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 epi... See more...

Aliases for PCDH19 Gene

Aliases for PCDH19 Gene

  • Protocadherin 19 2 3 5
  • Protocadherin-19 3 4
  • KIAA1313 2 4
  • EIEE9 2 3
  • Epilepsy, Female Restricted, With Mental Retardation (Juberg-Hellman Syndrome) 2
  • PCDH19 5
  • 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 Summary for PCDH19 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCDH19 Gene

Genomics for PCDH19 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PCDH19 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ100403 Promoter 1.5 EPDnew Ensembl CraniofacialAtlas 606.2 +2.8 2773 7.8 TARDBP PRDM1 ZSCAN4 POLR2A EZH2 ZNF600 ZNF341 ZBTB20 ZNF512B RAD21 PCDH19 ARL13A MN298708
GH0XJ100632 Promoter 0.3 EPDnew 600.1 -222.3 -222269 0.1 PCDH19 lnc-SYTL4-2 TSPAN6 LOC105373298 TNMD
GH0XJ100642 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 6.3 -236.7 -236740 8.9 GATAD2A ZNF629 REST SOX13 PRDM1 RBFOX2 RXRB IRF2 SP1 GABPA SRPX2 SYTL4 TSPAN6 ARMCX4 CSTF2 PPIAP90 PCDH19 HSALNG0139159 lnc-TSPAN6-1 RF00017-8584
GH0XJ100635 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 4.6 -226.0 -226028 2.6 CTCF PRDM10 GABPA PRDM1 RBFOX2 POLR2A ZNF600 CEBPA TAF1 SP1 TSPAN6 lnc-SYTL4-2 PCDH19 LOC105373298 TNMD
GH0XJ100379 Enhancer 0.5 Ensembl 12.8 +30.7 30672 1.6 CREB1 CTCF ZSCAN4 RAD21 SMC3 ZNF217 GATA3 ZNF654 ATF2 PCDH19 piR-57461-304 piR-31937-286
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDH19 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCDH19

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

Genomic Locations for PCDH19 Gene

Genomic Locations for PCDH19 Gene
chrX:100,291,644-100,410,273
(GRCh38/hg38)
Size:
118,630 bases
Orientation:
Minus strand
chrX:99,546,642-99,665,271
(GRCh37/hg19)
Size:
118,630 bases
Orientation:
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:
    Q8TAB3-PCD19_HUMAN
    Recommended name:
    Protocadherin-19
    Protein Accession:
    Q8TAB3
    Secondary Accessions:
    • B0LDS4
    • E9PAM6
    • Q5JTG1
    • Q5JTG2
    • Q68DT7
    • Q9P2N3

    Protein attributes for PCDH19 Gene

    Size:
    1148 amino acids
    Molecular mass:
    126253 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=CAH18133.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PCDH19 Gene

    Alternative splice isoforms for PCDH19 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDH19 Gene

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 & Families for PCDH19 Gene

Gene Families for PCDH19 Gene

HGNC:
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

GenScript: Design optimal peptide antigens:
  • cDNA FLJ39272 fis, clone OCBBF2010709, highly similar to Protocadherin-19 (B3KU71_HUMAN)
  • Protocadherin-19 (PCD19_HUMAN)
genes like me logo Genes that share domains with PCDH19: view

No data available for Graphical View of Domain Structure and 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

COMPARTMENTS
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 4
extracellular 2
cytoskeleton 1
mitochondrion 1
nucleus 1
cytosol 1
endoplasmic reticulum 0

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 21873635
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

PathCards logo

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 21873635
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
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

(1) Drugs for PCDH19 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra Target 6556
genes like me logo Genes that share compounds with PCDH19: view

Transcripts for PCDH19 Gene

mRNA/cDNA for PCDH19 Gene

3 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

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
PCDH19

Expression for PCDH19 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCDH19

SOURCE GeneReport for Unigene cluster for PCDH19 Gene:

Hs.4993

mRNA Expression by UniProt/SwissProt for PCDH19 Gene:

Q8TAB3-PCD19_HUMAN
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
Systems:
  • nervous
  • skeletal muscle
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
Limb:
  • lower limb
  • upper limb
General:
  • 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
Dog
(Canis familiaris)
Mammalia PCDH19 31
  • 97 (a)
OneToOne
LOC492013 30
  • 91.2 (n)
Chimpanzee
(Pan troglodytes)
Mammalia PCDH19 30 31
  • 96.3 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PCDH19 30 31
  • 91.03 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Pcdh19 30 17 31
  • 89.32 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Pcdh19 30
  • 88.31 (n)
Oppossum
(Monodelphis domestica)
Mammalia PCDH19 31
  • 82 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PCDH19 31
  • 76 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PCDH19 30 31
  • 78.48 (n)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia pcdh19 30
  • 72.25 (n)
Str.16394 30
Zebrafish
(Danio rerio)
Actinopterygii pcdh19 30
  • 68.35 (n)
si:ch211-199f5.1 31
  • 32 (a)
ManyToMany
Species where no ortholog for PCDH19 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

ENSEMBL:
Gene Tree for PCDH19 (if available)
TreeFam:
Gene Tree for PCDH19 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCDH19: view image

Paralogs for PCDH19 Gene

Pseudogenes.org Pseudogenes for PCDH19 Gene

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

Variants for PCDH19 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCDH19 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
206336 Uncertain Significance: Early infantile epileptic encephalopathy 9 100,406,941(-) T/C MISSENSE_VARIANT
635312 Uncertain Significance: Early infantile epileptic encephalopathy 9 100,407,456(-) T/C MISSENSE_VARIANT
637972 Likely Pathogenic: Early infantile epileptic encephalopathy 9 100,406,915(-) CG/C FRAMESHIFT_VARIANT
639503 Uncertain Significance: Early infantile epileptic encephalopathy 9 100,402,660(-) C/T MISSENSE_VARIANT
639643 Pathogenic: Early infantile epileptic encephalopathy 9; not provided 100,408,465(-) CT/C FRAMESHIFT_VARIANT

Additional dbSNP identifiers (rs#s) for PCDH19 Gene

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)

Additional Variant Information for PCDH19 Gene

Human Gene Mutation Database (HGMD)
PCDH19
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDH19

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

Disorders for PCDH19 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
epileptic encephalopathy, early infantile, 9
  • eiee9
childhood absence epilepsy
  • absence seizure
epileptic encephalopathy, early infantile, 6
  • ds
strabismus
  • strabismus, susceptibility to
encephalopathy
  • brain diseases
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

PCD19_HUMAN
  • 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
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 23 41
  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 23
  3. Protocadherin 19 mutations in girls with infantile-onset epilepsy. (PMID: 20713952) Marini C … Guerrini R (Neurology 2010) 3 4 41
  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 41
  5. Identification and characterization of three members of a novel subclass of protocadherins. (PMID: 11549318) Wolverton T … Lalande M (Genomics 2001) 2 3 4

Products for PCDH19 Gene

Sources for PCDH19 Gene