PCDH18 Gene (Protein Coding)

Protocadherin 18

GC04M137518
GIFtS:
37
This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. This gene encodes a protein which contains 6 extracellular cadherin domains, a transmembrane domain and a cytoplasmic tail differing from those of the classical cadherins. Although its specific function is undetermined, the cadherin-related neuronal receptor is thought to play a role in... See more...

Aliases for PCDH18 Gene

Aliases for PCDH18 Gene

  • Protocadherin 18 2 3 5
  • Protocadherin-18 3 4
  • KIAA1562 2 4
  • PCDH68L 2 3
  • Protocadherin 68-Like Protein 3
  • PCDH18 5

External Ids for PCDH18 Gene

Previous GeneCards Identifiers for PCDH18 Gene

  • GC04U990099
  • GC04M9M0022
  • GC04M138798
  • GC04M138660
  • GC04M138440
  • GC04M134169

Summaries for PCDH18 Gene

Entrez Gene Summary for PCDH18 Gene

  • This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. This gene encodes a protein which contains 6 extracellular cadherin domains, a transmembrane domain and a cytoplasmic tail differing from those of the classical cadherins. Although its specific function is undetermined, the cadherin-related neuronal receptor is thought to play a role in the establishment and function of specific cell-cell connections in the brain. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDH18 Gene

PCDH18 (Protocadherin 18) is a Protein Coding gene. Diseases associated with PCDH18 include Patent Foramen Ovale. 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 PCDH18 Gene

Gene Wiki entry for PCDH18 Gene

Additional gene information for PCDH18 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCDH18 Gene

Genomics for PCDH18 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PCDH18 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
GH04J137527 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +2.1 2083 8.1 CTCF PRDM10 PRDM1 PATZ1 ZNF341 PKNOX1 CEBPB FOXA2 ZBTB17 ZFHX2 PCDH18 piR-50399-022
GH04J137609 Enhancer 0.6 ENCODE CraniofacialAtlas 11.2 -77.8 -77819 2 CTCF NR2F2 ETS1 RAD21 NANOG POLR2A PCDH18 ENSG00000280352 RF00017-4415 LOC101927414 SLC7A11
GH04J137614 Enhancer 0.4 ENCODE 9.5 -82.2 -82172 0.2 FOXA1 CTBP1 FOXA2 SIX4 PCDH18 RF00017-4415 ENSG00000280352 LOC101927414 SLC7A11
GH04J137310 Enhancer 0.8 Ensembl ENCODE CraniofacialAtlas 4.5 +221.8 221788 2.3 JUND ZNF10 FOS POLR2A LINC02511 PCDH18 lnc-NOCT-17
GH04J137612 Enhancer 0.3 CraniofacialAtlas 9.5 -79.8 -79817 0.6 POLR2A PCDH18 ENSG00000280352 RF00017-4415 LOC101927414 SLC7A11
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDH18 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCDH18

Top Transcription factor binding sites by QIAGEN in the PCDH18 gene promoter:
  • AREB6
  • CUTL1
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • POU2F1
  • POU2F1a

Genomic Locations for PCDH18 Gene

Genomic Locations for PCDH18 Gene
chr4:137,518,918-137,532,530
(GRCh38/hg38)
Size:
13,613 bases
Orientation:
Minus strand
chr4:138,440,072-138,453,648
(GRCh37/hg19)
Size:
13,577 bases
Orientation:
Minus strand

Genomic View for PCDH18 Gene

Genes around PCDH18 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDH18 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDH18 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PCDH18 Gene

Proteins for PCDH18 Gene

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  • Protein details for PCDH18 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HCL0-PCD18_HUMAN
    Recommended name:
    Protocadherin-18
    Protein Accession:
    Q9HCL0
    Secondary Accessions:
    • A8K7K3
    • B7ZKT1
    • Q52LS2

    Protein attributes for PCDH18 Gene

    Size:
    1135 amino acids
    Molecular mass:
    126149 Da
    Quaternary structure:
    • Interacts with DAB1.
    SequenceCaution:
    • Sequence=BAB13388.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PCDH18 Gene

    Alternative splice isoforms for PCDH18 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDH18 Gene

Protein Expression for PCDH18 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PCDH18 Gene

  • Glycosylation at Asn103, Asn269, Asn420, Asn559, Asn583, and Asn641
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDH18 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Boster Bio Antibodies for PCDH18

No data available for DME Specific Peptides for PCDH18 Gene

Domains & Families for PCDH18 Gene

Gene Families for PCDH18 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for PCDH18 Gene

InterPro:
Blocks:
  • Cadherin
ProtoNet:

Suggested Antigen Peptide Sequences for PCDH18 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ57393, highly similar to Protocadherin-18 (B4DLR6_HUMAN)
  • cDNA FLJ57555, highly similar to Protocadherin-18 (B4DQ29_HUMAN)
  • Protocadherin-18 (PCD18_HUMAN)
genes like me logo Genes that share domains with PCDH18: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PCDH18 Gene

Function for PCDH18 Gene

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  2. CRISPR
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  6. Cell Line

Molecular function for PCDH18 Gene

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

Phenotypes From GWAS Catalog for PCDH18 Gene

Gene Ontology (GO) - Molecular Function for PCDH18 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDH18: view
genes like me logo Genes that share phenotypes with PCDH18: view

Animal Models for PCDH18 Gene

MGI Knock Outs for PCDH18:
  • Pcdh18 Pcdh18<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDH18

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for PCDH18 Gene

Localization for PCDH18 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDH18 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 PCDH18 gene
Compartment Confidence
plasma membrane 4
extracellular 2
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
peroxisome 0
cytosol 0
lysosome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCDH18 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 PCDH18: view

Pathways & Interactions for PCDH18 Gene

PathCards logo

SuperPathways for PCDH18 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDH18 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:0007399 nervous system development IEA --
GO:0007420 brain development ISS --
genes like me logo Genes that share ontologies with PCDH18: view

No data available for Pathways by source and SIGNOR curated interactions for PCDH18 Gene

Drugs & Compounds for PCDH18 Gene

Products:

  1. Drug

(1) Drugs for PCDH18 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6556
genes like me logo Genes that share compounds with PCDH18: view

Transcripts for PCDH18 Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for PCDH18 Gene

2 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
8 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 PCDH18

Alternative Splicing Database (ASD) splice patterns (SP) for PCDH18 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c
SP1: - - - -
SP2: - - - - -
SP3: -
SP4:
SP5: -
SP6: - -
SP7:

Relevant External Links for PCDH18 Gene

GeneLoc Exon Structure for
PCDH18

Expression for PCDH18 Gene

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  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCDH18 Gene

mRNA expression in normal human tissues for PCDH18 Gene
mRNA expression by GTEx for PCDH18 GenemRNA expression by BioGPS for PCDH18 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PCDH18 Gene

This gene is overexpressed in Plasma (66.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCDH18 Gene



Protein tissue co-expression partners for PCDH18 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCDH18

SOURCE GeneReport for Unigene cluster for PCDH18 Gene:

Hs.591691

mRNA Expression by UniProt/SwissProt for PCDH18 Gene:

Q9HCL0-PCD18_HUMAN
Tissue specificity: Expressed in all tissues, with highest expression in lung and ovary.

Evidence on tissue expression from TISSUES for PCDH18 Gene

  • Heart(5)
  • Liver(5)
  • Lung(5)
  • Nervous system(5)
  • Intestine(4.8)
  • Blood(4.4)
  • Spleen(4.1)
  • Pancreas(3.9)
genes like me logo Genes that share expression patterns with PCDH18: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDH18 Gene

Orthologs for PCDH18 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDH18 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia PCDH18 30 31
  • 99.74 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia PCDH18 31
  • 93 (a)
 OneToOne
Cow
(Bos Taurus)
 Mammalia PCDH18 30 31
  • 92.68 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Pcdh18 30 17 31
  • 86.92 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Pcdh18 30
  • 86.73 (n)
Dog
(Canis familiaris)
 Mammalia PCDH18 30 31
  • 82.19 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia PCDH18 31
  • 52 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves PCDH18 30 31
  • 78.96 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia PCDH18 31
  • 83 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia pcdh18 30
  • 73.88 (n)
Zebrafish
(Danio rerio)
 Actinopterygii pcdh18a 31
  • 68 (a)
 OneToMany
pcdh18b 31
  • 67 (a)
 OneToMany
Dr.19441 30
Species where no ortholog for PCDH18 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)
  • 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 PCDH18 Gene

ENSEMBL:
Gene Tree for PCDH18 (if available)
TreeFam:
Gene Tree for PCDH18 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCDH18: view image

Paralogs for PCDH18 Gene

Paralogs for PCDH18 Gene

(69) SIMAP similar genes for PCDH18 Gene using alignment to 5 proteins:

  • PCD18_HUMAN
  • B4DLR6_HUMAN
  • B4DQ29_HUMAN
  • D6RIG4_HUMAN
  • L8ECI2_HUMAN
genes like me logo Genes that share paralogs with PCDH18: view

Variants for PCDH18 Gene

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Additional dbSNP identifiers (rs#s) for PCDH18 Gene

Structural Variations from Database of Genomic Variants (DGV) for PCDH18 Gene

Variant ID Type Subtype PubMed ID
nsv516176 CNV gain+loss 19592680
nsv595521 CNV loss 21841781
nsv595576 CNV loss 21841781

Variation tolerance for PCDH18 Gene

Residual Variation Intolerance Score: 4.75% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.92; 48.95% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDH18 Gene

Human Gene Mutation Database (HGMD)
PCDH18
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDH18

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCDH18 Gene

Disorders for PCDH18 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PCDH18 Gene - From: DISEASES

Disorder Aliases PubMed IDs
patent foramen ovale
  • atrial septal defect within oval fossa
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDH18

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 PCDH18: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDH18 Gene

Publications for PCDH18 Gene

  1. Identification and characterization of three members of a novel subclass of protocadherins. (PMID: 11549318) Wolverton T … Lalande M (Genomics 2001) 2 3 4 23
  2. Disabled-1 interacts with a novel developmentally regulated protocadherin. (PMID: 11716507) Homayouni R … Curran T (Biochemical and biophysical research communications 2001) 3 23
  3. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10997877) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 3 4
  4. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. (PMID: 10835267) Nollet F … van Roy F (Journal of molecular biology 2000) 2 3
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

ExternalLinks

View latest publications for PCDH18 gene in Mastermind

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