U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

PCDH11Y protocadherin 11 Y-linked [ Homo sapiens (human) ]

Gene ID: 83259, updated on 11-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
PCDH11Yprovided by HGNC
Official Full Name
protocadherin 11 Y-linkedprovided by HGNC
Primary source
HGNC:HGNC:15813
See related
Ensembl:ENSG00000099715 MIM:400022; AllianceGenome:HGNC:15813
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PCDHX; PCDHY; PCDH22; PCDH-PC
Summary
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]
Expression
Biased expression in brain (RPKM 1.4), ovary (RPKM 0.6) and 5 other tissues See more
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
Yp11.2
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (5000296..5742228)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (4679814..5422252)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (4868337..5610269)

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene microRNA 9985 Neighboring gene SERPINE1 mRNA binding protein 1 pseudogene 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrY:4822044-4822666 Neighboring gene RNA, U2 small nuclear 57, pseudogene Neighboring gene voltage dependent anion channel 1 pseudogene 6 Neighboring gene NANOG hESC enhancer GRCh37_chrY:5192864-5193440 Neighboring gene eukaryotic translation initiation factor 4A1 pseudogene 2 Neighboring gene keratin 18 pseudogene 10 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrY:5577568-5578528 Neighboring gene sorting nexin 3 pseudogene 1 Y-linked Neighboring gene ribosomal protein L26 pseudogene 37 Neighboring gene TUSC2 pseudogene 1

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Expression of protocadherin 11Yb (PCDH11Yb) in seminal germ cells is correlated with fertility status in men. Anilkumar TR, et al. Reprod Fertil Dev, 2017 Oct. PMID 28241900
  2. Non-syndromic language delay in a child with disruption in the Protocadherin11X/Y gene pair. Speevak MD, et al. Am J Med Genet B Neuropsychiatr Genet, 2011 Jun. PMID 21480486
  3. Footprints of X-to-Y gene conversion in recent human evolution. Trombetta B, et al. Mol Biol Evol, 2010 Mar. PMID 19812029
  4. Evidence for positive selection on Protocadherin Y gene in Homo sapiens: implications for schizophrenia. Kalmady SV, et al. Schizophr Res, 2009 Mar. PMID 18938061
  5. Replication profile of PCDH11X and PCDH11Y, a gene pair located in the non-pseudoautosomal homologous region Xq21.3/Yp11.2. Wilson ND, et al. Chromosome Res, 2007. PMID 17671842, Free PMC Article

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. In the present study, PCDH11Yb, but not PCDH11Ya or PCDH11Yc, was expressed in germ cells isolated from the semen of all 13 men with proven fertility. However, in several subjects from various infertility classes, there was complete absence or a significant reduction in the expression of PCDH11Yb. In conclusion, expression levels of PCDH11Yb in germ cells in the semen were correlated with the fertility status of men.
    Title: Expression of protocadherin 11Yb (PCDH11Yb) in seminal germ cells is correlated with fertility status in men.
  2. PCDH11Y expression was detected in the fetal neocortex, ganglionic eminences, cerebellum, and inferior olive. In the adult brain, the cerebral cortex, hippocampal formation, and cerebellum and brain stem were immunoreactive.
    Title: Protocadherin 11X/Y a human-specific gene pair: an immunohistochemical survey of fetal and adult brains.
  3. the PCDH11X/Y gene pair determines cerebral asymmetry by initiating the right shift in Homo sapiens
    Title: The protocadherin 11X/Y (PCDH11X/Y) gene pair as determinant of cerebral asymmetry in modern Homo sapiens.
  4. Our data...extended the lack of association of late-onset Alzheimer's disease to common PCDH11Y variants.
    Title: Lack of association between protocadherin 11-X/Y (PCDH11X and PCDH11Y) polymorphisms and late onset Alzheimer's disease.
  5. The present article investigated the patterns of alternative splicing and expression of the PCDH11X/Y genes.
    Title: Quantitative analysis of alternative transcripts of human PCDH11X/Y genes.
  6. a candidate for the evolution of hominid-specific characteristics including the sexual dimorphism of cerebral asymmetry, a putative correlate of language
    Title: Accelerated evolution of Protocadherin11X/Y: a candidate gene-pair for cerebral asymmetry and language.
  7. This study provided the evidence for positive selection on Protocadherin Y gene in human lineage for schizophrenia.
    Title: Evidence for positive selection on Protocadherin Y gene in Homo sapiens: implications for schizophrenia.
  8. We consider that a stronger case can be mounted for the Protocadherin11X/Y gene pair located in the hominid specific Xq21.3/Yp11.2 region of homology that was generated by a duplication from the X
    Title: Where and what is the right shift factor or cerebral dominance gene? A critique of Francks et al. (2007).
  9. Findings do not support the role of PCDH11Y, or more generally of a frequent specific Y chromosome, in the susceptibility to these neuropsychiatric disorders.
    Title: Expression and genetic variability of PCDH11Y, a gene specific to Homo sapiens and candidate for susceptibility to psychiatric disorders.
  10. Our findings suggest a novel mechanism for the progression of CaP involving expression of PCDH-PC. This novel protocadherin induces Wnt signaling, promotes malignant behavior and hormone-resistance of CaP cells.
    Title: Protocadherin-PC promotes androgen-independent prostate cancer cell growth.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genetically distinct subsets within ANCA-associated vasculitis.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

Go to the top of the page Help
Preferred Names
protocadherin-11 Y-linked
Names
protocadherin 22
protocadherin on the Y chromosome
protocadherin prostate cancer
protocadherin-PC

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011652.1 RefSeqGene

    Range
    5071..746999
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001278619.2 → NP_001265548.1  protocadherin-11 Y-linked isoform a

    See identical proteins and their annotated locations for NP_001265548.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (d, also known as Ty2) contains an alternate exon in the 5' UTR, compared to variant a. Variants a and d encode the same isoform (a).
    Source sequence(s)
    AC010722, AF277053, AJ276803
    Consensus CDS
    CCDS14776.1
    UniProtKB/TrEMBL
    A8K0W1
    Related
    ENSP00000482115.1, ENST00000622698.4
    Conserved Domains (4) summary
    cd11304
    Location:493 → 587
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:405 → 485
    CA; Cadherin repeats
    pfam08374
    Location:796 → 997
    Protocadherin; Protocadherin
    cl09101
    Location:49 → 123
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  2. NM_001395587.1 → NP_001382516.1  protocadherin-11 Y-linked isoform d

    Status: REVIEWED

    Source sequence(s)
    AC010081, AC010722, AC012067, AC012667
    Consensus CDS
    CCDS94706.1
    UniProtKB/TrEMBL
    A0A8V8TP37
    Related
    ENSP00000513983.1, ENST00000698851.1
    Conserved Domains (2) summary
    cd11304
    Location:412 → 506
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:324 → 404
    CA; Cadherin repeats

  3. NM_032971.3 → NP_116753.1  protocadherin-11 Y-linked isoform a

    See identical proteins and their annotated locations for NP_116753.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (a, also known as Ty1) represents the shortest transcript and encodes the shortest isoform (a). Variants a and d encode the same isoform (a).
    Source sequence(s)
    AC010722, AJ276803
    Consensus CDS
    CCDS14776.1
    UniProtKB/TrEMBL
    A8K0W1
    Related
    ENSP00000330552.4, ENST00000333703.8
    Conserved Domains (4) summary
    cd11304
    Location:493 → 587
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:405 → 485
    CA; Cadherin repeats
    pfam08374
    Location:796 → 997
    Protocadherin; Protocadherin
    cl09101
    Location:49 → 123
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  4. NM_032972.3 → NP_116754.1  protocadherin-11 Y-linked isoform b precursor

    See identical proteins and their annotated locations for NP_116754.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (b, also known as Ty4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant a. The encoded isoform (b) is longer and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AC010722, AF332216, AJ276803
    Consensus CDS
    CCDS14777.1
    UniProtKB/TrEMBL
    A8K0W1
    Related
    ENSP00000355419.5, ENST00000362095.9
    Conserved Domains (4) summary
    cd11304
    Location:504 → 598
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:416 → 496
    CA; Cadherin repeats
    pfam08374
    Location:807 → 1008
    Protocadherin; Protocadherin
    cl09101
    Location:60 → 134
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  5. NM_032973.2 → NP_116755.1  protocadherin-11 Y-linked isoform c precursor

    See identical proteins and their annotated locations for NP_116755.1

    Status: REVIEWED

    Source sequence(s)
    AF332217, AJ564971
    Consensus CDS
    CCDS76066.1
    UniProtKB/Swiss-Prot
    Q70LR6, Q70LR8, Q70LS0, Q70LS1, Q70LS2, Q70LS3, Q70LS4, Q70LS5, Q8WY34, Q9BZA8, Q9BZA9, Q9H4E1
    Related
    ENSP00000383306.3, ENST00000400457.3
    Conserved Domains (5) summary
    cd11304
    Location:504 → 598
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:416 → 496
    CA; Cadherin repeats
    pfam08374
    Location:807 → 1008
    Protocadherin; Protocadherin
    pfam14650
    Location:1164 → 1270
    FAM75; FAM75 family
    cl09101
    Location:60 → 134
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

    Range
    5000296..5742228
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017030079.2 → XP_016885568.1  protocadherin-11 Y-linked isoform X1

  2. XM_017030081.2 → XP_016885570.1  protocadherin-11 Y-linked isoform X1

  3. XM_017030080.2 → XP_016885569.1  protocadherin-11 Y-linked isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060948.1 Alternate T2T-CHM13v2.0

    Range
    4679814..5422252
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054328379.1 → XP_054184354.1  protocadherin-11 Y-linked isoform X1

  2. XM_054328381.1 → XP_054184356.1  protocadherin-11 Y-linked isoform X1

  3. XM_054328380.1 → XP_054184355.1  protocadherin-11 Y-linked isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BZA8.1 GenPept UniProtKB/Swiss-Prot:Q9BZA8

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous