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Aliases for PCDHA9 Gene

Aliases for PCDHA9 Gene

  • Protocadherin Alpha 9 2 3 5
  • KIAA0345-Like 5 2 3
  • PCDH-Alpha-9 3 4
  • Protocadherin Alpha-9 3
  • KIAA0345 4

External Ids for PCDHA9 Gene

Previous GeneCards Identifiers for PCDHA9 Gene

  • GC05P140043
  • GC05P140756
  • GC05P140158
  • GC05P140213
  • GC05P140220
  • GC05P140175
  • GC05P140229
  • GC05P140234
  • GC05P140241
  • GC05P140250
  • GC05P140259
  • GC05P140268
  • GC05P140278
  • GC05P140288
  • GC05P140299
  • GC05P140308
  • GC05P140317
  • GC05P140333
  • GC05P140336
  • GC05P135372
  • GC05P140355
  • GC05P140370
  • GC05P140385
  • GC05P140399
  • GC05P140415
  • GC05P140428
  • GC05P140447
  • GC05P141271
  • GC05P141493
  • GC05P141600
  • GC05P141700
  • GC05P141802
  • GC05P141898
  • GC05P142007
  • GC05P142110

Summaries for PCDHA9 Gene

Entrez Gene Summary for PCDHA9 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 PCDHA9 Gene

PCDHA9 (Protocadherin Alpha 9) is a Protein Coding gene. Diseases associated with PCDHA9 include Hirschsprung Disease 1 and Hypoplastic Left Heart Syndrome. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHA7.

UniProtKB/Swiss-Prot for PCDHA9 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 PCDHA9 Gene

Additional gene information for PCDHA9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHA9 Gene

Genomics for PCDHA9 Gene

GeneHancer (GH) Regulatory Elements for PCDHA9 Gene

Promoters and enhancers for PCDHA9 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
GH05J140848 Promoter 0.7 EPDnew 650.7 +0.9 900 0.1 USF2 SMC3 RAD21 ENSG00000278907 GC05M140848 PCDHA9 PCDHA8 PCDHA7 PCDHA6 PCDHA5 PCDHA4 PCDHA3 PCDHA2
GH05J140545 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 7.5 -299.1 -299113 4.7 HDGF PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 YY1 POLR2B E2F8 EIF4EBP3 SRA1 CD14 PCDHA9 ANKHD1-EIF4EBP3
GH05J141039 Enhancer 1.4 FANTOM5 Ensembl ENCODE 10.7 +193.1 193071 2.6 PKNOX1 CLOCK ATF1 ARID4B SIN3A ZNF48 YY1 CBX5 ELK1 ZNF143 ANKHD1 PCDHB16 HDAC3 WDR55 LOC102723915 TMCO6 HARS2 PCDHA4 PCDHA9 DELE1
GH05J140663 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 7.1 -182.7 -182686 2.8 HDGF PKNOX1 SMAD1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B WDR55 SRA1 TMCO6 CD14 PCDHA9 PIR42041 GC05P142315
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHA9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHA9 gene promoter:
  • Zic3
  • AREB6
  • COMP1
  • E2F
  • E2F-1
  • Lmo2
  • FOXD3
  • Brachyury
  • Pax-4a

Genomic Locations for PCDHA9 Gene

Genomic Locations for PCDHA9 Gene
164,882 bases
Plus strand
164,882 bases
Plus strand

Genomic View for PCDHA9 Gene

Genes around PCDHA9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHA9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHA9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHA9 Gene

Proteins for PCDHA9 Gene

  • Protein details for PCDHA9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin alpha-9
    Protein Accession:
    Secondary Accessions:
    • O15053
    • Q2M3S5

    Protein attributes for PCDHA9 Gene

    950 amino acids
    Molecular mass:
    102402 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA20803.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PCDHA9 Gene


neXtProt entry for PCDHA9 Gene

Post-translational modifications for PCDHA9 Gene

  • Glycosylation at Asn548, isoforms=2265, and isoforms=2254
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHA9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHA9 Gene

Domains & Families for PCDHA9 Gene

Gene Families for PCDHA9 Gene

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

Protein Domains for PCDHA9 Gene

Suggested Antigen Peptide Sequences for PCDHA9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHA9: view

No data available for UniProtKB/Swiss-Prot for PCDHA9 Gene

Function for PCDHA9 Gene

Molecular function for PCDHA9 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 PCDHA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHA9: view
genes like me logo Genes that share phenotypes with PCDHA9: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHA9 Gene

Localization for PCDHA9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHA9 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 PCDHA9 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for PCDHA9 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 PCDHA9: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PCDHA9 Gene

Pathways & Interactions for PCDHA9 Gene

SuperPathways for PCDHA9 Gene

No Data Available

Interacting Proteins for PCDHA9 Gene

Gene Ontology (GO) - Biological Process for PCDHA9 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 PCDHA9: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHA9 Gene

Drugs & Compounds for PCDHA9 Gene

(1) Drugs for PCDHA9 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 PCDHA9: view

Transcripts for PCDHA9 Gene

mRNA/cDNA for PCDHA9 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHA9 Gene

No ASD Table

Relevant External Links for PCDHA9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHA9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHA9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PCDHA9 Gene

This gene is overexpressed in Testis (x11.6), Brain - Cerebellum (x6.6), and Brain - Cerebellar Hemisphere (x5.9).

Protein differential expression in normal tissues from HIPED for PCDHA9 Gene

This gene is overexpressed in Adipocyte (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCDHA9 Gene

Protein tissue co-expression partners for PCDHA9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHA9 Gene:


Evidence on tissue expression from TISSUES for PCDHA9 Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with PCDHA9: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHA9 Gene

Orthologs for PCDHA9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHA9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDHA9 33
  • 99.37 (n)
(Mus musculus)
Mammalia Pcdha8 16 33
  • 83.05 (n)
(Rattus norvegicus)
Mammalia Pcdha9 33
  • 82.42 (n)
(Bos Taurus)
Mammalia -- 34
  • 81 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 69 (a)
-- 34
  • 68 (a)
-- 34
  • 65 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 63 (a)
(Gallus gallus)
Aves PCDHA11 34
  • 54 (a)
-- 34
  • 47 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 57 (a)
-- 34
  • 56 (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
  • 55 (a)
-- 34
  • 55 (a)
-- 34
  • 54 (a)
-- 34
  • 53 (a)
-- 34
  • 53 (a)
-- 34
  • 50 (a)
(Danio rerio)
Actinopterygii pcdh2ab1 34
  • 42 (a)
pcdh2ab8 34
  • 42 (a)
pcdh1a6 34
  • 41 (a)
pcdh2ab11 34
  • 41 (a)
pcdh2ab12 34
  • 41 (a)
pcdh2ab3 34
  • 41 (a)
CT573264.5 34
  • 41 (a)
pcdh2ab2 34 34
  • 41 (a)
pcdh2ab7 34
  • 41 (a)
CT573264.4 34
  • 40 (a)
CR847851.8 34
  • 40 (a)
pcdh2ab9 34
  • 40 (a)
CR847851.6 34
  • 40 (a)
pcdh2ab6 34
  • 40 (a)
pcdh2ab10 34
  • 39 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 34 (a)
CSA.7308 34
  • 19 (a)
Species where no ortholog for PCDHA9 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)
  • 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 PCDHA9 Gene

Gene Tree for PCDHA9 (if available)
Gene Tree for PCDHA9 (if available)
Evolutionary constrained regions (ECRs) for PCDHA9: view image

Paralogs for PCDHA9 Gene

genes like me logo Genes that share paralogs with PCDHA9: view

Variants for PCDHA9 Gene

Sequence variations from dbSNP and Humsavar for PCDHA9 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
rs193920994 uncertain-significance, Malignant tumor of prostate 140,857,214(+) C/T genic_downstream_transcript_variant, intron_variant
rs139390480 likely-benign, not specified 140,856,945(+) A/T genic_downstream_transcript_variant, intron_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

Structural Variations from Database of Genomic Variants (DGV) for PCDHA9 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
dgv971n67 CNV loss 20364138
esv2421858 CNV deletion 20811451
esv2505753 CNV deletion 19546169
esv26168 CNV gain 19812545
esv2657537 CNV deletion 23128226
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
esv3606958 CNV loss 21293372
esv3606959 CNV gain 21293372
esv3890744 CNV loss 25118596
nsv1024237 CNV loss 25217958
nsv1031849 CNV loss 25217958
nsv10753 CNV gain 18304495
nsv10754 CNV gain 18304495
nsv1133616 CNV deletion 24896259
nsv1135376 CNV deletion 24896259
nsv1161301 OTHER complex 26073780
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
nsv823262 CNV gain 20364138
nsv823263 CNV gain 20364138
nsv823264 CNV gain 20364138
nsv830508 CNV loss 17160897
nsv950415 CNV duplication 24416366
nsv964953 CNV duplication 23825009
nsv964954 CNV duplication 23825009
nsv964955 CNV duplication 23825009
nsv964956 CNV duplication 23825009
nsv968252 CNV duplication 23825009
nsv968992 CNV duplication 23825009

Variation tolerance for PCDHA9 Gene

Residual Variation Intolerance Score: 99.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 16.60; 97.81% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHA9 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 PCDHA9 Gene

Disorders for PCDHA9 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PCDHA9 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
hirschsprung disease 1
  • hirschsprung disease, susceptibility to, 1
hypoplastic left heart syndrome
  • hlhs
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDHA9

genes like me logo Genes that share disorders with PCDHA9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDHA9 Gene

Publications for PCDHA9 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. 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. Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9205841) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 3 4 58
  5. Identification of two novel PCDHA9 mutations associated with Hirschsprung's disease. (PMID: 29477871) Shen Q … Tang W (Gene 2018) 3 58

Products for PCDHA9 Gene

Sources for PCDHA9 Gene

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