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Aliases for PCDH19 Gene

Aliases for PCDH19 Gene

  • Protocadherin 19 2 3 5
  • Epilepsy, Female Restricted, With Mental Retardation (Juberg-Hellman Syndrome) 2
  • Protocadherin-19 3
  • KIAA1313 4
  • EIEE9 3
  • EFMR 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 Dravet Syndrome. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH17.

UniProtKB/Swiss-Prot for PCDH19 Gene

  • Potential calcium-dependent cell-adhesion protein.

No data available for CIViC summary , 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

Enhancers for PCDH19 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XG100642 1.8 FANTOM5 Ensembl ENCODE dbSUPER 6.3 -236.7 -236740 8.9 TBP FOXA2 NFIB ARID4B DMAP1 RAD21 RARA YY1 SCRT2 FOS SYTL4 SRPX2 TSPAN6 CSTF2 PCDH19 GC0XP100679
GH0XG100615 0.7 ENCODE 6.8 -204.9 -204866 0.2 CTCF NFIA FEZF1 ZNF384 RAD21 RELA PRDM6 ZNF610 ZFP3 SMC3 PCDH19 LOC105373298 TNMD
GH0XG100314 0.8 FANTOM5 ENCODE 1.2 +94.1 94082 4.3 ZNF341 FOXP2 ZBTB7B TRIM28 ZNF18 PCDH19 PIR31157
GH0XG100416 0.4 ENCODE 0.4 -7.6 -7611 1.9 FOXP2 NR2F2 PCDH19 PIR46293
GH0XG100447 0.5 ENCODE 0.3 -37.9 -37861 0.7 ZNF263 CTCF ZNF143 RAD21 ZNF652 PIR46293 PCDH19
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PCDH19 on UCSC Golden Path with GeneCards custom track

Promoters for PCDH19 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000247575 -127 1200 ZNF777 SUZ12 ZNF133 CTBP1 POLR2A ZNF600 ZBTB20 EZH2 RNF2 ZNF398

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

Genes around PCDH19 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDH19 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Post-translational modifications for PCDH19 Gene

  • Glycosylation at Asn261, Asn420, posLast=485485, posLast=546546, posLast=570570, and Asn676
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDH19 Gene

No data available for DME Specific Peptides for PCDH19 Gene

Domains & Families for PCDH19 Gene

Gene Families for PCDH19 Gene

Suggested Antigen Peptide Sequences for PCDH19 Gene

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for PCDH19 Gene

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

Human Phenotype Ontology for PCDH19 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for PCDH19

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , 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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
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:0005887 integral component of plasma membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDH19: view

Pathways & Interactions for PCDH19 Gene

SuperPathways for PCDH19 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDH19 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IBA,IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007399 nervous system development IBA --
GO:0007420 brain development IEA --
genes like me logo Genes that share ontologies with PCDH19: view

No data available for Pathways by source and SIGNOR curated interactions for PCDH19 Gene

Drugs & Compounds for PCDH19 Gene

(4) Drugs for PCDH19 Gene - From: ClinicalTrials and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Anesthetics Pharma 9596
Central Nervous System Depressants Pharma 13403
Pregnanolone Pharma 20
calcium Nutra 0
genes like me logo Genes that share compounds with PCDH19: view

Transcripts for PCDH19 Gene

Unigene Clusters for PCDH19 Gene

Protocadherin 19:
Representative Sequences:

CRISPR Products

Inhibitory RNA 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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) (x5.8), Brain - Anterior cingulate cortex (BA24) (x5.7), Brain - Hypothalamus (x5.5), Brain - Hippocampus (x5.0), and Brain - Cortex (x4.4).

Protein differential expression in normal tissues from HIPED for PCDH19 Gene

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

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDH19 Gene

Protein tissue co-expression partners for PCDH19 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDH19 Gene:


SOURCE GeneReport for Unigene cluster for PCDH19 Gene:


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.

Evidence on tissue expression from TISSUES for PCDH19 Gene

  • Nervous system(4.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDH19 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
  • lower limb
  • upper limb
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with PCDH19: view

Primer 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
(Canis familiaris)
Mammalia PCDH19 35
  • 97 (a)
LOC492013 34
  • 91.2 (n)
(Pan troglodytes)
Mammalia PCDH19 34 35
  • 96.3 (n)
(Bos Taurus)
Mammalia PCDH19 34 35
  • 91.03 (n)
(Mus musculus)
Mammalia Pcdh19 34 16 35
  • 89.32 (n)
(Rattus norvegicus)
Mammalia Pcdh19 34
  • 88.31 (n)
(Monodelphis domestica)
Mammalia PCDH19 35
  • 82 (a)
(Ornithorhynchus anatinus)
Mammalia PCDH19 35
  • 76 (a)
(Gallus gallus)
Aves PCDH19 34 35
  • 78.48 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdh19 34
  • 72.25 (n)
Str.16394 34
(Danio rerio)
Actinopterygii pcdh19 34
  • 68.35 (n)
si:ch211-199f5.1 35
  • 32 (a)
Species where no ortholog for PCDH19 was found in the sources mined by GeneCards:
  • 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
rs132630323 Pathogenic, Epileptic encephalopathy, early infantile, 9 (EIEE9) [MIM:300088] 100,407,276(-) TACCG(A/T)GCTCA reference, missense
rs267606933 Pathogenic, Epileptic encephalopathy, early infantile, 9 (EIEE9) [MIM:300088] 100,406,927(-) GTCAA(C/G)GACAA reference, missense
rs587784299 Pathogenic, Epileptic encephalopathy, early infantile, 9 (EIEE9) [MIM:300088] 100,407,903(-) CTCCA(A/G/T)TGACA reference, missense
rs746274631 Epileptic encephalopathy, early infantile, 9 (EIEE9) [MIM:300088] 100,407,981(+) TTCGG(A/C)AGCTG reference, missense
rs753757730 Epileptic encephalopathy, early infantile, 9 (EIEE9) [MIM:300088] 100,408,027(+) CACCA(C/G)GAGTT reference, missense

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

Variant ID Type Subtype PubMed ID
esv2752340 CNV gain 17911159
esv3574250 CNV loss 25503493
nsv7007 CNV deletion 18451855
nsv953689 CNV deletion 24416366

Variation tolerance for PCDH19 Gene

Residual Variation Intolerance Score: 5.33% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.80; 47.54% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDH19 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for PCDH19 Gene

MalaCards: The human disease database

(9) MalaCards diseases for PCDH19 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
epileptic encephalopathy, early infantile, 9
  • early infantile epileptic encephalopathy 9
dravet syndrome
  • dravet syndrome, modifier of
pcdh19-related female-limited epilepsy
  • efmr
febrile infection-related epilepsy syndrome
  • acute encephalitis with refractory repetitive partial seizures
infantile epileptic encephalopathy
  • west syndrome
- elite association - COSMIC cancer census association via MalaCards


  • 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.

Relevant External Links for PCDH19

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with PCDH19: view

No data available for 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 22 46 64
  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 22 64
  3. Protocadherin 19 mutations in girls with infantile-onset epilepsy. (PMID: 20713952) Marini C. … Guerrini R. (Neurology 2010) 3 4 46 64
  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 46 64
  5. Identification and characterization of three members of a novel subclass of protocadherins. (PMID: 11549318) Wolverton T. … Lalande M. (Genomics 2001) 2 3 4 64

Products for PCDH19 Gene

Sources for PCDH19 Gene

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