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Aliases for PCDH11X Gene

Aliases for PCDH11X Gene

  • Protocadherin 11 X-Linked 2 3 5
  • Protein Phosphatase 1, Regulatory Subunit 119 2 3
  • Protocadherin On The X Chromosome 3 4
  • Protocadherin-S 3 4
  • PCDH11 3 4
  • PCDH-X 3 4
  • PCDHX 3 4
  • Protocadherin-11 X-Linked 3
  • Protocadherin 11X 3
  • Protocadherin-11 4
  • Protocadherin 11 2
  • PPP1R119 3
  • KIAA1326 4

External Ids for PCDH11X Gene

Previous HGNC Symbols for PCDH11X Gene

  • PCDH11

Previous GeneCards Identifiers for PCDH11X Gene

  • GC0XP086306
  • GC0XP088003
  • GC0XP089070
  • GC0XP089806
  • GC0XP090840
  • GC0XP090920
  • GC0XP091034

Summaries for PCDH11X Gene

Entrez Gene Summary for PCDH11X Gene

  • 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]

GeneCards Summary for PCDH11X Gene

PCDH11X (Protocadherin 11 X-Linked) is a Protein Coding gene. Diseases associated with PCDH11X include Dyslexia and Schizoaffective Disorder. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH11Y.

UniProtKB/Swiss-Prot for PCDH11X Gene

  • Potential calcium-dependent cell-adhesion protein.

Gene Wiki entry for PCDH11X Gene

Additional gene information for PCDH11X Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDH11X Gene

Genomics for PCDH11X Gene

GeneHancer (GH) Regulatory Elements for PCDH11X Gene

Promoters and enhancers for PCDH11X 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
GH0XJ092100 Enhancer 0.4 Ensembl ENCODE 0.1 +321.6 321560 1.3 EIF4A1P10 GC0XM091954 PCDH11X
GH0XJ092110 Enhancer 0.4 ENCODE dbSUPER 0.1 +331.4 331396 0.2 EIF4A1P10 GC0XM091954 PCDH11X
GH0XJ092098 Enhancer 0.3 dbSUPER 0.1 +320.2 320217 1.2 POLR2A EIF4A1P10 GC0XM091954 PCDH11X
GH0XJ092107 Enhancer 0.2 dbSUPER 0.1 +329.2 329192 1.2 EIF4A1P10 GC0XM091954 PCDH11X
GH0XJ092106 Enhancer 0.2 dbSUPER 0.1 +327.8 327838 0.5 EIF4A1P10 GC0XM091954 PCDH11X
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDH11X on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDH11X gene promoter:
  • FOXO4
  • Egr-2
  • MEF-2A
  • aMEF-2
  • CUTL1
  • p53
  • POU2F1
  • POU2F1a
  • POU2F1b
  • POU2F1c

Genomic Locations for PCDH11X Gene

Genomic Locations for PCDH11X Gene
843,970 bases
Plus strand
843,970 bases
Plus strand

Genomic View for PCDH11X Gene

Genes around PCDH11X on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDH11X Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDH11X Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDH11X Gene

Proteins for PCDH11X Gene

  • Protein details for PCDH11X Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin-11 X-linked
    Protein Accession:
    Secondary Accessions:
    • A6NIQ4
    • Q2TJH0
    • Q2TJH1
    • Q2TJH3
    • Q5JVZ0
    • Q70LR8
    • Q70LS7
    • Q70LS8
    • Q70LS9
    • Q70LT7
    • Q70LT8
    • Q70LT9
    • Q70LU0
    • Q70LU1
    • Q96RV4
    • Q96RW0
    • Q9BZA6
    • Q9H4E0
    • Q9P2M0
    • Q9P2X5

    Protein attributes for PCDH11X Gene

    1347 amino acids
    Molecular mass:
    147558 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDH11X Gene

neXtProt entry for PCDH11X Gene

Post-translational modifications for PCDH11X Gene

  • Glycosylation at Thr856, Asn773, Asn553, Asn344, Asn54, isoforms=2, 3, 4, 5, 6, 7, 848, and isoforms=2, 3, 4, 5, 6, 7, 827
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PCDH11X Gene

Domains & Families for PCDH11X Gene

Gene Families for PCDH11X Gene

Protein Domains for PCDH11X Gene

Suggested Antigen Peptide Sequences for PCDH11X Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDH11X: view

No data available for UniProtKB/Swiss-Prot for PCDH11X Gene

Function for PCDH11X Gene

Molecular function for PCDH11X Gene

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

Phenotypes From GWAS Catalog for PCDH11X Gene

Gene Ontology (GO) - Molecular Function for PCDH11X Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDH11X: view
genes like me logo Genes that share phenotypes with PCDH11X: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDH11X

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDH11X Gene

Localization for PCDH11X Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDH11X 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 PCDH11X gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 2
cytoskeleton 1
nucleus 1

Gene Ontology (GO) - Cellular Components for PCDH11X Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS 10644456
GO:0005887 integral component of plasma membrane TAS 10644456
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0070062 extracellular exosome HDA --
genes like me logo Genes that share ontologies with PCDH11X: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PCDH11X Gene

Pathways & Interactions for PCDH11X Gene

SuperPathways for PCDH11X Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDH11X 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 --
GO:0010923 negative regulation of phosphatase activity IDA 19389623
genes like me logo Genes that share ontologies with PCDH11X: view

No data available for Pathways by source and SIGNOR curated interactions for PCDH11X Gene

Drugs & Compounds for PCDH11X Gene

(1) Drugs for PCDH11X 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 PCDH11X: view

Transcripts for PCDH11X Gene

Unigene Clusters for PCDH11X Gene

Protocadherin 11 X-linked:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDH11X

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDH11X Gene

No ASD Table

Relevant External Links for PCDH11X Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDH11X Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDH11X Gene

mRNA differential expression in normal tissues according to GTEx for PCDH11X Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x9.7), Brain - Hypothalamus (x5.5), Brain - Caudate (basal ganglia) (x4.3), Brain - Amygdala (x4.3), and Brain - Putamen (basal ganglia) (x4.3).

Protein differential expression in normal tissues from HIPED for PCDH11X Gene

This gene is overexpressed in Breast (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCDH11X Gene

Protein tissue co-expression partners for PCDH11X Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDH11X Gene:


SOURCE GeneReport for Unigene cluster for PCDH11X Gene:


mRNA Expression by UniProt/SwissProt for PCDH11X 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.

Evidence on tissue expression from TISSUES for PCDH11X Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with PCDH11X: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDH11X Gene

Orthologs for PCDH11X Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDH11X Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LOC100611190 33
  • 99.01 (n)
PCDH11X 34
  • 99 (a)
(Bos Taurus)
Mammalia LOC538674 33
  • 87.78 (n)
-- 34
  • 86 (a)
(Canis familiaris)
Mammalia PCDH11X 33
  • 86.17 (n)
-- 34
  • 83 (a)
(Mus musculus)
Mammalia Pcdh11x 16 34 33
  • 84.7 (n)
(Rattus norvegicus)
Mammalia Pcdh11x 33
  • 84.37 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 71 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 58 (a)
(Gallus gallus)
Aves LOC422264 33
  • 72.52 (n)
-- 34
  • 72 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 71 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100493938 33
  • 69.28 (n)
(Danio rerio)
Actinopterygii pcdh11 33
  • 66.19 (n)
PCDH11Y 34
  • 66 (a)
Species where no ortholog for PCDH11X 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)
  • 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)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PCDH11X Gene

Gene Tree for PCDH11X (if available)
Gene Tree for PCDH11X (if available)
Evolutionary constrained regions (ECRs) for PCDH11X: view image

Paralogs for PCDH11X Gene

Variants for PCDH11X Gene

Sequence variations from dbSNP and Humsavar for PCDH11X Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
VAR_036109 A colorectal cancer sample p.Asp42Gly
rs1000003181 -- 92,175,355(+) T/C genic_downstream_transcript_variant, intron_variant
rs1000025593 -- 92,396,179(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000034583 -- 91,913,095(+) C/A genic_downstream_transcript_variant, intron_variant
rs1000037871 -- 92,316,874(+) C/A genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDH11X Gene

Variant ID Type Subtype PubMed ID
dgv2339e212 CNV loss 25503493
dgv2340e212 CNV loss 25503493
dgv2341e212 CNV loss 25503493
esv1001030 CNV gain 20482838
esv22341 CNV gain+loss 19812545
esv2656455 CNV deletion 23128226
esv2660593 CNV deletion 23128226
esv2661726 CNV deletion 23128226
esv2673530 CNV deletion 23128226
esv2673642 CNV deletion 23128226
esv2674815 CNV deletion 23128226
esv2675842 CNV deletion 23128226
esv27006 CNV gain 19812545
esv2740323 CNV deletion 23290073
esv2740324 CNV deletion 23290073
esv2740325 CNV deletion 23290073
esv2740326 CNV deletion 23290073
esv2740327 CNV deletion 23290073
esv2740329 CNV deletion 23290073
esv2740330 CNV deletion 23290073
esv3430522 CNV insertion 20981092
esv3559097 CNV deletion 23714750
esv3574199 CNV loss 25503493
esv3574202 CNV loss 25503493
esv3574203 CNV loss 25503493
esv3574204 CNV loss 25503493
esv3574207 CNV loss 25503493
esv3574210 CNV loss 25503493
esv3574211 CNV loss 25503493
esv3574212 CNV loss 25503493
esv3574216 CNV loss 25503493
esv3574217 CNV loss 25503493
esv3574218 CNV loss 25503493
nsv1133768 CNV deletion 24896259
nsv1148587 CNV duplication 26484159
nsv433341 CNV loss 18776910
nsv507982 OTHER sequence alteration 20534489
nsv510548 OTHER sequence alteration 20534489
nsv528258 CNV gain 19592680

Variation tolerance for PCDH11X Gene

Residual Variation Intolerance Score: 21.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.26; 52.83% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDH11X Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDH11X Gene

Disorders for PCDH11X Gene

MalaCards: The human disease database

(3) MalaCards diseases for PCDH11X Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
schizoaffective disorder
  • schizo-affective psychosis
spherocytosis, type 5
  • sph5
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDH11X

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PCDH11X: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDH11X Gene

Publications for PCDH11X Gene

  1. Identification of a novel protocadherin gene (PCDH11) on the human XY homology region in Xq21.3. (PMID: 10644456) Yoshida K … Sugano S (Genomics 1999) 2 3 4 22 58
  2. 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 22 58
  3. Failure to replicate an association of rs5984894 SNP in the PCDH11X gene in a collection of 1,222 Alzheimer's disease affected patients. (PMID: 20555150) Lescai F … Franceschi C (Journal of Alzheimer's disease : JAD 2010) 3 44 58
  4. Intermediate phenotypes identify divergent pathways to Alzheimer's disease. (PMID: 20574532) Shulman JM … De Jager PL (PloS one 2010) 3 44 58
  5. Lack of association between PCDH11X genetic variation and late-onset Alzheimer's disease in a Han Chinese population. (PMID: 20707987) Wu ZC … Tan L (Brain research 2010) 3 44 58

Products for PCDH11X Gene

Sources for PCDH11X Gene

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