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Aliases for PCDH9 Gene

Aliases for PCDH9 Gene

  • Protocadherin 9 2 3 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 Trichorhinophalangeal Syndrome, Type I. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH20.

UniProtKB/Swiss-Prot for PCDH9 Gene

  • Potential calcium-dependent cell-adhesion protein.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDH9 Gene

Genomics for PCDH9 Gene

Regulatory Elements for PCDH9 Gene

Enhancers for PCDH9 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 PCDH9 on UCSC Golden Path with GeneCards custom track

Promoters for PCDH9 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PCDH9 on UCSC Golden Path with GeneCards custom track

Genomic Location for PCDH9 Gene

66,302,834 bp from pter
67,230,445 bp from pter
927,612 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

Proteomics data for PCDH9 Gene at MOPED

Post-translational modifications for PCDH9 Gene

  • Glycosylation at Asn 48, Asn 148, Asn 306, Asn 307, Asn 347, Asn 368, Asn 450, Asn 511, Asn 630, Asn 681, Asn 734, Asn 754, Asn 775, and Asn 780
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PCDH9 Gene

Domains & Families for PCDH9 Gene

Gene Families for PCDH9 Gene

Protein Domains for PCDH9 Gene

Suggested Antigen Peptide Sequences for PCDH9 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 7 cadherin domains.
  • Contains 7 cadherin domains.
genes like me logo Genes that share domains with PCDH9: view

Function for PCDH9 Gene

Molecular function for PCDH9 Gene

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
UniProtKB/Swiss-Prot Function:
Potential calcium-dependent cell-adhesion protein.
genes like me logo Genes that share phenotypes with PCDH9: view

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , 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

Jensen Localization Image for PCDH9 Gene COMPARTMENTS Subcellular localization image for PCDH9 gene
Compartment Confidence
plasma membrane 5
cytosol 1
endoplasmic reticulum 1
extracellular 1
golgi apparatus 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for PCDH9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016021 integral component of membrane IEA --
GO:0044291 cell-cell contact zone IEA --
genes like me logo Genes that share ontologies with PCDH9: view

Pathways & Interactions for PCDH9 Gene

SuperPathways for PCDH9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDH9 Gene


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 0
genes like me logo Genes that share compounds with PCDH9: view

Transcripts for PCDH9 Gene

Unigene Clusters for PCDH9 Gene

Protocadherin 9:
Representative Sequences:

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
ECgene alternative splicing isoforms for

Expression for PCDH9 Gene

mRNA expression in normal human tissues 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, PaxDb, MOPED, and MaxQB for PCDH9 Gene

SOURCE GeneReport for Unigene cluster for PCDH9 Gene Hs.654709

genes like me logo Genes that share expression patterns with PCDH9: view

Protein tissue co-expression partners for PCDH9 Gene

- Elite partner

Primer Products

No data available for mRNA Expression by UniProt/SwissProt 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
(Bos Taurus)
Mammalia PCDH9 35
  • 95.63 (n)
  • 99.19 (a)
PCDH9 36
  • 98 (a)
(Canis familiaris)
Mammalia PCDH9 35
  • 96.42 (n)
  • 99.6 (a)
PCDH9 36
  • 99 (a)
(Mus musculus)
Mammalia Pcdh9 35
  • 92.51 (n)
  • 98.22 (a)
Pcdh9 16
Pcdh9 36
  • 98 (a)
(Pan troglodytes)
Mammalia PCDH9 35
  • 99.49 (n)
  • 99.68 (a)
PCDH9 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Pcdh9 35
  • 92.7 (n)
  • 98.54 (a)
(Monodelphis domestica)
Mammalia PCDH9 36
  • 97 (a)
(Gallus gallus)
Aves PCDH9 35
  • 86.99 (n)
  • 96.24 (a)
PCDH9 36
  • 97 (a)
(Anolis carolinensis)
Reptilia PCDH9 36
  • 97 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdh9 35
  • 80.25 (n)
  • 91.19 (a)
(Danio rerio)
Actinopterygii pcdh9 35
  • 74.4 (n)
  • 84.71 (a)
PCDH9 36
  • 86 (a)
Species with no ortholog for PCDH9:
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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)

Paralogs for PCDH9 Gene

Paralogs for PCDH9 Gene

genes like me logo Genes that share paralogs with PCDH9: view

Variants for PCDH9 Gene

Sequence variations from dbSNP and Humsavar for PCDH9 Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type
rs149448 -- 67,049,632(+) GCACC(A/G)AGCAC intron-variant
rs155008 -- 67,018,184(+) TTATA(C/T)TGGAG intron-variant
rs155009 -- 67,017,933(+) ATAAC(A/G)TTATT intron-variant
rs155010 -- 67,017,360(+) AATTA(C/T)ACCAT intron-variant
rs155011 -- 67,067,619(+) AAAGT(A/T)TTTAA intron-variant

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

Variant ID Type Subtype PubMed ID
nsv900352 CNV Loss 21882294
nsv900388 CNV Loss 21882294
nsv900389 CNV Loss 21882294
esv2672074 CNV Deletion 23128226
nsv900390 CNV Loss 21882294
dgv567e1 CNV Complex 17122850
nsv9084 CNV Gain 18304495
essv4340 CNV CNV 17122850
nsv1074 CNV Insertion 18451855
esv2422196 CNV Deletion 17116639
nsv832639 CNV Gain 17160897
esv2747551 CNV Deletion 23290073
nsv900391 CNV Loss 21882294
dgv1658n71 CNV Loss 21882294
nsv471142 CNV Loss 18288195
dgv228n27 CNV Loss 19166990
nsv455926 CNV Loss 19166990
esv2747553 CNV Deletion 23290073
esv2661300 CNV Deletion 23128226
esv2747554 CNV Deletion 23290073
nsv511510 CNV Loss 21212237
nsv512325 CNV Loss 21212237
esv2747555 CNV Deletion 23290073
esv2667555 CNV Deletion 23128226
esv28367 CNV Loss 19812545
nsv900398 CNV Loss 21882294
nsv455928 CNV Loss 19166990
esv2664008 CNV Deletion 23128226
nsv826687 CNV Loss 20364138
nsv455929 CNV Loss 19166990
nsv826688 CNV Loss 20364138
esv34348 CNV Loss 17911159
dgv568e1 CNV Complex 17122850
nsv455931 CNV Loss 19166990
dgv1659n71 CNV Loss 21882294
nsv900400 CNV Loss 21882294
nsv455932 CNV Loss 19166990
nsv471143 CNV Loss 18288195
nsv523360 CNV Loss 19592680
nsv900403 CNV Loss 21882294
nsv900404 CNV Loss 21882294
esv2747556 CNV Deletion 23290073
esv2657997 CNV Deletion 23128226
nsv900405 CNV Loss 21882294
nsv528416 CNV Loss 19592680
nsv455933 CNV Loss 19166990
esv2660269 CNV Deletion 23128226
nsv64575 CNV Loss 16902084
nsv900406 CNV Loss 21882294
nsv900407 CNV Loss 21882294
esv2678519 CNV Deletion 23128226
nsv832640 CNV Gain 17160897
nsv437166 CNV Loss 16327808
nsv507708 CNV Insertion 20534489
dgv1660n71 CNV Loss 21882294
nsv818971 CNV Loss 17921354
dgv1661n71 CNV Loss 21882294
esv2667447 CNV Deletion 23128226
nsv900412 CNV Loss 21882294
nsv438254 CNV Loss 16468122
nsv900414 CNV Loss 21882294
nsv900415 CNV Loss 21882294
nsv518201 CNV Loss 19592680
nsv832641 CNV Loss 17160897
esv267821 CNV Insertion 20981092
esv269191 CNV Insertion 20981092
nsv522396 CNV Loss 19592680

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)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for PCDH9 Gene

Disorders for PCDH9 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PCDH9 Gene - From: DISEASES

Disorder Aliases PubMed IDs
trichorhinophalangeal syndrome, type i
  • trichorhinophalangeal syndrome, type iii
- elite association - COSMIC cancer census association via MalaCards
Search PCDH9 in MalaCards View complete list of genes associated with diseases

Relevant External Links for PCDH9

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 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 67
  2. Loss of PCDH9 is associated with the differentiation of tumor cells and metastasis and predicts poor survival in gastric cancer. (PMID: 25869928) Chen Y. … Yu G. (Clin. Exp. Metastasis 2015) 3
  3. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  4. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. (PMID: 24722188) Corominas R. … Iakoucheva L.M. (Nat. Commun. 2014) 3
  5. Protocadherin 9 inhibits epithelial-mesenchymal transition and cell migration through activating GSK-3I^ in hepatocellular carcinoma. (PMID: 25172662) Zhu P. … Lu F. (Biochem. Biophys. Res. Commun. 2014) 3

Products for PCDH9 Gene

Sources for PCDH9 Gene