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Aliases for PCDHA13 Gene

Aliases for PCDHA13 Gene

  • Protocadherin Alpha 13 2 3 5
  • Ortholog Of Mouse CNR5 2 3
  • KIAA0345-Like 1 2 3
  • PCDH-Alpha-13 3 4
  • CNRS5 3 4
  • Protocadherin Alpha-13 3
  • PCDH-ALPHA13 3
  • CNRN5 3
  • CRNR5 3
  • CNR5 3

External Ids for PCDHA13 Gene

Previous HGNC Symbols for PCDHA13 Gene

  • CNRS5

Previous GeneCards Identifiers for PCDHA13 Gene

  • GC05P140078
  • GC05P140760
  • GC05P140205
  • GC05P140198
  • GC05P140169
  • GC05P140242
  • GC05P140251
  • GC05P140260
  • GC05P140270
  • GC05P140279
  • GC05P140289
  • GC05P140300
  • GC05P140309
  • GC05P140330
  • GC05P140337
  • GC05P135406
  • GC05P140353
  • GC05P140374
  • GC05P140393
  • GC05P140407
  • GC05P140423
  • GC05P140440
  • GC05P140458
  • GC05P141436
  • GC05P141571
  • GC05P141673
  • GC05P141774
  • GC05P141875
  • GC05P141983
  • GC05P142084

Summaries for PCDHA13 Gene

Entrez Gene Summary for PCDHA13 Gene

  • This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDHA13 Gene

PCDHA13 (Protocadherin Alpha 13) is a Protein Coding gene. Diseases associated with PCDHA13 include Protocadherin-Alpha Gene Cluster. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHA3.

UniProtKB/Swiss-Prot for PCDHA13 Gene

  • Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

Additional gene information for PCDHA13 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHA13 Gene

Genomics for PCDHA13 Gene

GeneHancer (GH) Regulatory Elements for PCDHA13 Gene

Promoters and enhancers for PCDHA13 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
GH05I140883 Promoter 0.8 EPDnew 550.8 0.0 -11 0.1 CTCF CREB1 SIN3A ZBTB33 FOS RAD21 ENSG00000278901 PCDHA13 ENSG00000278915 PCDHA12 PCDHA11 PCDHA10 PCDHA9 PCDHA8 PCDHA7 PCDHA6
GH05I140882 Enhancer 0.5 ENCODE 550.8 +0.5 493 0.1 ZNF217 CTCF GATA3 MNT REST CUX1 ENSG00000278901 PCDHA13 PCDHA12 PCDHA11 PCDHA10 PCDHA9 PCDHA8 PCDHAC1 PCDHA7 PCDHA6
GH05I140965 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 16.8 +84.3 84308 1.3 SIN3A ZNF335 GLIS2 ZNF366 ZNF143 SP3 ZNF398 REST ZFP69B ZNF217 ENSG00000279028 PCDHAC2 PCDHA11 PCDHA13 PCDHACT PCDHAC1 PCDHA12 PCDHA10 PCDHA8 PCDHA9
GH05I141725 Enhancer 0.6 ENCODE 6.4 +843.9 843866 1.4 GTF3C2 SCRT1 MAFF POLR3A SCRT2 MAX RCOR1 CHD2 NFE2L2 PCDH1 PCDHA13 ARAP3 ENSG00000278925
GH05I140943 Enhancer 0.2 FANTOM5 3.9 +61.2 61179 0.1 PCDHA13 PCDHA3 PCDHGA6 PCDHA2 PCDHA1 PCDHAC2 PCDHA7 PCDHA4 PCDHA5 PCDHB15
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCDHA13 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHA13 gene promoter:

Genomic Locations for PCDHA13 Gene

Genomic Locations for PCDHA13 Gene
130,137 bases
Plus strand

Genomic View for PCDHA13 Gene

Genes around PCDHA13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHA13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHA13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHA13 Gene

Proteins for PCDHA13 Gene

  • Protein details for PCDHA13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin alpha-13
    Protein Accession:
    Secondary Accessions:
    • O75277

    Protein attributes for PCDHA13 Gene

    950 amino acids
    Molecular mass:
    102483 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHA13 Gene


neXtProt entry for PCDHA13 Gene

Post-translational modifications for PCDHA13 Gene

  • Glycosylation at isoforms=2257, isoforms=2265, and isoforms=2548
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHA13 Gene

No data available for DME Specific Peptides for PCDHA13 Gene

Domains & Families for PCDHA13 Gene

Gene Families for PCDHA13 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for PCDHA13 Gene

Suggested Antigen Peptide Sequences for PCDHA13 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHA13: view

No data available for UniProtKB/Swiss-Prot for PCDHA13 Gene

Function for PCDHA13 Gene

Molecular function for PCDHA13 Gene

UniProtKB/Swiss-Prot Function:
Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

Gene Ontology (GO) - Molecular Function for PCDHA13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHA13: view
genes like me logo Genes that share phenotypes with PCDHA13: view

Animal Model Products

miRNA for PCDHA13 Gene

miRTarBase miRNAs that target PCDHA13

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHA13 Gene

Localization for PCDHA13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHA13 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 PCDHA13 gene
Compartment Confidence
plasma membrane 3

Gene Ontology (GO) - Cellular Components for PCDHA13 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 PCDHA13: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PCDHA13 Gene

Pathways & Interactions for PCDHA13 Gene

SuperPathways for PCDHA13 Gene

No Data Available

Interacting Proteins for PCDHA13 Gene

Gene Ontology (GO) - Biological Process for PCDHA13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IBA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007399 nervous system development IBA --
genes like me logo Genes that share ontologies with PCDHA13: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHA13 Gene

Drugs & Compounds for PCDHA13 Gene

(1) Drugs for PCDHA13 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with PCDHA13: view

Transcripts for PCDHA13 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHA13 Gene

No ASD Table

Relevant External Links for PCDHA13 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHA13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHA13 Gene

mRNA differential expression in normal tissues according to GTEx for PCDHA13 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x7.4) and Brain - Cerebellum (x4.7).

Protein differential expression in normal tissues from HIPED for PCDHA13 Gene

This gene is overexpressed in Tlymphocyte (49.6) and Heart (19.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PCDHA13 Gene

Protein tissue co-expression partners for PCDHA13 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDHA13 Gene:


Evidence on tissue expression from TISSUES for PCDHA13 Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with PCDHA13: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHA13 Gene

Orthologs for PCDHA13 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHA13 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia PCDHA13 33 34
  • 87.37 (n)
(Mus musculus)
Mammalia Pcdha12 33 16
  • 83.68 (n)
(Rattus norvegicus)
Mammalia Pcdha13 33
  • 82.98 (n)
(Canis familiaris)
Mammalia -- 34
  • 74 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 68 (a)
-- 34
  • 68 (a)
-- 34
  • 67 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 64 (a)
(Gallus gallus)
Aves PCDHA11 34
  • 53 (a)
-- 34
  • 47 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 58 (a)
-- 34
  • 57 (a)
-- 34
  • 57 (a)
-- 34
  • 57 (a)
-- 34
  • 57 (a)
-- 34
  • 56 (a)
-- 34
  • 56 (a)
-- 34
  • 56 (a)
-- 34
  • 56 (a)
-- 34
  • 56 (a)
-- 34
  • 56 (a)
-- 34
  • 55 (a)
-- 34
  • 55 (a)
-- 34
  • 53 (a)
-- 34
  • 52 (a)
-- 34
  • 50 (a)
(Danio rerio)
Actinopterygii pcdh2ab1 34
  • 43 (a)
pcdh2ab12 34
  • 43 (a)
pcdh2ab8 34
  • 43 (a)
CR847851.6 34
  • 42 (a)
CR847851.8 34
  • 42 (a)
CT573264.4 34
  • 42 (a)
CT573264.5 34
  • 42 (a)
pcdh1a6 34
  • 42 (a)
pcdh2ab11 34
  • 42 (a)
pcdh2ab2 34 34
  • 42 (a)
pcdh2ab3 34
  • 42 (a)
pcdh2ab6 34
  • 42 (a)
pcdh2ab7 34
  • 42 (a)
pcdh2ab10 34
  • 41 (a)
pcdh2ab9 34
  • 41 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 33 (a)
CSA.7308 34
  • 20 (a)
Species where no ortholog for PCDHA13 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)
  • chimpanzee (Pan troglodytes)
  • 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 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PCDHA13 Gene

Gene Tree for PCDHA13 (if available)
Gene Tree for PCDHA13 (if available)

Paralogs for PCDHA13 Gene

Variants for PCDHA13 Gene

Sequence variations from dbSNP and Humsavar for PCDHA13 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs150254638 uncertain-significance, Hirschsprung disease 1 140,978,974(+) G/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs386352346 uncertain-significance, not provided 140,929,288(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000122176 -- 140,965,777(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000158608 -- 140,908,533(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000222500 -- 140,957,863(+) T/G genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHA13 Gene

Variant ID Type Subtype PubMed ID
esv2505753 CNV deletion 19546169
esv2759382 CNV gain 17122850
esv3606959 CNV gain 21293372
nsv1031849 CNV loss 25217958
nsv10754 CNV gain 18304495
nsv599904 CNV loss 21841781
nsv823264 CNV gain 20364138
nsv968252 CNV duplication 23825009
nsv968992 CNV duplication 23825009

Variation tolerance for PCDHA13 Gene

Residual Variation Intolerance Score: 42% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.51; 43.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHA13 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 PCDHA13 Gene

Disorders for PCDHA13 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PCDHA13 Gene - From: HGMD and GeneCards

Disorder Aliases PubMed IDs
protocadherin-alpha gene cluster
  • pcdha@
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDHA13

genes like me logo Genes that share disorders with PCDHA13: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDHA13 Gene

Publications for PCDHA13 Gene

  1. A striking organization of a large family of human neural cadherin-like cell adhesion genes. (PMID: 10380929) Wu Q … Maniatis T (Cell 1999) 2 3 4 58
  2. The DNA sequence and comparative analysis of human chromosome 5. (PMID: 15372022) Schmutz J … Rubin EM (Nature 2004) 3 4 58
  3. Genomic organization of the family of CNR cadherin genes in mice and humans. (PMID: 10662547) Sugino H … Yagi T (Genomics 2000) 2 3 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. (PMID: 22589738) Fox CS … Borecki IB (PLoS genetics 2012) 3 58

Products for PCDHA13 Gene

Sources for PCDHA13 Gene

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