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Aliases for PCDHA3 Gene

Aliases for PCDHA3 Gene

  • Protocadherin Alpha 3 2 3 5
  • KIAA0345-Like 11 2 3
  • PCDH-Alpha-3 3 4
  • Protocadherin Alpha-3 3

External Ids for PCDHA3 Gene

Previous GeneCards Identifiers for PCDHA3 Gene

  • GC05P139998
  • GC05P140750
  • GC05P140152
  • GC05P140207
  • GC05P140200
  • GC05P140161
  • GC05P135325
  • GC05P141235
  • GC05P141480
  • GC05P141589
  • GC05P141691

Summaries for PCDHA3 Gene

Entrez Gene Summary for PCDHA3 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 PCDHA3 Gene

PCDHA3 (Protocadherin Alpha 3) is a Protein Coding gene. Diseases associated with PCDHA3 include Restless Legs Syndrome. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHA4.

UniProtKB/Swiss-Prot for PCDHA3 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 PCDHA3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHA3 Gene

Genomics for PCDHA3 Gene

Regulatory Elements for PCDHA3 Gene

Enhancers for PCDHA3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05F140399 1.2 ENCODE 27.1 -399.0 -399000 4.7 CREB3L1 ZFP64 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 ZNF610 PURA PCDHA3 PCDHA2 PCDHA7 SRA1 VTRNA1-1 CD14 PCDHA1 PCDHB18P PCDHGA6
GH05F139962 1.2 ENCODE 26.6 -839.0 -839047 1.2 HDGF PKNOX1 ARNT CREB3L1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 PURA PCDHA3 VTRNA1-1 TMCO6 PSD2 PCDHA2 PCDHA7 LINC01024 GC05P139956 GC05P140021
GH05F140725 1.1 ENCODE 19.8 -75.0 -75046 1.1 PKNOX1 ARNT ARID4B SIN3A ZNF2 FOS KLF13 DEK ZNF263 SP3 HDAC3 LOC102723915 PCDHA4 TMCO6 PCDHA3 FCHSD1 HARS LOC101929719 PCDHB19P PCDHB17P
GH05F140112 2.1 ENCODE 9.9 -687.1 -687053 3.6 HDGF ARID4B SIN3A ZNF2 ZNF416 ZNF207 ZNF263 SP5 MXD4 REST VTRNA1-1 LINC01024 PCDHA3 GC05P140117 PIR63019
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PCDHA3 on UCSC Golden Path with GeneCards custom track

Promoters for PCDHA3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001874409 272 600 TBP ELF3 CTCF IRF2 SAP130 CREB3L1 ZNF644 KMT2B ZNF316 GATA2

Genomic Location for PCDHA3 Gene

140,801,028 bp from pter
141,012,344 bp from pter
211,317 bases
Plus strand

Genomic View for PCDHA3 Gene

Genes around PCDHA3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHA3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHA3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHA3 Gene

Proteins for PCDHA3 Gene

  • Protein details for PCDHA3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin alpha-3
    Protein Accession:
    Secondary Accessions:
    • O75286

    Protein attributes for PCDHA3 Gene

    950 amino acids
    Molecular mass:
    102428 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHA3 Gene


neXtProt entry for PCDHA3 Gene

Post-translational modifications for PCDHA3 Gene

  • Glycosylation at Asn 257, Asn 265, and Asn 548
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHA3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHA3 Gene

Domains & Families for PCDHA3 Gene

Gene Families for PCDHA3 Gene

Protein Domains for PCDHA3 Gene

Suggested Antigen Peptide Sequences for PCDHA3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 6 cadherin domains.
  • Contains 6 cadherin domains.
genes like me logo Genes that share domains with PCDHA3: view

Function for PCDHA3 Gene

Molecular function for PCDHA3 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 PCDHA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHA3: view

Phenotypes for PCDHA3 Gene

GenomeRNAi human phenotypes for PCDHA3:
genes like me logo Genes that share phenotypes with PCDHA3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for PCDHA3

miRNA for PCDHA3 Gene

miRTarBase miRNAs that target PCDHA3

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHA3 Gene

Localization for PCDHA3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHA3 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 PCDHA3 gene
Compartment Confidence
plasma membrane 4

Gene Ontology (GO) - Cellular Components for PCDHA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane TAS 10380929
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDHA3: view

Pathways & Interactions for PCDHA3 Gene

SuperPathways for PCDHA3 Gene

No Data Available

Interacting Proteins for PCDHA3 Gene

Gene Ontology (GO) - Biological Process for PCDHA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion TAS 10380929
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007399 nervous system development TAS 10380929
genes like me logo Genes that share ontologies with PCDHA3: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHA3 Gene

Drugs & Compounds for PCDHA3 Gene

(1) Drugs for PCDHA3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with PCDHA3: view

Transcripts for PCDHA3 Gene

mRNA/cDNA for PCDHA3 Gene

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHA3 Gene

No ASD Table

Relevant External Links for PCDHA3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHA3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCDHA3 Gene

Protein differential expression in normal tissues from HIPED for PCDHA3 Gene

This gene is overexpressed in Heart (52.9) and Fetal heart (14.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PCDHA3 Gene

Protein tissue co-expression partners for PCDHA3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHA3 Gene:

genes like me logo Genes that share expression patterns with PCDHA3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PCDHA3 Gene

Orthologs for PCDHA3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHA3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDHA3 34
  • 99.26 (n)
(Canis familiaris)
Mammalia PCDHA3 34
  • 86.16 (n)
(Mus musculus)
Mammalia Pcdha3 34 16
  • 84.08 (n)
(Rattus norvegicus)
Mammalia Pcdha3 34
  • 84.01 (n)
(Bos Taurus)
Mammalia PCDHA3 35
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 70 (a)
-- 35
  • 69 (a)
-- 35
  • 67 (a)
(Monodelphis domestica)
Mammalia -- 35
  • 64 (a)
(Gallus gallus)
Aves PCDHA11 35
  • 54 (a)
-- 35
  • 48 (a)
(Anolis carolinensis)
Reptilia -- 35
  • 57 (a)
-- 35
  • 57 (a)
-- 35
  • 56 (a)
-- 35
  • 56 (a)
-- 35
  • 56 (a)
-- 35
  • 56 (a)
-- 35
  • 56 (a)
-- 35
  • 56 (a)
-- 35
  • 55 (a)
-- 35
  • 55 (a)
-- 35
  • 55 (a)
-- 35
  • 55 (a)
-- 35
  • 55 (a)
-- 35
  • 54 (a)
-- 35
  • 53 (a)
-- 35
  • 51 (a)
(Danio rerio)
Actinopterygii pcdh1a6 35
  • 43 (a)
pcdh2ab1 35
  • 43 (a)
pcdh2ab8 35
  • 43 (a)
CT573264.5 35
  • 42 (a)
pcdh2ab12 35
  • 42 (a)
pcdh2ab3 35
  • 42 (a)
pcdh2ab6 35
  • 42 (a)
pcdh2ab7 35
  • 42 (a)
CR847851.6 35
  • 41 (a)
CR847851.8 35
  • 41 (a)
CT573264.4 35
  • 41 (a)
pcdh2ab10 35
  • 41 (a)
pcdh2ab11 35
  • 41 (a)
pcdh2ab2 35 35
  • 41 (a)
pcdh2ab9 35
  • 41 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 35 (a)
CSA.7308 35
  • 19 (a)
Species where no ortholog for PCDHA3 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)
  • 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 PCDHA3 Gene

Gene Tree for PCDHA3 (if available)
Gene Tree for PCDHA3 (if available)

Paralogs for PCDHA3 Gene

genes like me logo Genes that share paralogs with PCDHA3: view

Variants for PCDHA3 Gene

Sequence variations from dbSNP and Humsavar for PCDHA3 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs193920994 Uncertain significance 140,857,214(+) TCTGA(C/T)GCCTC intron-variant, reference, missense
rs386352345 Uncertain significance 140,803,127(+) CCCCG(C/T)GCCAT intron-variant, reference, missense
rs386352346 Uncertain significance 140,929,288(+) GATTC(A/G)GAATA intron-variant, reference, missense
rs587776956 Uncertain significance 140,802,947(+) CGCGG(C/T)CAGTG intron-variant, reference, missense
rs10036183 -- 140,996,918(+) ATATT(A/T)AAAAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHA3 Gene

Variant ID Type Subtype PubMed ID
dgv10092n54 CNV loss 21841781
dgv10093n54 CNV loss 21841781
dgv10094n54 CNV loss 21841781
dgv10095n54 CNV loss 21841781
dgv10096n54 CNV loss 21841781
dgv10097n54 CNV loss 21841781
dgv10098n54 CNV loss 21841781
dgv10099n54 CNV loss 21841781
dgv10100n54 CNV loss 21841781
dgv10101n54 CNV loss 21841781
dgv10102n54 CNV loss 21841781
dgv10103n54 CNV loss 21841781
dgv10104n54 CNV loss 21841781
dgv10105n54 CNV loss 21841781
dgv1043e199 CNV deletion 23128226
dgv1044e199 CNV deletion 23128226
dgv138e203 CNV loss 21179565
dgv1651e212 CNV loss 25503493
dgv1652e212 CNV loss 25503493
dgv1653e212 CNV loss 25503493
dgv3182n106 CNV deletion 24896259
dgv724n27 CNV loss 19166990
dgv970n67 CNV gain 20364138
dgv971n67 CNV loss 20364138
dgv972n67 CNV gain 20364138
esv21596 CNV gain 19812545
esv2421858 CNV deletion 20811451
esv2505753 CNV deletion 19546169
esv26168 CNV gain 19812545
esv2657537 CNV deletion 23128226
esv2659321 CNV deletion 23128226
esv27071 CNV loss 19812545
esv2730838 CNV deletion 23290073
esv2730839 CNV deletion 23290073
esv2759382 CNV gain 17122850
esv2861013 CNV duplication 24192839
esv29977 CNV gain 17803354
esv33939 CNV gain+loss 17666407
esv3566721 CNV deletion 23714750
esv3606956 CNV loss 21293372
esv3606957 CNV gain 21293372
esv3606958 CNV loss 21293372
esv3606959 CNV gain 21293372
esv3890744 CNV loss 25118596
esv8310 CNV loss 19470904
nsv1024237 CNV loss 25217958
nsv1031849 CNV loss 25217958
nsv10752 CNV gain+loss 18304495
nsv10753 CNV gain 18304495
nsv10754 CNV gain 18304495
nsv1133616 CNV deletion 24896259
nsv1135376 CNV deletion 24896259
nsv1161301 OTHER complex 26073780
nsv330045 CNV deletion 16902084
nsv436885 CNV insertion 17901297
nsv437955 CNV loss 16468122
nsv442962 CNV loss 18776908
nsv514324 CNV loss 21397061
nsv515909 CNV loss 19592680
nsv599839 CNV gain 21841781
nsv599841 CNV loss 21841781
nsv599842 CNV loss 21841781
nsv599859 CNV loss 21841781
nsv599864 CNV loss 21841781
nsv599870 CNV loss 21841781
nsv599894 CNV loss 21841781
nsv599902 CNV loss 21841781
nsv599903 CNV loss 21841781
nsv599904 CNV loss 21841781
nsv819207 CNV gain 19587683
nsv820841 CNV deletion 20802225
nsv823251 CNV gain 20364138
nsv823262 CNV gain 20364138
nsv823263 CNV gain 20364138
nsv823264 CNV gain 20364138
nsv830508 CNV loss 17160897
nsv950415 CNV duplication 24416366
nsv964948 CNV duplication 23825009
nsv964949 CNV duplication 23825009
nsv964950 CNV duplication 23825009
nsv964951 CNV duplication 23825009
nsv964953 CNV duplication 23825009
nsv964954 CNV duplication 23825009
nsv964955 CNV duplication 23825009
nsv964956 CNV duplication 23825009
nsv968251 CNV duplication 23825009
nsv968252 CNV duplication 23825009
nsv968992 CNV duplication 23825009
nsv980734 CNV duplication 23825009

Variation tolerance for PCDHA3 Gene

Residual Variation Intolerance Score: 11% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.85; 74.00% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDHA3 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 PCDHA3 Gene

Disorders for PCDHA3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PCDHA3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
restless legs syndrome
  • wed
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for PCDHA3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with PCDHA3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDHA3 Gene

Publications for PCDHA3 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 64
  2. Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence. (PMID: 19054571) GregA^rio S.P. … Dias-Neto E. (Psychiatry Res 2009) 3 46 64
  3. The DNA sequence and comparative analysis of human chromosome 5. (PMID: 15372022) Schmutz J. … Rubin E.M. (Nature 2004) 3 4 64
  4. Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. (PMID: 22589738) Fox C.S. … Borecki I.B. (PLoS Genet. 2012) 3 64
  5. Exome sequencing in a family with restless legs syndrome. (PMID: 23192925) Weissbach A. … Lohmann K. (Mov. Disord. 2012) 3 64

Products for PCDHA3 Gene

Sources for PCDHA3 Gene

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