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... See more...

Aliases for PCDH11Y Gene

Aliases for PCDH11Y Gene

  • Protocadherin 11 Y-Linked 2 3 5
  • PCDHY 2 3 4
  • Protocadherin On The Y Chromosome 3 4
  • Protocadherin Prostate Cancer 3 4
  • Protocadherin-11 Y-Linked 3 4
  • Protocadherin 22 2 3
  • Protocadherin-PC 3 4
  • PCDH22 3 4
  • Protocadherin-11 4
  • Protocadherin-22 4
  • PCDH-PC 3
  • PCDH11Y 5
  • PCDH11 4
  • PCDH-Y 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 Summary for PCDH11Y Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCDH11Y Gene

Genomics for PCDH11Y Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PCDH11Y Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0YJ004992 Enhancer 0.3 Ensembl 0.4 -7.9 -7943 0.2 CTCF RAD21 PCDH11Y piR-32287-197 RF00017-8201
GH0YJ005324 Enhancer 0.2 ENCODE 0.1 +325.0 324971 0.2 piR-41245-323 piR-37567-247 RF00017-8203 RF00017-8201 RF00017-8204 RF00017-8202 PCDH11Y TSPY2
GH0YJ005333 Enhancer 0.2 Ensembl 0.1 +333.7 333657 0.6 piR-32287-201 piR-49097-125 KY945980 RF00017-8203 RF00017-8201 RF00017-8204 PCDH11Y TSPY2
GH0YJ004035 Enhancer 0.2 ENCODE 0 -963.4 -963367 3.3 ENSG00000229308 piR-31534-720 RF00017-8197 TGIF2LY 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCDH11Y

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

Genomic Locations for PCDH11Y Gene

Latest Assembly
chrY:5,000,044-5,742,228
(GRCh38/hg38)
Size:
742,185 bases
Orientation:
Plus strand

Previous Assembly
chrY:4,868,337-5,610,269
(GRCh37/hg19 by Entrez Gene)
Size:
741,933 bases
Orientation:
Plus strand

chrY:4,868,267-5,610,265
(GRCh37/hg19 by Ensembl)
Size:
741,999 bases
Orientation:
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:
    Q9BZA8-PC11Y_HUMAN
    Recommended name:
    Protocadherin-11 Y-linked
    Protein Accession:
    Q9BZA8
    Secondary Accessions:
    • Q70LR6
    • Q70LR8
    • Q70LS0
    • Q70LS1
    • Q70LS2
    • Q70LS3
    • Q70LS4
    • Q70LS5
    • Q8WY34
    • Q9BZA9
    • Q9H4E1

    Protein attributes for PCDH11Y Gene

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

    Alternative splice isoforms for PCDH11Y Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDH11Y Gene

Post-translational modifications for PCDH11Y Gene

  • Glycosylation at Asn59, Asn80, Asn86, Asn376, Asn585, and Asn805
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PCDH11Y Gene

Domains & Families for PCDH11Y Gene

Gene Families for PCDH11Y Gene

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

Protein Domains for PCDH11Y Gene

InterPro:
Blocks:
  • Cadherin
  • Protocadherin

Suggested Antigen Peptide Sequences for PCDH11Y Gene

GenScript: Design optimal peptide antigens:
  • Protocadherin-22 (PC11Y_HUMAN)
  • Protocadherin (Q6KER0_HUMAN)
  • Protocadherin (Q70LR4_HUMAN)
  • Protocadherin (Q70LR5_HUMAN)
  • Protocadherin (Q70LR7_HUMAN)
genes like me logo Genes that share domains with PCDH11Y: view

No data available for Graphical View of Domain Structure and 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.

Phenotypes From GWAS Catalog for PCDH11Y Gene

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

Inhibitory RNAs for research

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

No data available for Enzyme Numbers (IUBMB) , 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.

Gene Ontology (GO) - Cellular Components for PCDH11Y 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:0061827 sperm head IDA --
genes like me logo Genes that share ontologies with PCDH11Y: view

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

Pathways & Interactions for PCDH11Y Gene

PathCards logo

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 IBA 21873635
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007283 spermatogenesis IMP --
GO:0030177 positive regulation of Wnt signaling pathway IMP --
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 Nutra 6959
genes like me logo Genes that share compounds with PCDH11Y: view

Transcripts for PCDH11Y Gene

mRNA/cDNA for PCDH11Y Gene

4 REFSEQ mRNAs :
29 NCBI additional mRNA sequence :
7 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 PCDH11Y

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

No ASD Table

Relevant External Links for PCDH11Y Gene

GeneLoc Exon Structure for
PCDH11Y

Expression for PCDH11Y Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCDH11Y

SOURCE GeneReport for Unigene cluster for PCDH11Y Gene:

Hs.661308

mRNA Expression by UniProt/SwissProt for PCDH11Y Gene:

Q9BZA8-PC11Y_HUMAN
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.
genes like me logo Genes that share expression patterns with PCDH11Y: view

Primer products for research

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 , Evidence on tissue expression from TISSUES 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
Cow
(Bos Taurus)
Mammalia -- 30
  • 85 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia -- 30
  • 82 (a)
OneToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 71 (a)
OneToMany
Mouse
(Mus musculus)
Mammalia Pcdh11x 30
  • 64 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 49 (a)
OneToMany
Chicken
(Gallus gallus)
Aves -- 30
  • 71 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 70 (a)
OneToMany
Zebrafish
(Danio rerio)
Actinopterygii PCDH11Y 30
  • 65 (a)
OneToMany
Species where no ortholog for PCDH11Y 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)
  • 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 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for PCDH11Y Gene

ENSEMBL:
Gene Tree for PCDH11Y (if available)
TreeFam:
Gene Tree for PCDH11Y (if available)
Alliance of Genome Resources:
Additional Orthologs for PCDH11Y

Paralogs for PCDH11Y Gene

Variants for PCDH11Y Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCDH11Y Gene

SNP ID Clinical significance and condition Chr 0Y pos Variation AA Info Type
rs2524543 -- p.Val917Phe
rs2556900 -- p.Ala1320Thr
rs2563389 -- p.Asn1012Lys

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PCDH11Y 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 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
PCDH11Y
Leiden Open Variation Database (LOVD)
PCDH11Y

SNP Genotyping and Copy Number Assays for research

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

Disorders for PCDH11Y Gene

UniProtKB/Swiss-Prot

PC11Y_HUMAN
  • 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

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

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
  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
  3. 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
  4. 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
  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

Products for PCDH11Y Gene

Sources for PCDH11Y Gene