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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. 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]

GeneCards Summary for PCDH19 Gene

PCDH19 (Protocadherin 19) is a Protein Coding gene. Diseases associated with PCDH19 include Epileptic Encephalopathy, Early Infantile, 9 and Childhood Absence Epilepsy. Gene Ontology (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.

Additional gene information for PCDH19 Gene

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

GeneHancer (GH) Regulatory Elements for PCDH19 Gene

Promoters and enhancers for PCDH19 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ100409 Promoter 1.5 EPDnew Ensembl 650.7 -0.1 -127 1.2 ZNF777 ZBTB6 SUZ12 ZNF133 ZNF335 CTBP1 POLR2A ZNF600 ZBTB20 ZNF16 PCDH19 ARL13A PIR46293
GH0XJ100632 Promoter 0.5 EPDnew 650.1 -222.3 -222269 0.1 PCDH19 TSPAN6 LOC105373298
GH0XJ100642 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 6.3 -236.7 -236740 8.9 FOXA2 ARID4B DMAP1 YY1 FOS RXRA SP5 REST PPARG NFIL3 SRPX2 SYTL4 TSPAN6 ARMCX4 CSTF2 PPIAP90 PCDH19 GC0XP100679
GH0XJ100615 Enhancer 0.6 ENCODE 6.8 -204.9 -204866 0.2 CTCF NFIA ZNF384 FEZF1 BATF RAD21 RELA PRDM6 ZNF610 ZFP3 PCDH19 LOC105373298 TNMD
GH0XJ100314 Enhancer 0.6 FANTOM5 ENCODE 1.2 +94.1 94082 4.3 ZNF341 FOXP2 PCDH19 PIR31157
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCDH19 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDH19 gene promoter:
  • E2F-2
  • E2F
  • E2F-1
  • AREB6
  • E2F-3a
  • E2F-4
  • E2F-5
  • IRF-2
  • CUTL1
  • HFH-1

Genomic Locations for PCDH19 Gene

Genomic Locations for PCDH19 Gene
118,630 bases
Minus strand
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 isoforms=2, 3676, Asn570, Asn546, Asn485, Asn420, and Asn261
  • 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

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains 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 Models for PCDH19 Gene

MGI Knock Outs for PCDH19:

Animal Model Products

  • Taconic Biosciences Mouse Models for PCDH19

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDH19

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

Subcellular locations from the

Human Protein Atlas (HPA)

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 IEA,IBA --
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: DrugBank, ClinicalTrials, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra Target 0
Anesthetics Pharma 10650
Central Nervous System Depressants Pharma 14508
Pregnanolone Pharma 23
genes like me logo Genes that share compounds with PCDH19: view

Transcripts for PCDH19 Gene

mRNA/cDNA for PCDH19 Gene

Unigene Clusters for PCDH19 Gene

Protocadherin 19:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDH19

Clone 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 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

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 34
  • 97 (a)
LOC492013 33
  • 91.2 (n)
(Pan troglodytes)
Mammalia PCDH19 34 33
  • 96.3 (n)
(Bos Taurus)
Mammalia PCDH19 34 33
  • 91.03 (n)
(Mus musculus)
Mammalia Pcdh19 16 34 33
  • 89.32 (n)
(Rattus norvegicus)
Mammalia Pcdh19 33
  • 88.31 (n)
(Monodelphis domestica)
Mammalia PCDH19 34
  • 82 (a)
(Ornithorhynchus anatinus)
Mammalia PCDH19 34
  • 76 (a)
(Gallus gallus)
Aves PCDH19 34 33
  • 78.48 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdh19 33
  • 72.25 (n)
Str.16394 33
(Danio rerio)
Actinopterygii pcdh19 33
  • 68.35 (n)
si:ch211-199f5.1 34
  • 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)
Evolutionary constrained regions (ECRs) for PCDH19: view image

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 Variation AA Info Type
rs1002430549 likely-benign, Early infantile epileptic encephalopathy 9 100,408,433(-) G/C coding_sequence_variant, synonymous_variant
rs1057521256 likely-benign, likely-pathogenic, not specified, Early infantile epileptic encephalopathy 9, not provided 100,406,783(-) G/A/C coding_sequence_variant, stop_gained, synonymous_variant
rs1060502175 pathogenic, Early infantile epileptic encephalopathy 9 100,402,799(-) TTTTTTT/TTTTTT coding_sequence_variant, frameshift
rs1060502176 uncertain-significance, likely-pathogenic, Early infantile epileptic encephalopathy 9, not provided 100,407,891(-) G/C coding_sequence_variant, missense_variant
rs1060502177 uncertain-significance, Early infantile epileptic encephalopathy 9 100,407,120(-) A/T coding_sequence_variant, missense_variant

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

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

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)

Additional Variant Information 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

(11) MalaCards diseases for PCDH19 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- 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, ECO:0000269 PubMed:25818041, ECO:0000269 PubMed:26993267}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PCDH19

Genetic Association Database
Human Genome Epidemiology 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 IE (Journal of medical genetics 2010) 2 3 4 22 44 58
  2. X-linked protocadherin 19 mutations cause female-limited epilepsy and cognitive impairment. (PMID: 18469813) Dibbens LM … Gécz J (Nature genetics 2008) 2 3 4 22 58
  3. Protocadherin 19 mutations in girls with infantile-onset epilepsy. (PMID: 20713952) Marini C … Guerrini R (Neurology 2010) 3 4 44 58
  4. Sporadic infantile epileptic encephalopathy caused by mutations in PCDH19 resembles Dravet syndrome but mainly affects females. (PMID: 19214208) Depienne C … Leguern E (PLoS genetics 2009) 3 4 44 58
  5. Identification and characterization of three members of a novel subclass of protocadherins. (PMID: 11549318) Wolverton T … Lalande M (Genomics 2001) 2 3 4 58

Products for PCDH19 Gene

Sources for PCDH19 Gene

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