This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notabl... See more...

Aliases for PCDH9 Gene

Aliases for PCDH9 Gene

  • Protocadherin 9 2 3 5
  • Protocadherin-9 3 4
  • Cadherin Superfamily Protein VR4-11 3
  • PCDH9 5

External Ids for PCDH9 Gene

Previous GeneCards Identifiers for PCDH9 Gene

  • GC13M065766
  • GC13M061794
  • GC13M065597
  • GC13M064677
  • GC13M065774
  • GC13M066876
  • GC13M047575

Summaries for PCDH9 Gene

Entrez Gene Summary for PCDH9 Gene

  • This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Nov 2012]

GeneCards Summary for PCDH9 Gene

PCDH9 (Protocadherin 9) is a Protein Coding gene. Diseases associated with PCDH9 include Auditory Neuropathy, Autosomal Dominant, 1 and Chromosome 9P Deletion Syndrome. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH1.

UniProtKB/Swiss-Prot Summary for PCDH9 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCDH9 Gene

Genomics for PCDH9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PCDH9 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
GH13J067228 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 259 +0.6 645 7.6 TBP SP1 MXD4 IKZF1 SMAD5 ELF1 NONO HOMEZ ZNF610 THAP11 PCDH9 lnc-KLHL1-9 ENSG00000285588 HSALNG0097704
GH13J067146 Enhancer 1.1 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 13.4 +82.8 82750 2.9 ZNF316 MAFK ZBTB48 JUND ZNF384 BHLHE40 TRIM28 FOS EP300 PCDH9 piR-41141-006 ENSG00000285588 HSALNG0097704
GH13J067047 Enhancer 1 Ensembl ENCODE dbSUPER 11.3 +181.7 181657 1.6 FEZF1 BATF EGR1 IKZF1 ZNF561 TRIM28 L3MBTL2 PKNOX1 LEF1 EGR2 HSALNG0097702 PCDH9 PCDH9-AS3 lnc-KLHL1-10
GH13J067223 Promoter/Enhancer 1.3 ENCODE CraniofacialAtlas dbSUPER 8.5 +6.3 6325 0.9 FEZF1 DEK CTCF ZEB1 CEBPB REST ZNF639 VEZF1 EP300 RXRA PCDH9 lnc-KLHL1-9 ENSG00000285588 HSALNG0097704
GH13J067155 Enhancer 0.5 FANTOM5 dbSUPER 16.5 +74.3 74322 0.3 ZFP91 ZBTB5 piR-41141-006 PCDH9 HSALNG0097704 ENSG00000285588
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDH9 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCDH9

Top Transcription factor binding sites by QIAGEN in the PCDH9 gene promoter:
  • C/EBPalpha
  • CHOP-10
  • CUTL1
  • ER-alpha
  • Evi-1
  • FOXO4
  • Pax-5
  • POU6F1 (c2)
  • SRF
  • SRF (504 AA)

Genomic Locations for PCDH9 Gene

Latest Assembly
927,612 bases
Minus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
927,503 bases
Minus strand

(GRCh37/hg19 by Ensembl)
927,502 bases
Minus strand

Genomic View for PCDH9 Gene

Genes around PCDH9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDH9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDH9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDH9 Gene

Proteins for PCDH9 Gene

  • Protein details for PCDH9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A2A6U1
    • Q5VT83
    • Q7Z3U0
    • Q8N3K7

    Protein attributes for PCDH9 Gene

    1237 amino acids
    Molecular mass:
    136064 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for PCDH9 Gene

    Alternative splice isoforms for PCDH9 Gene


neXtProt entry for PCDH9 Gene

Post-translational modifications for PCDH9 Gene

  • Glycosylation at Asn48, Asn148, Asn306, Asn307, Asn347, Asn368, Asn450, Asn511, Asn630, Asn681, Asn734, Asn754, Asn775, and Asn780
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • PCDH9_HUMAN (1969)

No data available for DME Specific Peptides for PCDH9 Gene

Domains & Families for PCDH9 Gene

Gene Families for PCDH9 Gene

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

Protein Domains for PCDH9 Gene

  • Protocadherin

Suggested Antigen Peptide Sequences for PCDH9 Gene

GenScript: Design optimal peptide antigens:
  • PCDH9 protein (A7E2D9_HUMAN)
  • PCDH9 protein (B7ZM79_HUMAN)
  • Protocadherin-9 (PCDH9_HUMAN)
genes like me logo Genes that share domains with PCDH9: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PCDH9 Gene

Function for PCDH9 Gene

Molecular function for PCDH9 Gene

UniProtKB/Swiss-Prot Function:
Potential calcium-dependent cell-adhesion protein.
GENATLAS Biochemistry:
BH protocadherin 9 cadherin-related neuronal receptor,predominantly expressed in brain,localizing to synaptic junctions and putatively involved in specific neuronal connections and signal transduction,also expressed in other tissues with a developmentally regulated expression pattern,cadherin superfamily of calcium dependant cell-cell adhesion glycoproteins

Phenotypes From GWAS Catalog for PCDH9 Gene

Gene Ontology (GO) - Molecular Function for PCDH9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDH9: view
genes like me logo Genes that share phenotypes with PCDH9: view

Animal Models for PCDH9 Gene

MGI Knock Outs for PCDH9:
  • Pcdh9 Pcdh9<tm1Mjhk>
  • Pcdh9 Pcdh9<tm1.1(KOMP)Vlcg>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDH9

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PCDH9 Gene

Localization for PCDH9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDH9 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 PCDH9 gene
Compartment Confidence
plasma membrane 4
extracellular 2
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
cytosol 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centrosome (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCDH9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030426 growth cone IEA --
genes like me logo Genes that share ontologies with PCDH9: view

Pathways & Interactions for PCDH9 Gene

PathCards logo

SuperPathways for PCDH9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDH9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA,IBA 21873635
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0030900 forebrain development IEA --
genes like me logo Genes that share ontologies with PCDH9: view

No data available for Pathways by source and SIGNOR curated interactions for PCDH9 Gene

Drugs & Compounds for PCDH9 Gene

(1) Drugs for PCDH9 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6876
genes like me logo Genes that share compounds with PCDH9: view

Transcripts for PCDH9 Gene

mRNA/cDNA for PCDH9 Gene

18 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDH9

Alternative Splicing Database (ASD) splice patterns (SP) for PCDH9 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c
SP1: -
SP2: - -
SP3: - - -

Relevant External Links for PCDH9 Gene

GeneLoc Exon Structure for

Expression for PCDH9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCDH9 Gene

mRNA differential expression in normal tissues according to GTEx for PCDH9 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x5.1), Brain - Amygdala (x4.5), Brain - Anterior cingulate cortex (BA24) (x4.4), Brain - Hippocampus (x4.3), and Brain - Substantia nigra (x4.2).

Protein differential expression in normal tissues from HIPED for PCDH9 Gene

This gene is overexpressed in Frontal cortex (28.7), Brain (26.9), and Fetal Brain (7.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PCDH9 Gene

Protein tissue co-expression partners for PCDH9 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCDH9

SOURCE GeneReport for Unigene cluster for PCDH9 Gene:


Evidence on tissue expression from TISSUES for PCDH9 Gene

  • Nervous system(4.9)
  • Heart(2.3)
  • Kidney(2.1)
genes like me logo Genes that share expression patterns with PCDH9: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDH9 Gene

Orthologs for PCDH9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDH9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDH9 30 31
  • 99.49 (n)
(Monodelphis domestica)
Mammalia PCDH9 31
  • 97 (a)
(Canis familiaris)
Mammalia PCDH9 30 31
  • 96.42 (n)
(Bos Taurus)
Mammalia PCDH9 30 31
  • 95.63 (n)
(Rattus norvegicus)
Mammalia Pcdh9 30
  • 92.7 (n)
(Mus musculus)
Mammalia Pcdh9 30 17 31
  • 92.51 (n)
(Gallus gallus)
Aves PCDH9 30 31
  • 86.99 (n)
(Anolis carolinensis)
Reptilia PCDH9 31
  • 97 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia pcdh9 30
  • 80.25 (n)
(Danio rerio)
Actinopterygii PCDH9 31
  • 86 (a)
pcdh9 30
  • 74.4 (n)
Species where no ortholog for PCDH9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for PCDH9 Gene

Gene Tree for PCDH9 (if available)
Gene Tree for PCDH9 (if available)
Evolutionary constrained regions (ECRs) for PCDH9: view image

Paralogs for PCDH9 Gene

Variants for PCDH9 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCDH9 Gene

SNP ID Clinical significance and condition Chr 13 pos Variation AA Info Type
rs3764117 Benign: not provided 66,631,388(-) A/G
NM_203487.3(PCDH9):c.3162T>C (p.His1054=)

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PCDH9 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PCDH9 Gene

Variant ID Type Subtype PubMed ID
dgv110e215 CNV deletion 23714750
dgv1699n100 CNV loss 25217958
dgv1700n100 CNV loss 25217958
dgv228n27 CNV loss 19166990
dgv3219n54 CNV loss 21841781
dgv3220n54 CNV loss 21841781
dgv3221n54 CNV loss 21841781
dgv3222n54 CNV loss 21841781
dgv3223n54 CNV loss 21841781
dgv3224n54 CNV loss 21841781
dgv341e214 CNV loss 21293372
dgv342e214 CNV gain 21293372
dgv553e212 CNV loss 25503493
dgv554e212 CNV loss 25503493
dgv555e212 CNV loss 25503493
esv2422196 CNV deletion 17116639
esv2657997 CNV deletion 23128226
esv2660269 CNV deletion 23128226
esv2661300 CNV deletion 23128226
esv2664008 CNV deletion 23128226
esv2667447 CNV deletion 23128226
esv2667555 CNV deletion 23128226
esv2672074 CNV deletion 23128226
esv2678519 CNV deletion 23128226
esv2747551 CNV deletion 23290073
esv2747553 CNV deletion 23290073
esv2747554 CNV deletion 23290073
esv2747555 CNV deletion 23290073
esv2747556 CNV deletion 23290073
esv2759943 CNV loss 17122850
esv2759944 CNV loss 17122850
esv2760282 CNV loss 21179565
esv2761797 CNV loss 21179565
esv2761798 CNV loss 21179565
esv2761800 CNV loss 21179565
esv28367 CNV loss 19812545
esv3303542 CNV mobile element insertion 20981092
esv3304913 CNV mobile element insertion 20981092
esv3329136 CNV insertion 20981092
esv3377371 CNV insertion 20981092
esv3414442 CNV insertion 20981092
esv34348 CNV loss 17911159
esv3550613 CNV deletion 23714750
esv3550614 CNV deletion 23714750
esv3580710 CNV loss 25503493
esv3580711 CNV loss 25503493
esv3580721 CNV loss 25503493
esv3582583 CNV gain 25503493
esv3582594 CNV gain 25503493
esv3582605 CNV gain 25503493
esv3582616 CNV gain 25503493
esv3632502 CNV loss 21293372
esv3632503 CNV loss 21293372
esv3632505 CNV loss 21293372
esv3632506 CNV loss 21293372
esv3632507 CNV loss 21293372
esv3632510 CNV loss 21293372
esv3632511 CNV loss 21293372
esv3632512 CNV loss 21293372
esv3632513 CNV loss 21293372
esv3632515 CNV loss 21293372
esv3632517 CNV loss 21293372
esv3632522 CNV loss 21293372
esv3632523 CNV loss 21293372
esv3632524 CNV loss 21293372
esv3632525 CNV gain 21293372
esv3632526 CNV loss 21293372
esv3632528 CNV loss 21293372
esv3632529 CNV loss 21293372
esv3632533 CNV loss 21293372
esv3632534 CNV gain 21293372
esv3632536 CNV loss 21293372
esv3892376 CNV loss 25118596
esv3892377 CNV loss 25118596
esv3892378 CNV loss 25118596
nsv1037217 CNV gain 25217958
nsv1040715 CNV gain 25217958
nsv1042756 CNV loss 25217958
nsv1043110 CNV loss 25217958
nsv1043603 CNV gain 25217958
nsv1044881 CNV loss 25217958
nsv1051576 CNV loss 25217958
nsv1053874 CNV loss 25217958
nsv1074 CNV insertion 18451855
nsv1122839 CNV deletion 24896259
nsv437166 CNV loss 16327808
nsv438254 CNV loss 16468122
nsv455926 CNV loss 19166990
nsv455928 CNV loss 19166990
nsv455929 CNV loss 19166990
nsv455931 CNV loss 19166990
nsv455932 CNV loss 19166990
nsv455933 CNV loss 19166990
nsv471142 CNV loss 18288195
nsv471143 CNV loss 18288195
nsv474082 CNV novel sequence insertion 20440878
nsv507708 OTHER sequence alteration 20534489
nsv511510 CNV loss 21212237
nsv512325 CNV loss 21212237
nsv518201 CNV loss 19592680
nsv522396 CNV loss 19592680
nsv523360 CNV loss 19592680
nsv528416 CNV loss 19592680
nsv562100 CNV loss 21841781
nsv562102 CNV loss 21841781
nsv562128 CNV loss 21841781
nsv562129 CNV loss 21841781
nsv562130 CNV loss 21841781
nsv562131 CNV loss 21841781
nsv562132 CNV loss 21841781
nsv562133 CNV loss 21841781
nsv562134 CNV loss 21841781
nsv562135 CNV loss 21841781
nsv562136 CNV gain 21841781
nsv562137 CNV loss 21841781
nsv562138 CNV loss 21841781
nsv562139 CNV loss 21841781
nsv64575 CNV deletion 16902084
nsv818971 CNV loss 17921354
nsv826687 CNV loss 20364138
nsv826688 CNV loss 20364138
nsv832639 CNV gain 17160897
nsv832640 CNV gain 17160897
nsv832641 CNV loss 17160897
nsv9084 CNV gain 18304495
nsv958070 CNV deletion 24416366
nsv976260 CNV deletion 23825009
nsv977254 CNV duplication 23825009

Variation tolerance for PCDH9 Gene

Residual Variation Intolerance Score: 7.45% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.19; 61.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDH9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDH9 Gene

Disorders for PCDH9 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PCDH9 Gene - From: COP

Disorder Aliases PubMed IDs
auditory neuropathy, autosomal dominant, 1
  • auna1
chromosome 9p deletion syndrome
  • monosomy 9p syndrome
- elite association - COSMIC cancer census association via MalaCards
Search PCDH9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PCDH9

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with PCDH9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDH9 Gene

Publications for PCDH9 Gene

  1. Characterization of two novel protocadherins (PCDH8 and PCDH9) localized on human chromosome 13 and mouse chromosome 14. (PMID: 9787079) Strehl S … Lalande M (Genomics 1998) 2 3 23
  2. A genome-wide association study on obesity and obesity-related traits. (PMID: 21552555) Wang K … Price RA (PloS one 2011) 3 41
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41
  5. The DNA sequence and analysis of human chromosome 13. (PMID: 15057823) Dunham A … Ross MT (Nature 2004) 3 4

Products for PCDH9 Gene

Sources for PCDH9 Gene