Gene

No ASD Table

Relevant External Links for PCDH19 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDH19 Gene

mRNA expression in normal human tissues for PCDH19 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PCDH19 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (5.8), Brain - Anterior cingulate cortex (BA24) (5.7), Brain - Hypothalamus (5.5), Brain - Hippocampus (5.0), and Brain - Cortex (4.4).

Protein differential expression in normal tissues for PCDH19 Gene

This gene is overexpressed in Fetal Brain (44.5) and Stomach (19.0).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for PCDH19 Gene

SOURCE GeneReport for Unigene cluster for PCDH19 Gene Hs.4993

mRNA Expression by UniProt/SwissProt for PCDH19 Gene

Tissue specificity: Moderately expressed in all regions of the brain examined, with lowest levels found in the cerebellum. Moderate expression is also found in ovary, and low expression in all other tissues tested. Also detected in primary skin fibroblast.
genes like me logo Genes that share expressions with PCDH19: view

Expression partners for PCDH19 Gene

* - Elite partner

Primer Products

In Situ Assay Products

Orthologs for PCDH19 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDH19 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia PCDH19 35
  • 91.03 (n)
  • 97.64 (a)
PCDH19 36
  • 98 (a)
(Canis familiaris)
Mammalia LOC492013 35
  • 91.2 (n)
  • 97.63 (a)
PCDH19 36
  • 97 (a)
(Mus musculus)
Mammalia Pcdh19 35
  • 89.32 (n)
  • 96.68 (a)
Pcdh19 16
Pcdh19 36
  • 97 (a)
(Pan troglodytes)
Mammalia PCDH19 35
  • 96.3 (n)
  • 95.94 (a)
PCDH19 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Pcdh19 35
  • 88.31 (n)
  • 96.36 (a)
(Monodelphis domestica)
Mammalia PCDH19 36
  • 82 (a)
(Ornithorhynchus anatinus)
Mammalia PCDH19 36
  • 76 (a)
(Gallus gallus)
Aves PCDH19 35
  • 78.48 (n)
  • 85.26 (a)
PCDH19 36
  • 85 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdh19 35
  • 72.25 (n)
  • 83.24 (a)
Str.16394 35
(Danio rerio)
Actinopterygii pcdh19 35
  • 68.35 (n)
  • 72.31 (a)
si:ch211-199f5.1 36
  • 32 (a)
Species with no ortholog for PCDH19:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PCDH19 Gene

Gene Tree for PCDH19 (if available)
Gene Tree for PCDH19 (if available)

Paralogs for PCDH19 Gene Pseudogenes for PCDH19 Gene

genes like me logo Genes that share paralogs with PCDH19: view

Variants for PCDH19 Gene

Sequence variations from dbSNP and Humsavar for PCDH19 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs871781 -- 100,360,835(-) ATGAA(A/G)TGATG intron-variant
rs915256 -- 100,378,415(-) AGAAC(C/T)GTATT intron-variant
rs915257 -- 100,312,161(+) ATTGG(A/G)TGGGA intron-variant
rs915258 -- 100,399,003(+) TCTGT(A/C)TTTCT intron-variant
rs915259 -- 100,399,162(+) AGAAC(A/T)ATGTA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PCDH19 Gene

Variant ID Type Subtype PubMed ID
esv2752340 CNV Gain 17911159
nsv7007 CNV Loss 18451855

Relevant External Links for PCDH19 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

PCR Panel Products

  • Copy Number PCR Panels: for PCDH19

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDH19 Gene

Disorders for PCDH19 Gene

(1) OMIM Diseases for PCDH19 Gene (300460)


  • Epileptic encephalopathy, early infantile, 9 (EIEE9) [MIM:300088]: A condition characterized by seizure with onset in infancy or early childhood, cognitive impairment, and delayed development of variable severity in some patients. Additional features include autistic signs and psychosis. The disorder is sex-limited, with the phenotype being restricted to females. {ECO:0000269 PubMed:18469813, ECO:0000269 PubMed:19214208, ECO:0000269 PubMed:19752159, ECO:0000269 PubMed:20713952, ECO:0000269 PubMed:20830798, ECO:0000269 PubMed:21053371, ECO:0000269 PubMed:21480887, ECO:0000269 PubMed:21519002, ECO:0000269 PubMed:22050978, ECO:0000269 PubMed:22267240}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(4) University of Copenhagen DISEASES for PCDH19 Gene

Relevant External Links for PCDH19

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with PCDH19: view

No data available for Novoseek inferred disease relationships and Genatlas for PCDH19 Gene

Publications for PCDH19 Gene

  1. Epilepsy and mental retardation limited to females with PCDH19 mutations can present de novo or in single generation families. (PMID: 19752159) Hynes K. … Scheffer I.E. (J. Med. Genet. 2010) 2 3 4 23 48
  2. X-linked protocadherin 19 mutations cause female-limited epilepsy and cognitive impairment. (PMID: 18469813) Dibbens L.M. … Gecz J. (Nat. Genet. 2008) 2 3 4 23
  3. Identification and characterization of three members of a novel subclass of protocadherins. (PMID: 11549318) Wolverton T. … Lalande M. (Genomics 2001) 2 3 4
  4. Sporadic infantile epileptic encephalopathy caused by mutations in PCDH19 resembles Dravet syndrome but mainly affects females. (PMID: 19214208) Depienne C. … Leguern E. (PLoS Genet. 2009) 3 4 48
  5. Protocadherin 19 mutations in girls with infantile-onset epilepsy. (PMID: 20713952) Marini C. … Guerrini R. (Neurology 2010) 3 4 48

Products for PCDH19 Gene

Sources for PCDH19 Gene

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