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Aliases for PCDH11Y Gene

Aliases for PCDH11Y Gene

  • Protocadherin 11 Y-Linked 2 3 5
  • Protocadherin On The Y Chromosome 3 4
  • Protocadherin Prostate Cancer 3 4
  • Protocadherin-PC 3 4
  • Protocadherin 22 2 3
  • PCDH22 3 4
  • PCDHY 3 4
  • Protocadherin-11 Y-Linked 3
  • Protocadherin-11 4
  • Protocadherin-22 4
  • PCDH-PC 3
  • PCDH-Y 4
  • PCDH11 4
  • PCDHX 3

External Ids for PCDH11Y Gene

Previous HGNC Symbols for PCDH11Y Gene

  • PCDH22

Previous GeneCards Identifiers for PCDH11Y Gene

  • GC0YP004833
  • GC0YP004571
  • GC0YP004911
  • GC0YP004868

Summaries for PCDH11Y Gene

Entrez Gene Summary for PCDH11Y Gene

  • This gene belongs to the protocadherin family, a subfamily of the cadherin superfamily. The encoded protein consists of an extracellular domain containing seven cadherin repeats, a transmembrane domain, and a cytoplasmic tail that differs from those of the classical cadherins. This gene is located on the Y chromosome in a block of X/Y homology and is very closely related to its paralog on the X chromosome. The protein is thought to play a role in cell-cell recognition during development of the central nervous system. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

GeneCards Summary for PCDH11Y Gene

PCDH11Y (Protocadherin 11 Y-Linked) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH11X.

UniProtKB/Swiss-Prot for PCDH11Y Gene

  • Potential calcium-dependent cell-adhesion protein.

Additional gene information for PCDH11Y Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDH11Y Gene

Genomics for PCDH11Y Gene

GeneHancer (GH) Regulatory Elements for PCDH11Y Gene

Promoters and enhancers for PCDH11Y 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
GH0YJ005324 Enhancer 0.2 ENCODE 0.1 +324.8 324789 0.2 PIR60612 PIR42097 PCDH11Y
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDH11Y on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDH11Y gene promoter:
  • c-Myb
  • MEF-2A
  • aMEF-2
  • CUTL1
  • p53
  • POU2F1
  • POU2F1a
  • POU2F1b
  • POU2F1c

Genomic Locations for PCDH11Y Gene

Genomic Locations for PCDH11Y Gene
742,003 bases
Plus strand
741,999 bases
Plus strand

Genomic View for PCDH11Y Gene

Genes around PCDH11Y on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDH11Y Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDH11Y Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDH11Y Gene

Proteins for PCDH11Y Gene

  • Protein details for PCDH11Y Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin-11 Y-linked
    Protein Accession:
    Secondary Accessions:
    • Q70LR6
    • Q70LR8
    • Q70LS0
    • Q70LS1
    • Q70LS2
    • Q70LS3
    • Q70LS4
    • Q70LS5
    • Q8WY34
    • Q9BZA9
    • Q9H4E1

    Protein attributes for PCDH11Y Gene

    1340 amino acids
    Molecular mass:
    146775 Da
    Quaternary structure:
    • Interacts with CTNNB1.

    Alternative splice isoforms for PCDH11Y Gene


neXtProt entry for PCDH11Y Gene

Post-translational modifications for PCDH11Y Gene

  • Glycosylation at Asn805, Asn585, isoforms=2, 3, 4376, isoforms=2, 3, 486, isoforms=2, 3, 480, and isoforms=2, 3, 459
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PCDH11Y Gene

Domains & Families for PCDH11Y Gene

Gene Families for PCDH11Y Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for PCDH11Y Gene

Suggested Antigen Peptide Sequences for PCDH11Y Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDH11Y: view

No data available for UniProtKB/Swiss-Prot for PCDH11Y Gene

Function for PCDH11Y Gene

Molecular function for PCDH11Y Gene

UniProtKB/Swiss-Prot Function:
Potential calcium-dependent cell-adhesion protein.

Gene Ontology (GO) - Molecular Function for PCDH11Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDH11Y: view
genes like me logo Genes that share phenotypes with PCDH11Y: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDH11Y

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDH11Y Gene

Localization for PCDH11Y Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDH11Y 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 PCDH11Y gene
Compartment Confidence
plasma membrane 5
extracellular 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for PCDH11Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDH11Y: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PCDH11Y Gene

Pathways & Interactions for PCDH11Y Gene

SuperPathways for PCDH11Y Gene

No Data Available

Interacting Proteins for PCDH11Y Gene

Gene Ontology (GO) - Biological Process for PCDH11Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
genes like me logo Genes that share ontologies with PCDH11Y: view

No data available for Pathways by source and SIGNOR curated interactions for PCDH11Y Gene

Drugs & Compounds for PCDH11Y Gene

(1) Drugs for PCDH11Y 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 PCDH11Y: view

Transcripts for PCDH11Y Gene

mRNA/cDNA for PCDH11Y Gene

(9) REFSEQ mRNAs :
(20) Additional mRNA sequences :
(2) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PCDH11Y Gene

Protocadherin 11 Y-linked:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDH11Y

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDH11Y Gene

No ASD Table

Relevant External Links for PCDH11Y Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDH11Y Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDH11Y Gene

mRNA differential expression in normal tissues according to GTEx for PCDH11Y Gene

This gene is overexpressed in Brain - Hypothalamus (x8.1), Brain - Amygdala (x7.1), Brain - Hippocampus (x6.6), Brain - Anterior cingulate cortex (BA24) (x6.2), Brain - Frontal Cortex (BA9) (x4.5), and Brain - Cortex (x4.2).

NURSA nuclear receptor signaling pathways regulating expression of PCDH11Y Gene:


SOURCE GeneReport for Unigene cluster for PCDH11Y Gene:


mRNA Expression by UniProt/SwissProt for PCDH11Y Gene:

Tissue specificity: Expressed strongly in fetal brain and brain (cortex, amygdala, thalamus, substantia nigra, hippocampus, caudate nucleus and corpus callosum). Expressed at low level in testis. Expressed in apoptosis-resistant cells.

Evidence on tissue expression from TISSUES for PCDH11Y Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with PCDH11Y: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDH11Y Gene

Orthologs for PCDH11Y Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDH11Y Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia -- 34
  • 85 (a)
(Canis familiaris)
Mammalia -- 34
  • 82 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 71 (a)
(Mus musculus)
Mammalia Pcdh11x 34
  • 64 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 49 (a)
(Gallus gallus)
Aves -- 34
  • 71 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 70 (a)
(Danio rerio)
Actinopterygii PCDH11Y 34
  • 65 (a)
Species where no ortholog for PCDH11Y 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)
  • chimpanzee (Pan troglodytes)
  • 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)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PCDH11Y Gene

Gene Tree for PCDH11Y (if available)
Gene Tree for PCDH11Y (if available)

Paralogs for PCDH11Y Gene

Variants for PCDH11Y Gene

Sequence variations from dbSNP and Humsavar for PCDH11Y Gene

SNP ID Clin Chr 0Y pos Variation AA Info Type
rs1000297456 -- 5,219,368(+) C/A genic_downstream_transcript_variant, intron_variant
rs1002232889 -- 5,012,189(+) C/A genic_upstream_transcript_variant, intron_variant
rs1002346118 -- 5,708,355(+) C/T genic_downstream_transcript_variant, intron_variant
rs1003055389 -- 5,393,721(+) C/A genic_downstream_transcript_variant, intron_variant
rs1003261694 -- 5,593,444(+) G/A genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDH11Y Gene

Variant ID Type Subtype PubMed ID
esv3577576 CNV gain 25503493
esv3577577 CNV gain 25503493
nsv1110640 CNV duplication 24896259
nsv1149113 CNV duplication 26484159
nsv958558 CNV deletion 24416366

Additional Variant Information for PCDH11Y Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for PCDH11Y Gene

Disorders for PCDH11Y Gene


  • Note=A chromosomal aberration involving PCDH11Y is a cause of multiple congenital abnormalities, including severe bilateral vesicoureteral reflux (VUR) with ureterovesical junction defects. Translocation t(Y;3)(p11;p12) with ROBO2.

Additional Disease Information for PCDH11Y

No disorders were found for PCDH11Y Gene.

No data available for MalaCards and Genatlas for PCDH11Y Gene

Publications for PCDH11Y Gene

  1. Conservation of PCDHX in mammals; expression of human X/Y genes predominantly in brain. (PMID: 11003707) Blanco P … Affara NA (Mammalian genome : official journal of the International Mammalian Genome Society 2000) 2 3 4 58
  2. Disruption of ROBO2 is associated with urinary tract anomalies and confers risk of vesicoureteral reflux. (PMID: 17357069) Lu W … Maas RL (American journal of human genetics 2007) 3 4 58
  3. PCDH11 is X/Y homologous in Homo sapiens but not in Gorilla gorilla and Pan troglodytes. (PMID: 16825765) Wilson ND … Volpi EV (Cytogenetic and genome research 2006) 3 22 58
  4. Expression and genetic variability of PCDH11Y, a gene specific to Homo sapiens and candidate for susceptibility to psychiatric disorders. (PMID: 16331680) Durand CM … Bourgeron T (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2006) 3 4 58
  5. Protocadherin X ( PCDHX) and Y ( PCDHY) genes; multiple mRNA isoforms encoding variant signal peptides and cytoplasmic domains. (PMID: 14727141) Blanco-Arias P … Affara NA (Mammalian genome : official journal of the International Mammalian Genome Society 2004) 3 4 58

Products for PCDH11Y Gene

Sources for PCDH11Y Gene

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