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Aliases for PCDHA1 Gene

Aliases for PCDHA1 Gene

  • Protocadherin Alpha 1 2 3 5
  • KIAA0345-Like 13 2 3
  • PCDH-Alpha-1 3 4

External Ids for PCDHA1 Gene

Previous GeneCards Identifiers for PCDHA1 Gene

  • GC05P139982
  • GC05P140748
  • GC05P140150
  • GC05P140194
  • GC05P140146
  • GC05P135311
  • GC05P141231
  • GC05P141476

Summaries for PCDHA1 Gene

Entrez Gene Summary for PCDHA1 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 PCDHA1 Gene

PCDHA1 (Protocadherin Alpha 1) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGA5.

UniProtKB/Swiss-Prot for PCDHA1 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 PCDHA1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHA1 Gene

Genomics for PCDHA1 Gene

Regulatory Elements for PCDHA1 Gene

Enhancers for PCDHA1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PCDHA1 on UCSC Golden Path with GeneCards custom track

Genomic Location for PCDHA1 Gene

140,786,136 bp from pter
141,012,347 bp from pter
226,212 bases
Plus strand

Genomic View for PCDHA1 Gene

Genes around PCDHA1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHA1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHA1 Gene

Proteins for PCDHA1 Gene

  • Protein details for PCDHA1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin alpha-1
    Protein Accession:
    Secondary Accessions:
    • O75288
    • Q9NRT7

    Protein attributes for PCDHA1 Gene

    950 amino acids
    Molecular mass:
    102952 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHA1 Gene


neXtProt entry for PCDHA1 Gene

Proteomics data for PCDHA1 Gene at MOPED

Post-translational modifications for PCDHA1 Gene

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

Other Protein References for PCDHA1 Gene

Antibody Products

  • R&D Systems Antibodies for PCDHA1 (Protocadherin alpha 1)

No data available for DME Specific Peptides for PCDHA1 Gene

Domains & Families for PCDHA1 Gene

Gene Families for PCDHA1 Gene

Protein Domains for PCDHA1 Gene

Suggested Antigen Peptide Sequences for PCDHA1 Gene

GenScript: Design optimal peptide antigens:

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 PCDHA1: view

Function for PCDHA1 Gene

Molecular function for PCDHA1 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.
genes like me logo Genes that share phenotypes with PCDHA1: view

Animal Models for PCDHA1 Gene

MGI Knock Outs for PCDHA1:

Animal Model Products

miRNA for PCDHA1 Gene

miRTarBase miRNAs that target PCDHA1

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PCDHA1 Gene

Localization for PCDHA1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHA1 Gene

Isoform 1: Cell membrane; Single-pass type I membrane protein.
Isoform 2: Secreted.

Subcellular locations from

Jensen Localization Image for PCDHA1 Gene COMPARTMENTS Subcellular localization image for PCDHA1 gene
Compartment Confidence
plasma membrane 4
extracellular 3
endoplasmic reticulum 2

Gene Ontology (GO) - Cellular Components for PCDHA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PCDHA1: view

Pathways & Interactions for PCDHA1 Gene

SuperPathways for PCDHA1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA,TAS 10380929
genes like me logo Genes that share ontologies with PCDHA1: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHA1 Gene

Drugs & Compounds for PCDHA1 Gene

(1) Drugs for PCDHA1 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 PCDHA1: view

Transcripts for PCDHA1 Gene

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHA1 Gene

No ASD Table

Relevant External Links for PCDHA1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHA1 Gene

mRNA expression in normal human tissues for PCDHA1 Gene

mRNA differential expression in normal tissues according to GTEx for PCDHA1 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x5.7) and Brain - Cerebellar Hemisphere (x4.2).

Protein differential expression in normal tissues from HIPED for PCDHA1 Gene

This gene is overexpressed in Pancreatic juice (51.1) and Bone marrow mesenchymal stem cell (17.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDHA1 Gene

genes like me logo Genes that share expression patterns with PCDHA1: view

Protein tissue co-expression partners for PCDHA1 Gene

- Elite partner

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for PCDHA1 Gene

Orthologs for PCDHA1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHA1 Gene

Organism Taxonomy Gene Similarity Type Details
(Mus musculus)
Mammalia Pcdha1 35
  • 83.91 (n)
  • 84.79 (a)
Pcdha1 16
(Rattus norvegicus)
Mammalia Pcdha1 35
  • 83.39 (n)
  • 84.69 (a)
(Monodelphis domestica)
Mammalia -- 36
  • 64 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 66 (a)
-- 36
  • 68 (a)
-- 36
  • 69 (a)
(Pan troglodytes)
Mammalia PCDHA1 36
  • 98 (a)
(Gallus gallus)
Aves -- 36
  • 47 (a)
PCDHA11 36
  • 53 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 52 (a)
-- 36
  • 54 (a)
-- 36
  • 54 (a)
-- 36
  • 52 (a)
-- 36
  • 55 (a)
-- 36
  • 56 (a)
-- 36
  • 54 (a)
-- 36
  • 55 (a)
-- 36
  • 55 (a)
-- 36
  • 55 (a)
-- 36
  • 55 (a)
-- 36
  • 56 (a)
-- 36
  • 56 (a)
-- 36
  • 55 (a)
-- 36
  • 51 (a)
-- 36
  • 54 (a)
(Danio rerio)
Actinopterygii Dr.19866 35
CR847851.6 36
  • 41 (a)
CR847851.8 36
  • 40 (a)
CT573264.4 36
  • 41 (a)
CT573264.5 36
  • 40 (a)
pcdh1a6 36
  • 42 (a)
pcdh2ab1 36
  • 42 (a)
pcdh2ab10 36
  • 40 (a)
pcdh2ab11 36
  • 41 (a)
pcdh2ab12 36
  • 41 (a)
pcdh2ab2 36
  • 40 (a)
pcdh2ab2 36
  • 40 (a)
pcdh2ab3 36
  • 41 (a)
pcdh2ab6 36
  • 41 (a)
pcdh2ab7 36
  • 41 (a)
pcdh2ab8 36
  • 42 (a)
pcdh2ab9 36
  • 39 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 32 (a)
CSA.7308 36
  • 20 (a)
Species with no ortholog for PCDHA1:
  • 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)
  • cow (Bos Taurus)
  • 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)
  • 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 PCDHA1 Gene

Gene Tree for PCDHA1 (if available)
Gene Tree for PCDHA1 (if available)

Paralogs for PCDHA1 Gene

genes like me logo Genes that share paralogs with PCDHA1: view

Variants for PCDHA1 Gene

Sequence variations from dbSNP and Humsavar for PCDHA1 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs3733712 - 140,787,635(-) GTCAT(G/T)CACGT reference, missense
rs2240696 - 140,788,485(-) GCACA(C/T)ACGCA intron-variant, reference, missense
rs34575154 - 140,787,368(-) CTCTC(C/T)GATAG reference, missense
rs2240695 - 140,788,566(-) TAGAG(A/C)ACACC intron-variant, reference, missense
rs6579965 -- 140,789,226(+) GGGCG(G/T)ATCAC intron-variant, downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for PCDHA1 Gene

Variant ID Type Subtype PubMed ID
nsv830508 CNV Loss 17160897
nsv882950 CNV Loss 21882294
dgv6343n71 CNV Loss 21882294
dgv1856e1 CNV Complex 17122850
dgv1857e1 CNV Complex 17122850
nsv882952 CNV Loss 21882294
dgv6344n71 CNV Loss 21882294
dgv970n67 CNV Gain 20364138
nsv330045 CNV Loss 16902084
esv8310 CNV Loss 19470904
esv2659321 CNV Deletion 23128226
nsv882956 CNV Loss 21882294
nsv882957 CNV Loss 21882294
dgv6345n71 CNV Loss 21882294
nsv882960 CNV Gain 21882294
esv2730838 CNV Deletion 23290073
nsv10752 CNV Gain+Loss 18304495
dgv6346n71 CNV Loss 21882294
esv21596 CNV Gain 19812545
nsv882965 CNV Gain+Loss 21882294
nsv436885 CNV Insertion 17901297
esv27071 CNV Loss 19812545
esv33939 CNV Gain+Loss 17666407
dgv6347n71 CNV Loss 21882294
nsv823251 CNV Gain 20364138
dgv1043e199 CNV Deletion 23128226
esv2730839 CNV Deletion 23290073
esv26168 CNV Gain 19812545
dgv971n67 CNV Loss 20364138
nsv820841 CNV Deletion 20802225
nsv10753 CNV Gain 18304495
nsv819207 CNV Gain 19587683
dgv972n67 CNV Gain 20364138
dgv1044e199 CNV Deletion 23128226
esv29977 CNV Gain 17803354
nsv514324 CNV Loss 21397061
esv2421858 CNV Deletion 20811451
nsv442962 CNV CNV 18776908
dgv724n27 CNV Loss 19166990
nsv437955 CNV Loss 16468122
nsv515909 CNV Loss 19592680
esv2657537 CNV Deletion 23128226
nsv823262 CNV Gain 20364138
nsv823263 CNV Gain 20364138
nsv823264 CNV Gain 20364138
nsv882970 CNV Loss 21882294
nsv10754 CNV Gain 18304495
esv2505753 CNV Deletion 19546169

Variation tolerance for PCDHA1 Gene

Residual Variation Intolerance Score: 60.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.35; 63.30% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for PCDHA1 Gene

Disorders for PCDHA1 Gene

Relevant External Links for PCDHA1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for PCDHA1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHA1 Gene

Publications for PCDHA1 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 67
  2. 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
  3. CTCF/cohesin-mediated DNA looping is required for protocadherin I+ promoter choice. (PMID: 23204437) Guo Y. … Wu Q. (Proc. Natl. Acad. Sci. U.S.A. 2012) 3
  4. Analysis of protocadherin alpha gene deletion variant in bipolar disorder and schizophrenia. (PMID: 18496207) Lachman H.M. … Stopkova P. (Psychiatr. Genet. 2008) 3
  5. Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. (PMID: 17474147) Wu C. … Li S.S. (Proteomics 2007) 3

Products for PCDHA1 Gene

Sources for PCDHA1 Gene