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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
  • PCDH-ALPHA3 3

External Ids for PCDHA3 Gene

Previous GeneCards Identifiers for PCDHA3 Gene

  • GC05P139998
  • GC05P140750
  • GC05P140152
  • GC05P140207
  • GC05P140200
  • GC05P140161
  • GC05P135325
  • GC05P141235
  • GC05P141480
  • GC05P141589
  • GC05P141691
  • GC05P141793
  • GC05P141890

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 PCDHA7.

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

Additional gene information for PCDHA3 Gene

No data available for CIViC summary , 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
GH05H140036 1.6 FANTOM5 Ensembl ENCODE 20.1 -760.5 -760542 7 SIN3A ZNF2 GLIS2 ZNF143 ZNF207 FOS ATF7 KLF7 RUNX3 SP3 PCDHA2 PCDHA3 PCDHA7 PURA PCDHA6 PCDHA10 DNAJC18 PFDN1 MATR3 PCDHA4
GH05H140190 1.7 FANTOM5 Ensembl ENCODE dbSUPER 10.5 -610.2 -610206 1 HDAC1 PKNOX1 ATF1 CHAMP1 TCF12 ZNF302 GATA2 ZNF366 ZSCAN5C SIRT6 PFDN1 ENSG00000272108 PCDHB5 PCDHB4 PCDHB9 PCDHB6 PCDHB3 PCDHB17P PCDHB8 PCDHB7
GH05H141563 1.6 Ensembl ENCODE dbSUPER 10.3 +763.4 763385 1 FOXA2 PKNOX1 ARNT DMAP1 ZNF2 YY1 ZNF143 ZNF207 FOS SP3 HARS2 IK PCDHB8 PCDHB3 PCDHA6 PCDHB9 PCDHB7 ENSG00000272108 PCDHB15 PCDHGC3
GH05H141039 1.6 FANTOM5 Ensembl ENCODE 10 +239.5 239507 2 PKNOX1 ATF1 ARID4B SIN3A YY1 CBX5 ELK1 ZNF143 KLF7 ATF7 ANKHD1 PCDHB16 HDAC3 WDR55 LOC102723915 TMCO6 HARS2 PCDHA4 PCDHA9 KIAA0141
GH05H141557 1.5 Ensembl ENCODE dbSUPER 9.9 +758.5 758477 4 PKNOX1 ATF1 SIN3A YY1 ETS1 ZNF766 ZNF143 ZNF207 FOS ATF7 PCDHGA6 PCDHA2 PCDHB18P PCDHA7 PCDHGA7 GNPDA1 PCDHA3 SLC35A4 RELL2 DIAPH1
- 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
ENSR00000187823 272 200 CTCF

Genomic Location for PCDHA3 Gene

Chromosome:
5
Start:
140,801,028 bp from pter
End:
141,012,344 bp from pter
Size:
211,317 bases
Orientation:
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:
    Q9Y5H8-PCDA3_HUMAN
    Recommended name:
    Protocadherin alpha-3
    Protein Accession:
    Q9Y5H8
    Secondary Accessions:
    • O75286

    Protein attributes for PCDHA3 Gene

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

    Alternative splice isoforms for PCDHA3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHA3 Gene

Post-translational modifications for PCDHA3 Gene

  • Glycosylation at posLast=257257, Asn265, and posLast=548548
  • 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

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

Protein Domains for PCDHA3 Gene

Suggested Antigen Peptide Sequences for PCDHA3 Gene

Graphical View of Domain Structure for InterPro Entry

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

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

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

CRISPR Products

miRNA for PCDHA3 Gene

miRTarBase miRNAs that target PCDHA3

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PCDHA3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

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 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

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PCDHA3 Gene

Pathways & Interactions for PCDHA3 Gene

SuperPathways for PCDHA3 Gene

No Data Available

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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PCDHA3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

No ASD Table

Relevant External Links for PCDHA3 Gene

GeneLoc Exon Structure for
PCDHA3
ECgene alternative splicing isoforms for
PCDHA3

Expression for PCDHA3 Gene

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

PCDHA3

Evidence on tissue expression from TISSUES for PCDHA3 Gene

  • Nervous system(4)
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 , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia PCDHA3 33
  • 99.26 (n)
dog
(Canis familiaris)
Mammalia PCDHA3 33
  • 86.16 (n)
mouse
(Mus musculus)
Mammalia Pcdha3 33 16
  • 84.08 (n)
rat
(Rattus norvegicus)
Mammalia Pcdha3 33
  • 84.01 (n)
cow
(Bos Taurus)
Mammalia PCDHA3 34
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 70 (a)
ManyToMany
-- 34
  • 69 (a)
ManyToMany
-- 34
  • 67 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 64 (a)
OneToMany
chicken
(Gallus gallus)
Aves PCDHA11 34
  • 54 (a)
ManyToMany
-- 34
  • 48 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 57 (a)
ManyToMany
-- 34
  • 57 (a)
ManyToMany
-- 34
  • 56 (a)
ManyToMany
-- 34
  • 56 (a)
ManyToMany
-- 34
  • 56 (a)
ManyToMany
-- 34
  • 56 (a)
ManyToMany
-- 34
  • 56 (a)
ManyToMany
-- 34
  • 56 (a)
ManyToMany
-- 34
  • 55 (a)
ManyToMany
-- 34
  • 55 (a)
ManyToMany
-- 34
  • 55 (a)
ManyToMany
-- 34
  • 55 (a)
ManyToMany
-- 34
  • 55 (a)
ManyToMany
-- 34
  • 54 (a)
ManyToMany
-- 34
  • 53 (a)
ManyToMany
-- 34
  • 51 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii pcdh1a6 34
  • 43 (a)
ManyToMany
pcdh2ab1 34
  • 43 (a)
ManyToMany
pcdh2ab8 34
  • 43 (a)
ManyToMany
CT573264.5 34
  • 42 (a)
ManyToMany
pcdh2ab12 34
  • 42 (a)
ManyToMany
pcdh2ab3 34
  • 42 (a)
ManyToMany
pcdh2ab6 34
  • 42 (a)
ManyToMany
pcdh2ab7 34
  • 42 (a)
ManyToMany
CR847851.6 34
  • 41 (a)
ManyToMany
CR847851.8 34
  • 41 (a)
ManyToMany
CT573264.4 34
  • 41 (a)
ManyToMany
pcdh2ab10 34
  • 41 (a)
ManyToMany
pcdh2ab11 34
  • 41 (a)
ManyToMany
pcdh2ab2 34 34
  • 41 (a)
ManyToMany
pcdh2ab9 34
  • 41 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 35 (a)
ManyToMany
CSA.7308 34
  • 19 (a)
ManyToMany
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

ENSEMBL:
Gene Tree for PCDHA3 (if available)
TreeFam:
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
rs1000079934 -- 140,816,794(+) CCAGC(C/T)TTTTT 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)
PCDHA3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHA3

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: HGMD, 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)
PCDHA3
Human Genome Epidemiology (HuGE) Navigator
PCDHA3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCDHA3
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 60
  2. Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence. (PMID: 19054571) Gregório SP … Dias-Neto E (Psychiatry research 2009) 3 45 60
  3. The DNA sequence and comparative analysis of human chromosome 5. (PMID: 15372022) Schmutz J … Rubin EM (Nature 2004) 3 4 60
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  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 60

Products for PCDHA3 Gene

Sources for PCDHA3 Gene

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