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PCDH11X protocadherin 11 X-linked [ Homo sapiens (human) ]

Gene ID: 27328, updated on 2-Nov-2024

Summary

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Official Symbol
PCDH11Xprovided by HGNC
Official Full Name
protocadherin 11 X-linkedprovided by HGNC
Primary source
HGNC:HGNC:8656
See related
Ensembl:ENSG00000102290 MIM:300246; AllianceGenome:HGNC:8656
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; PCDH-X; PCDH-Y; PCDH11; PCDH22; PCDH11Y; PPP1R119
Summary
This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The encoded protein consists of an extracellular domain containing 7 cadherin repeats, a transmembrane domain and a cytoplasmic tail that differs from those of the classical cadherins. The gene is located in a major X/Y block of homology and its Y homolog, despite divergence leading to coding region changes, is the most closely related cadherin family member. The protein is thought to play a fundamental role in cell-cell recognition essential for the segmental development and function of the central nervous system. Disruption of this gene may be associated with developmental dyslexia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
Expression
Biased expression in ovary (RPKM 3.1), brain (RPKM 2.5) and 2 other tissues See more
Orthologs
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Genomic context

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See PCDH11X in Genome Data Viewer
Location:
Xq21.31
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (91779375..92623230)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (90231454..91073463)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (91034374..91878229)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene SERPINE1 mRNA binding protein 1 pseudogene 4 Neighboring gene uncharacterized LOC105373293 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:91116529-91116701 Neighboring gene RNA, U2 small nuclear 26, pseudogene Neighboring gene voltage dependent anion channel 1 pseudogene 3 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:91354906-91355678 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:91355679-91356451 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:91357997-91358770 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:91358771-91359542 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:91360316-91361087 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:91365337-91366118 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:91417763-91418440 Neighboring gene eukaryotic translation initiation factor 4A1 pseudogene 10 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:91525883-91526412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:91715176-91715676 Neighboring gene keratin 18 pseudogene 11 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:91796763-91796972 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:91844408-91845108 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:91845109-91845809 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:91845810-91846510 Neighboring gene sorting nexin 3 pseudogene 1 X-linked Neighboring gene ribosomal protein L26 pseudogene 36 Neighboring gene TUSC2 pseudogene 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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Related articles in PubMed

  1. The 'big bang' theory of the origin of psychosis and the faculty of language. Crow TJ. Schizophr Res, 2008 Jul. PMID 18502103
  2. Identification of a novel protocadherin gene (PCDH11) on the human XY homology region in Xq21.3. Yoshida K, et al. Genomics, 1999 Dec 15. PMID 10644456
  3. Genetic variation in PCDH11X is associated with susceptibility to late-onset Alzheimer's disease. Carrasquillo MM, et al. Nat Genet, 2009 Feb. PMID 19136949, Free PMC Article
  4. Genome-wide copy number scan identifies disruption of PCDH11X in developmental dyslexia. Veerappa AM, et al. Am J Med Genet B Neuropsychiatr Genet, 2013 Dec. PMID 24591081
  5. PCDH11X variation is not associated with late-onset Alzheimer disease susceptibility. Beecham GW, et al. Psychiatr Genet, 2010 Dec. PMID 20523261, Free PMC Article

See all (41) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PCDH11X, expressed in brain is implicated in cell-cell communication, verbal ability, cerebral asymmetry, and dendritic synaptic plasticity, may be regarded as a new candidate gene for dyslexia.
    Title: Genome-wide copy number scan identifies disruption of PCDH11X in developmental dyslexia.
  2. PCDH11X 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...failed to confirm the association between PCDH11X polymorphisms and late-onset Alzheimer's disease
    Title: Lack of association between protocadherin 11-X/Y (PCDH11X and PCDH11Y) polymorphisms and late onset Alzheimer's disease.
  5. An association between late-onset Alzheimer disease and the PCDH11X polymorphisms, was not detected.
    Title: PCDH11X variation is not associated with late-onset Alzheimer disease susceptibility.
  6. PCDH11X gene polymorphism does not play a major role in the genetic predisposition to late-onset Alzheimer disease in this Han Chinese population.
    Title: Lack of association between PCDH11X genetic variation and late-onset Alzheimer's disease in a Han Chinese population.
  7. association not found for rs5984894 polymorphism in PCDH11X in Alzheimer's disease in Italy
    Title: Failure to replicate an association of rs5984894 SNP in the PCDH11X gene in a collection of 1,222 Alzheimer's disease affected patients.
  8. 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.
  9. This paper proposes that the PCDH11X/Y gene pair generates epigenetic diversity relating to the species capacity for language including predisposition to psychosis.
    Title: The 'big bang' theory of the origin of psychosis and the faculty of language.
  10. 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.
Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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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
Genetic variation in PCDH11X is associated with susceptibility to late-onset Alzheimer's disease.
EBI GWAS Catalog
Genetically distinct subsets within ANCA-associated vasculitis.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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
  

General protein information

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Preferred Names
protocadherin-11 X-linked
Names
Protocadherin on the Y chromosome
Protocadherin prostate cancer
Protocadherin-11 Y-linked
Protocadherin-22
Protocadherin-PC
protein phosphatase 1, regulatory subunit 119
protocadherin 11X
protocadherin on the X chromosome
protocadherin-S

NCBI Reference Sequences (RefSeq)

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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_016251.1 RefSeqGene

    Range
    5115..848970
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001168360.1 → NP_001161832.1  protocadherin-11 X-linked isoform e precursor

    See identical proteins and their annotated locations for NP_001161832.1

    Status: REVIEWED

    Source sequence(s)
    AB037747, AJ564931, AJ564945, AY861432, BQ184367
    Consensus CDS
    CCDS55459.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Related
    ENSP00000384758.1, ENST00000406881.3
    Conserved Domains (5) summary
    cd11304
    Location:253 → 351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384 → 464
    CA; Cadherin repeats
    pfam08374
    Location:775 → 976
    Protocadherin; Protocadherin
    pfam14650
    Location:1199 → 1269
    FAM75; FAM75 family
    cl09101
    Location:28 → 102
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  2. NM_001168361.1 → NP_001161833.1  protocadherin-11 X-linked isoform f precursor

    See identical proteins and their annotated locations for NP_001161833.1

    Status: REVIEWED

    Source sequence(s)
    AJ564931, AJ564945, AY861435, BQ184367
    Consensus CDS
    CCDS55458.1
    UniProtKB/TrEMBL
    B7ZAE8
    Related
    ENSP00000423762.1, ENST00000504220.6
    Conserved Domains (4) summary
    cd11304
    Location:253 → 351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384 → 464
    CA; Cadherin repeats
    pfam08374
    Location:775 → 976
    Protocadherin; Protocadherin
    cl09101
    Location:28 → 102
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  3. NM_001168362.1 → NP_001161834.1  protocadherin-11 X-linked isoform g precursor

    See identical proteins and their annotated locations for NP_001161834.1

    Status: REVIEWED

    Source sequence(s)
    AB037747, AJ564931, AJ564945, AY861433, BQ184367
    Consensus CDS
    CCDS55461.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Related
    ENSP00000362180.1, ENST00000373088.5
    Conserved Domains (5) summary
    cd11304
    Location:253 → 351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384 → 464
    CA; Cadherin repeats
    pfam08374
    Location:775 → 976
    Protocadherin; Protocadherin
    pfam14650
    Location:1170 → 1240
    FAM75; FAM75 family
    cl09101
    Location:28 → 102
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  4. NM_001168363.1 → NP_001161835.1  protocadherin-11 X-linked isoform h precursor

    See identical proteins and their annotated locations for NP_001161835.1

    Status: REVIEWED

    Source sequence(s)
    AB037747, AJ564931, AJ564945, AY861434, BQ184367
    Consensus CDS
    CCDS55460.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Related
    ENSP00000355105.2, ENST00000361655.6
    Conserved Domains (5) summary
    cd11304
    Location:253 → 351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384 → 464
    CA; Cadherin repeats
    pfam08374
    Location:775 → 976
    Protocadherin; Protocadherin
    pfam14650
    Location:1189 → 1259
    FAM75; FAM75 family
    cl09101
    Location:28 → 102
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  5. NM_032968.5 → NP_116750.1  protocadherin-11 X-linked isoform c precursor

    See identical proteins and their annotated locations for NP_116750.1

    Status: REVIEWED

    Source sequence(s)
    AC004388, AL121869, AL133274, AL133321
    Consensus CDS
    CCDS14461.1
    UniProtKB/Swiss-Prot
    A6NIQ4, Q2TJH0, Q2TJH1, Q2TJH3, Q5JVZ0, Q70LR8, Q70LS7, Q70LS8, Q70LS9, Q70LT7, Q70LT8, Q70LT9, Q70LU0, Q70LU1, Q96RV4, Q96RW0, Q9BZA6, Q9BZA7, Q9H4E0, Q9P2M0, Q9P2X5
    Related
    ENSP00000507225.1, ENST00000682573.1
    Conserved Domains (5) summary
    cd11304
    Location:253 → 351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384 → 464
    CA; Cadherin repeats
    pfam08374
    Location:775 → 976
    Protocadherin; Protocadherin
    pfam14650
    Location:1207 → 1277
    FAM75; FAM75 family
    cl09101
    Location:28 → 102
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  6. NM_032969.4 → NP_116751.1  protocadherin-11 X-linked isoform d precursor

    See identical proteins and their annotated locations for NP_116751.1

    Status: REVIEWED

    Source sequence(s)
    AF332219, AJ564945, BQ184367
    Consensus CDS
    CCDS14462.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Related
    ENSP00000362189.1, ENST00000373097.5
    Conserved Domains (5) summary
    cd11304
    Location:253 → 351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384 → 464
    CA; Cadherin repeats
    pfam08374
    Location:775 → 976
    Protocadherin; Protocadherin
    pfam14650
    Location:1197 → 1267
    FAM75; FAM75 family
    cl09101
    Location:28 → 102
    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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    91779375..92623230
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011530911.3 → XP_011529213.1  protocadherin-11 X-linked isoform X2

    See identical proteins and their annotated locations for XP_011529213.1

    Conserved Domains (5) summary
    cd11304
    Location:282 → 380
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:413 → 493
    CA; Cadherin repeats
    pfam08374
    Location:804 → 1005
    Protocadherin; Protocadherin
    pfam14650
    Location:1236 → 1306
    FAM75; FAM75 family
    cl09101
    Location:57 → 131
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  2. XM_011530910.1 → XP_011529212.1  protocadherin-11 X-linked isoform X2

    See identical proteins and their annotated locations for XP_011529212.1

    Conserved Domains (5) summary
    cd11304
    Location:282 → 380
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:413 → 493
    CA; Cadherin repeats
    pfam08374
    Location:804 → 1005
    Protocadherin; Protocadherin
    pfam14650
    Location:1236 → 1306
    FAM75; FAM75 family
    cl09101
    Location:57 → 131
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  3. XM_011530914.3 → XP_011529216.1  protocadherin-11 X-linked isoform X5

    See identical proteins and their annotated locations for XP_011529216.1

    UniProtKB/Swiss-Prot
    A6NIQ4, Q2TJH0, Q2TJH1, Q2TJH3, Q5JVZ0, Q70LR8, Q70LS7, Q70LS8, Q70LS9, Q70LT7, Q70LT8, Q70LT9, Q70LU0, Q70LU1, Q96RV4, Q96RW0, Q9BZA6, Q9BZA7, Q9H4E0, Q9P2M0, Q9P2X5
    Related
    ENSP00000362186.1, ENST00000373094.5
    Conserved Domains (5) summary
    cd11304
    Location:253 → 351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384 → 464
    CA; Cadherin repeats
    pfam08374
    Location:775 → 976
    Protocadherin; Protocadherin
    pfam14650
    Location:1207 → 1277
    FAM75; FAM75 family
    cl09101
    Location:28 → 102
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  4. XM_047441993.1 → XP_047297949.1  protocadherin-11 X-linked isoform X3

  5. XM_047441994.1 → XP_047297950.1  protocadherin-11 X-linked isoform X4

  6. XM_047441995.1 → XP_047297951.1  protocadherin-11 X-linked isoform X7

  7. XM_017029416.2 → XP_016884905.1  protocadherin-11 X-linked isoform X1

  8. XM_017029419.2 → XP_016884908.1  protocadherin-11 X-linked isoform X6

  9. XM_017029421.2 → XP_016884910.1  protocadherin-11 X-linked isoform X8

    UniProtKB/TrEMBL
    B7ZAE8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    90231454..91073463
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054326839.1 → XP_054182814.1  protocadherin-11 X-linked isoform X2

  2. XM_054326840.1 → XP_054182815.1  protocadherin-11 X-linked isoform X2

  3. XM_054326843.1 → XP_054182818.1  protocadherin-11 X-linked isoform X5

    UniProtKB/Swiss-Prot
    A6NIQ4, Q2TJH0, Q2TJH1, Q2TJH3, Q5JVZ0, Q70LR8, Q70LS7, Q70LS8, Q70LS9, Q70LT7, Q70LT8, Q70LT9, Q70LU0, Q70LU1, Q96RV4, Q96RW0, Q9BZA6, Q9BZA7, Q9H4E0, Q9P2M0, Q9P2X5

  4. XM_054326841.1 → XP_054182816.1  protocadherin-11 X-linked isoform X3

  5. XM_054326842.1 → XP_054182817.1  protocadherin-11 X-linked isoform X4

  6. XM_054326845.1 → XP_054182820.1  protocadherin-11 X-linked isoform X7

  7. XM_054326838.1 → XP_054182813.1  protocadherin-11 X-linked isoform X1

  8. XM_054326844.1 → XP_054182819.1  protocadherin-11 X-linked isoform X6

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_014522.1: Suppressed sequence

    Description
    NM_014522.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

  2. NM_032967.2: Suppressed sequence

    Description
    NM_032967.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BZA7.1 GenPept UniProtKB/Swiss-Prot:Q9BZA7

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