Free for academic non-profit institutions. Other users need a Commercial license

Aliases for PCDHB13 Gene

Aliases for PCDHB13 Gene

  • Protocadherin Beta 13 2 3 5
  • Protocadherin Beta-13 3
  • PCDH-Beta-13 4
  • PCDH-BETA13 3

External Ids for PCDHB13 Gene

Previous GeneCards Identifiers for PCDHB13 Gene

  • GC05P140409
  • GC05P141176
  • GC05P140576
  • GC05P140623
  • GC05P140624
  • GC05P140573
  • GC05P140657
  • GC05P140662
  • GC05P135738
  • GC05P140668
  • GC05P140673
  • GC05P140678
  • GC05P140684
  • GC05P140694
  • GC05P141285
  • GC05P141366
  • GC05P141426
  • GC05P141511
  • GC05P141617
  • GC05P141720
  • GC05P141819
  • GC05P141918
  • GC05P142026
  • GC05P142134

Summaries for PCDHB13 Gene

Entrez Gene Summary for PCDHB13 Gene

  • This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDHB13 Gene

PCDHB13 (Protocadherin Beta 13) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB8.

UniProtKB/Swiss-Prot for PCDHB13 Gene

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

Gene Wiki entry for PCDHB13 Gene

Additional gene information for PCDHB13 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHB13 Gene

Genomics for PCDHB13 Gene

GeneHancer (GH) Regulatory Elements for PCDHB13 Gene

Promoters and enhancers for PCDHB13 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
GH05J141968 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 16.6 +755.6 755648 3 CLOCK DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 NFYC GLIS1 RNF14 PCDH12 LOC102723915 HDAC3 PCDHB18P PCDHGA6 PCDHGA7 DELE1 PCDHGA5 ENSG00000271871
GH05J140717 Promoter/Enhancer 1.6 Ensembl ENCODE 20.4 -494.8 -494783 2.7 MLX IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 SP3 PPARGC1A MEF2D GC05P142304 VTRNA1-2 ANKHD1 PURA HARS2 PCDHB18P PCDHB19P HDAC3 WDR55 PCDHGA6
GH05J141868 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.8 +660.5 660491 11 PKNOX1 FOXA2 ARID4B SIN3A YBX1 ZNF2 ZBTB7B IRF4 YY1 ZNF766 PCDH1 GC05P142308 MRPL11P2 PCDHB19P PCDHB5 PCDHB12 PCDHB3 PCDHB11 DELE1 HDAC3
GH05J141563 Enhancer 1.4 Ensembl ENCODE dbSUPER 12 +350.5 350494 1.4 FOXA2 PKNOX1 ARNT SIN3A DMAP1 ZNF2 IRF4 YY1 ZNF213 ZNF207 HARS2 IK PCDHB8 PCDHB3 PCDHA6 PCDHB9 PCDHB7 ENSG00000272108 PCDHB15 PCDHGC3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHB13 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHB13 gene promoter:
  • HEN1
  • GR
  • PPAR-alpha
  • Arnt
  • AhR
  • GR-beta
  • GR-alpha
  • E47
  • LUN-1

Genomic Locations for PCDHB13 Gene

Genomic Locations for PCDHB13 Gene
5,061 bases
Plus strand
3,485 bases
Plus strand

Genomic View for PCDHB13 Gene

Genes around PCDHB13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHB13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHB13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHB13 Gene

Proteins for PCDHB13 Gene

  • Protein details for PCDHB13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin beta-13
    Protein Accession:
    Secondary Accessions:
    • A8K9V6

    Protein attributes for PCDHB13 Gene

    798 amino acids
    Molecular mass:
    87552 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PCDHB13 Gene

Post-translational modifications for PCDHB13 Gene

  • Glycosylation at Asn567, Asn463, isoforms=436, and isoforms=418
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHB13 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHB13 Gene

Domains & Families for PCDHB13 Gene

Gene Families for PCDHB13 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted membrane proteins

Protein Domains for PCDHB13 Gene

Suggested Antigen Peptide Sequences for PCDHB13 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHB13: view

No data available for UniProtKB/Swiss-Prot for PCDHB13 Gene

Function for PCDHB13 Gene

Molecular function for PCDHB13 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 PCDHB13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHB13: view
genes like me logo Genes that share phenotypes with PCDHB13: view

Animal Model Products

  • Taconic Biosciences Mouse Models for PCDHB13

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHB13

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHB13 Gene

Localization for PCDHB13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHB13 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 PCDHB13 gene
Compartment Confidence
plasma membrane 5
extracellular 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for PCDHB13 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 NAS 11322959
genes like me logo Genes that share ontologies with PCDHB13: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PCDHB13 Gene

Pathways & Interactions for PCDHB13 Gene

SuperPathways for PCDHB13 Gene

No Data Available

Interacting Proteins for PCDHB13 Gene

Gene Ontology (GO) - Biological Process for PCDHB13 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:0007268 chemical synaptic transmission TAS 12231349
GO:0007416 synapse assembly TAS 12231349
genes like me logo Genes that share ontologies with PCDHB13: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHB13 Gene

Drugs & Compounds for PCDHB13 Gene

(1) Drugs for PCDHB13 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 PCDHB13: view

Transcripts for PCDHB13 Gene

mRNA/cDNA for PCDHB13 Gene

(1) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(30) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PCDHB13 Gene

Protocadherin beta 13:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHB13

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHB13 Gene

No ASD Table

Relevant External Links for PCDHB13 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHB13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHB13 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDHB13 Gene:


SOURCE GeneReport for Unigene cluster for PCDHB13 Gene:


Evidence on tissue expression from TISSUES for PCDHB13 Gene

  • Lung(4)
  • Nervous system(2.3)
genes like me logo Genes that share expression patterns with PCDHB13: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHB13 Gene

Orthologs for PCDHB13 Gene

This gene was present in the common ancestor of mammals.

Orthologs for PCDHB13 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDHB13 34 33
  • 98.58 (n)
(Bos Taurus)
Mammalia -- 34
  • 82 (a)
(Mus musculus)
Mammalia Pcdhb16 34
  • 74 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 64 (a)
-- 34
  • 64 (a)
-- 34
  • 64 (a)
-- 34
  • 64 (a)
-- 34
  • 64 (a)
-- 34
  • 64 (a)
-- 34
  • 64 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 63 (a)
-- 34
  • 63 (a)
-- 34
  • 60 (a)
Species where no ortholog for PCDHB13 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)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • 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)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for PCDHB13 Gene

Gene Tree for PCDHB13 (if available)
Gene Tree for PCDHB13 (if available)
Evolutionary constrained regions (ECRs) for PCDHB13: view image

Paralogs for PCDHB13 Gene

genes like me logo Genes that share paralogs with PCDHB13: view

Variants for PCDHB13 Gene

Sequence variations from dbSNP and Humsavar for PCDHB13 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1003513879 -- 141,216,534(+) T/C 3_prime_UTR_variant
rs1007951967 -- 141,217,179(+) G/A 3_prime_UTR_variant
rs1008046759 -- 141,216,975(+) A/G 3_prime_UTR_variant
rs1014244794 -- 141,217,765(+) A/G downstream_transcript_variant
rs1019533751 -- 141,216,804(+) T/C 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHB13 Gene

Variant ID Type Subtype PubMed ID
dgv1142e214 CNV loss 21293372
dgv958e201 CNV deletion 23290073
esv26005 CNV gain 19812545
esv2759382 CNV gain 17122850
esv3606977 CNV gain 21293372
nsv1024594 CNV loss 25217958
nsv10757 CNV gain 18304495
nsv428127 CNV loss 18775914
nsv471634 CNV gain+loss 15918152
nsv599908 CNV loss 21841781
nsv599920 CNV gain 21841781
nsv823266 CNV gain 20364138
nsv823277 CNV gain 20364138
nsv823278 CNV gain 20364138
nsv980738 CNV duplication 23825009

Variation tolerance for PCDHB13 Gene

Residual Variation Intolerance Score: 83.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.70; 78.61% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHB13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHB13 Gene

Disorders for PCDHB13 Gene

Additional Disease Information for PCDHB13

No disorders were found for PCDHB13 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHB13 Gene

Publications for PCDHB13 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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4 58
  5. The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number. (PMID: 11322959) Vanhalst K … van Roy F (FEBS letters 2001) 3 4 58

Products for PCDHB13 Gene

Sources for PCDHB13 Gene

Loading form....