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Aliases for PCDHA6 Gene

Aliases for PCDHA6 Gene

  • Protocadherin Alpha 6 2 3 5
  • KIAA0345-Like 8 2 3
  • PCDH-Alpha-6 3 4
  • CNRS2 3 4
  • Protocadherin Alpha-6 3
  • PCDH-ALPHA6 3
  • CNRN2 3
  • CRNR2 3
  • CNR2 3

External Ids for PCDHA6 Gene

Previous HGNC Symbols for PCDHA6 Gene

  • CNRS2

Previous GeneCards Identifiers for PCDHA6 Gene

  • GC05P140024
  • GC05P140753
  • GC05P140155
  • GC05P140210
  • GC05P140217
  • GC05P140172
  • GC05P140187
  • GC05P140321
  • GC05P140342
  • GC05P135352
  • GC05P140362
  • GC05P140378
  • GC05P140392
  • GC05P140406
  • GC05P140422
  • GC05P140439
  • GC05P140456
  • GC05P141238
  • GC05P141487
  • GC05P141594
  • GC05P141695

Summaries for PCDHA6 Gene

Entrez Gene Summary for PCDHA6 Gene

  • This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDHA6 Gene

PCDHA6 (Protocadherin Alpha 6) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHA8.

UniProtKB/Swiss-Prot for PCDHA6 Gene

  • Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

Gene Wiki entry for PCDHA6 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHA6 Gene

Genomics for PCDHA6 Gene

Regulatory Elements for PCDHA6 Gene

Enhancers for PCDHA6 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05F140996 0.5 FANTOM5 1.5 +168.7 168654 0.3 ZNF121 ZNF512 PCDHGC4 PCDHA13 PCDHGA6 PCDHA3 PCDHA2 PCDHB12 PCDHA4 PCDHGA8 PCDHB15 PCDHA6
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around PCDHA6 on UCSC Golden Path with GeneCards custom track

Promoters for PCDHA6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001874410 179 199 CTCF EED IKZF1 RAD21

Genomic Location for PCDHA6 Gene

Chromosome:
5
Start:
140,827,922 bp from pter
End:
141,012,344 bp from pter
Size:
184,423 bases
Orientation:
Plus strand

Genomic View for PCDHA6 Gene

Genes around PCDHA6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHA6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHA6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHA6 Gene

Proteins for PCDHA6 Gene

  • Protein details for PCDHA6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UN73-PCDA6_HUMAN
    Recommended name:
    Protocadherin alpha-6
    Protein Accession:
    Q9UN73
    Secondary Accessions:
    • O75283
    • Q9NRT8

    Protein attributes for PCDHA6 Gene

    Size:
    950 amino acids
    Molecular mass:
    102716 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAF89691.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PCDHA6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHA6 Gene

Post-translational modifications for PCDHA6 Gene

  • Glycosylation at Asn 257, Asn 265, Asn 386, and Asn 548
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHA6 Gene

No data available for DME Specific Peptides for PCDHA6 Gene

Domains & Families for PCDHA6 Gene

Gene Families for PCDHA6 Gene

Protein Domains for PCDHA6 Gene

Suggested Antigen Peptide Sequences for PCDHA6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UN73

UniProtKB/Swiss-Prot:

PCDA6_HUMAN :
  • Contains 6 cadherin domains.
Domain:
  • Contains 6 cadherin domains.
genes like me logo Genes that share domains with PCDHA6: view

Function for PCDHA6 Gene

Molecular function for PCDHA6 Gene

UniProtKB/Swiss-Prot Function:
Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

Gene Ontology (GO) - Molecular Function for PCDHA6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHA6: view

Phenotypes for PCDHA6 Gene

genes like me logo Genes that share phenotypes with PCDHA6: view

Animal Model Products

miRNA for PCDHA6 Gene

miRTarBase miRNAs that target PCDHA6

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHA6 Gene

Localization for PCDHA6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHA6 Gene

Isoform 1: Cell membrane; Single-pass type I membrane protein.
Isoform 2: Secreted.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PCDHA6 Gene COMPARTMENTS Subcellular localization image for PCDHA6 gene
Compartment Confidence
plasma membrane 4
extracellular 3

Gene Ontology (GO) - Cellular Components for PCDHA6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane TAS 10380929
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDHA6: view

Pathways & Interactions for PCDHA6 Gene

SuperPathways for PCDHA6 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHA6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion TAS 10380929
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007399 nervous system development TAS 10380929
genes like me logo Genes that share ontologies with PCDHA6: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHA6 Gene

Drugs & Compounds for PCDHA6 Gene

(1) Drugs for PCDHA6 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with PCDHA6: view

Transcripts for PCDHA6 Gene

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHA6 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b
SP1: - - - - - - - - - - - - - - - -
SP2: - - - - - - - - - - - - - - - - - -
SP3: - - - - - -
SP4: - - -
SP5: -
SP6:
SP7: - - - - - - - - - - - - - - -
SP8: - - - - - - - - - - - -
SP9: - - - - - - - - - - - - -
SP10: - - - - - - - - - - -
SP11: - - - - - - - - - - - - - - - - -
SP12: - - - - - - - - - -
SP13: - - - - - - - - -
SP14: - - - - - - - -
SP15: - - - - - - -
SP16: - - - - -
SP17: - - - -
SP18: - -

Relevant External Links for PCDHA6 Gene

GeneLoc Exon Structure for
PCDHA6
ECgene alternative splicing isoforms for
PCDHA6

Expression for PCDHA6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCDHA6 Gene

mRNA differential expression in normal tissues according to GTEx for PCDHA6 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x6.0) and Brain - Frontal Cortex (BA9) (x5.1).

NURSA nuclear receptor signaling pathways regulating expression of PCDHA6 Gene:

PCDHA6
genes like me logo Genes that share expression patterns with PCDHA6: view

Primer Products

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 and mRNA Expression by UniProt/SwissProt for PCDHA6 Gene

Orthologs for PCDHA6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHA6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHA6 34 35
  • 99.23 (n)
dog
(Canis familiaris)
Mammalia PCDHA6 34
  • 85.97 (n)
-- 35
  • 82 (a)
OneToMany
cow
(Bos Taurus)
Mammalia -- 35
  • 84 (a)
OneToMany
LOC540057 34
  • 76.87 (n)
mouse
(Mus musculus)
Mammalia Pcdha6 34 16
  • 83.65 (n)
rat
(Rattus norvegicus)
Mammalia Pcdha6 34
  • 83.16 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 69 (a)
ManyToMany
-- 35
  • 68 (a)
ManyToMany
-- 35
  • 66 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 64 (a)
OneToMany
chicken
(Gallus gallus)
Aves PCDHA11 35
  • 54 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 58 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
-- 35
  • 55 (a)
ManyToMany
-- 35
  • 55 (a)
ManyToMany
-- 35
  • 55 (a)
ManyToMany
-- 35
  • 55 (a)
ManyToMany
-- 35
  • 55 (a)
ManyToMany
-- 35
  • 55 (a)
ManyToMany
-- 35
  • 55 (a)
ManyToMany
-- 35
  • 55 (a)
ManyToMany
-- 35
  • 54 (a)
ManyToMany
-- 35
  • 53 (a)
ManyToMany
-- 35
  • 52 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100490196 34
  • 55.33 (n)
zebrafish
(Danio rerio)
Actinopterygii pcdh2ab12 35
  • 43 (a)
ManyToMany
pcdh2ab3 35
  • 43 (a)
ManyToMany
pcdh2ab8 35
  • 43 (a)
ManyToMany
CR847851.6 35
  • 42 (a)
ManyToMany
CT573264.4 35
  • 42 (a)
ManyToMany
CT573264.5 35
  • 42 (a)
ManyToMany
pcdh2ab1 35
  • 42 (a)
ManyToMany
pcdh2ab11 35
  • 42 (a)
ManyToMany
pcdh2ab6 35
  • 42 (a)
ManyToMany
CR847851.8 35
  • 41 (a)
ManyToMany
pcdh1a6 35
  • 41 (a)
ManyToMany
pcdh2ab10 35
  • 41 (a)
ManyToMany
pcdh2ab2 35 35
  • 41 (a)
ManyToMany
pcdh2ab7 35
  • 41 (a)
ManyToMany
pcdh2ab9 35
  • 41 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 32 (a)
ManyToMany
CSA.7308 35
  • 20 (a)
ManyToMany
Species where no ortholog for PCDHA6 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 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 PCDHA6 Gene

ENSEMBL:
Gene Tree for PCDHA6 (if available)
TreeFam:
Gene Tree for PCDHA6 (if available)

Paralogs for PCDHA6 Gene

genes like me logo Genes that share paralogs with PCDHA6: view

Variants for PCDHA6 Gene

Sequence variations from dbSNP and Humsavar for PCDHA6 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs193920994 Uncertain significance 140,857,214(+) TCTGA(C/T)GCCTC intron-variant, reference, missense
rs386352346 Uncertain significance 140,929,288(+) GATTC(A/G)GAATA intron-variant, reference, missense
rs10036183 -- 140,996,918(+) ATATT(A/T)AAAAA intron-variant
rs10038174 -- 140,831,031(+) ATTCC(A/G)GGAGG intron-variant
rs10040019 -- 140,921,372(+) TATTT(A/C)TACAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHA6 Gene

Variant ID Type Subtype PubMed ID
dgv10092n54 CNV loss 21841781
dgv10093n54 CNV loss 21841781
dgv10094n54 CNV loss 21841781
dgv10095n54 CNV loss 21841781
dgv10096n54 CNV loss 21841781
dgv10097n54 CNV loss 21841781
dgv10098n54 CNV loss 21841781
dgv10099n54 CNV loss 21841781
dgv10100n54 CNV loss 21841781
dgv10101n54 CNV loss 21841781
dgv10102n54 CNV loss 21841781
dgv10103n54 CNV loss 21841781
dgv10104n54 CNV loss 21841781
dgv10105n54 CNV loss 21841781
dgv1043e199 CNV deletion 23128226
dgv1044e199 CNV deletion 23128226
dgv138e203 CNV loss 21179565
dgv1651e212 CNV loss 25503493
dgv1652e212 CNV loss 25503493
dgv1653e212 CNV loss 25503493
dgv3182n106 CNV deletion 24896259
dgv724n27 CNV loss 19166990
dgv970n67 CNV gain 20364138
dgv971n67 CNV loss 20364138
dgv972n67 CNV gain 20364138
esv21596 CNV gain 19812545
esv2421858 CNV deletion 20811451
esv2505753 CNV deletion 19546169
esv26168 CNV gain 19812545
esv2657537 CNV deletion 23128226
esv27071 CNV loss 19812545
esv2730838 CNV deletion 23290073
esv2730839 CNV deletion 23290073
esv2759382 CNV gain 17122850
esv2861013 CNV duplication 24192839
esv29977 CNV gain 17803354
esv33939 CNV gain+loss 17666407
esv3566721 CNV deletion 23714750
esv3606956 CNV loss 21293372
esv3606957 CNV gain 21293372
esv3606958 CNV loss 21293372
esv3606959 CNV gain 21293372
esv3890744 CNV loss 25118596
esv8310 CNV loss 19470904
nsv1024237 CNV loss 25217958
nsv1031849 CNV loss 25217958
nsv10752 CNV gain+loss 18304495
nsv10753 CNV gain 18304495
nsv10754 CNV gain 18304495
nsv1133616 CNV deletion 24896259
nsv1135376 CNV deletion 24896259
nsv1161301 OTHER complex 26073780
nsv436885 CNV insertion 17901297
nsv437955 CNV loss 16468122
nsv442962 CNV loss 18776908
nsv514324 CNV loss 21397061
nsv515909 CNV loss 19592680
nsv599839 CNV gain 21841781
nsv599841 CNV loss 21841781
nsv599842 CNV loss 21841781
nsv599859 CNV loss 21841781
nsv599864 CNV loss 21841781
nsv599870 CNV loss 21841781
nsv599894 CNV loss 21841781
nsv599902 CNV loss 21841781
nsv599903 CNV loss 21841781
nsv599904 CNV loss 21841781
nsv819207 CNV gain 19587683
nsv820841 CNV deletion 20802225
nsv823251 CNV gain 20364138
nsv823262 CNV gain 20364138
nsv823263 CNV gain 20364138
nsv823264 CNV gain 20364138
nsv830508 CNV loss 17160897
nsv950415 CNV duplication 24416366
nsv964951 CNV duplication 23825009
nsv964953 CNV duplication 23825009
nsv964954 CNV duplication 23825009
nsv964955 CNV duplication 23825009
nsv964956 CNV duplication 23825009
nsv968251 CNV duplication 23825009
nsv968252 CNV duplication 23825009
nsv968992 CNV duplication 23825009
nsv980734 CNV duplication 23825009

Variation tolerance for PCDHA6 Gene

Residual Variation Intolerance Score: 46.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.29; 53.12% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDHA6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHA6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHA6 Gene

Disorders for PCDHA6 Gene

Relevant External Links for PCDHA6

Genetic Association Database (GAD)
PCDHA6
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCDHA6

No disorders were found for PCDHA6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHA6 Gene

Publications for PCDHA6 Gene

  1. A striking organization of a large family of human neural cadherin- like cell adhesion genes. (PMID: 10380929) Wu Q. … Maniatis T. (Cell 1999) 2 3 4 64
  2. The DNA sequence and comparative analysis of human chromosome 5. (PMID: 15372022) Schmutz J. … Rubin E.M. (Nature 2004) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. Genomic organization of the family of CNR cadherin genes in mice and humans. (PMID: 10662547) Sugino H. … Yagi T. (Genomics 2000) 2 3 64
  5. Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. (PMID: 22589738) Fox C.S. … Borecki I.B. (PLoS Genet. 2012) 3 64

Products for PCDHA6 Gene

Sources for PCDHA6 Gene

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