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

    Gene ID: 27328, updated on 27-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
    mouse all
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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
    • 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)

    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

    Gene LinkOut

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

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