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Aliases for PCDHAC1 Gene

Aliases for PCDHAC1 Gene

  • Protocadherin Alpha Subfamily C, 1 2 3 5
  • PCDH-ALPHA-C1 2 3 4
  • Protocadherin Alpha-C1 3

External Ids for PCDHAC1 Gene

Previous GeneCards Identifiers for PCDHAC1 Gene

  • GC05U990126
  • GC05P140149
  • GC05P140214
  • GC05P140221
  • GC05P140176
  • GC05P140178
  • GC05P140286
  • GC05P140252
  • GC05P140261
  • GC05P140271
  • GC05P140280
  • GC05P140291
  • GC05P140301
  • GC05P140310
  • GC05P140313
  • GC05P140320
  • GC05P140343
  • GC05P135451
  • GC05P140354
  • GC05P140375
  • GC05P140394
  • GC05P140408
  • GC05P140424
  • GC05P140443
  • GC05P140461
  • GC05P141437
  • GC05P141572
  • GC05P141674
  • GC05P141775
  • GC05P141876
  • GC05P141984
  • GC05P142085

Summaries for PCDHAC1 Gene

Entrez Gene Summary for PCDHAC1 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 PCDHAC1 Gene

PCDHAC1 (Protocadherin Alpha Subfamily C, 1) is a Protein Coding gene. Diseases associated with PCDHAC1 include Protocadherin-Alpha Gene Cluster and Spherocytosis, Type 5. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHAC2.

UniProtKB/Swiss-Prot for PCDHAC1 Gene

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

Additional gene information for PCDHAC1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHAC1 Gene

Genomics for PCDHAC1 Gene

GeneHancer (GH) Regulatory Elements for PCDHAC1 Gene

Promoters and enhancers for PCDHAC1 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
GH05I140926 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 550.8 +0.2 231 0.8 KLF17 SIN3A ZNF2 RAD21 ZEB1 ZNF335 GLIS2 ZNF143 KLF7 SP3 PCDHAC1 PCDHA11 PCDHA10 PIR58635 PCDHA13 PCDHA12 PCDHA9 PCDHA8 PCDHA7 PCDHA6
GH05I140927 Enhancer 0.3 ENCODE 550.8 +0.8 777 0 ZNF335 PIR58635 PCDHAC1 PCDHA13 PCDHA12 PCDHA11 PCDHA10 PCDHA9 PCDHA8 PCDHA7 PCDHA6
GH05I141084 Enhancer 1.2 FANTOM5 Ensembl ENCODE 11.6 +158.4 158376 1.4 CTCF SAP130 RAD21 YY1 ZNF335 E2F1 ZNF23 GATA3 POLR2A ZNF143 PCDHAC2 PCDHB17P PCDHB1 MALINC1 IGIP PCDHGC4 PCDHB3 PCDHB10 PCDHAC1 PCDHA12
GH05I141832 Enhancer 0.9 ENCODE dbSUPER 11 +906.5 906505 1.5 ZNF449 NFIB ETV1 ZNF23 GATA3 PRDM10 RCOR1 TCF7L2 STAT1 CBFA2T3 PCDH1 PCDHAC2 PCDHA12 ARAP3 PCDHAC1 PCDHB17P KIAA0141 ENSG00000272108 PCDHA10 ENSG00000278925
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCDHAC1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHAC1 gene promoter:

Genomic Locations for PCDHAC1 Gene

Genomic Locations for PCDHAC1 Gene
85,976 bases
Plus strand

Genomic View for PCDHAC1 Gene

Genes around PCDHAC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHAC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHAC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHAC1 Gene

Proteins for PCDHAC1 Gene

  • Protein details for PCDHAC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin alpha-C1
    Protein Accession:
    Secondary Accessions:
    • Q9Y5F5
    • Q9Y5I5

    Protein attributes for PCDHAC1 Gene

    963 amino acids
    Molecular mass:
    103942 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHAC1 Gene


neXtProt entry for PCDHAC1 Gene

Post-translational modifications for PCDHAC1 Gene

  • Glycosylation at isoforms=238, isoforms=2248, Asn274, and isoforms=2562
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHAC1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHAC1 Gene

Domains & Families for PCDHAC1 Gene

Gene Families for PCDHAC1 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for PCDHAC1 Gene

Suggested Antigen Peptide Sequences for PCDHAC1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHAC1: view

No data available for UniProtKB/Swiss-Prot for PCDHAC1 Gene

Function for PCDHAC1 Gene

Molecular function for PCDHAC1 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.

Phenotypes From GWAS Catalog for PCDHAC1 Gene

Gene Ontology (GO) - Molecular Function for PCDHAC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHAC1: view
genes like me logo Genes that share phenotypes with PCDHAC1: view

Animal Models for PCDHAC1 Gene

MGI Knock Outs for PCDHAC1:

Animal Model Products

miRNA for PCDHAC1 Gene

miRTarBase miRNAs that target PCDHAC1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PCDHAC1 Gene

Localization for PCDHAC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHAC1 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 PCDHAC1 gene
Compartment Confidence
plasma membrane 4

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleus (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCDHAC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
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 PCDHAC1: view

Pathways & Interactions for PCDHAC1 Gene

SuperPathways for PCDHAC1 Gene

No Data Available

Interacting Proteins for PCDHAC1 Gene

Gene Ontology (GO) - Biological Process for PCDHAC1 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 PCDHAC1: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHAC1 Gene

Drugs & Compounds for PCDHAC1 Gene

(1) Drugs for PCDHAC1 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 PCDHAC1: view

Transcripts for PCDHAC1 Gene

mRNA/cDNA for PCDHAC1 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHAC1 Gene

No ASD Table

Relevant External Links for PCDHAC1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHAC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHAC1 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDHAC1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDHAC1 Gene:


Evidence on tissue expression from TISSUES for PCDHAC1 Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with PCDHAC1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHAC1 Gene

Orthologs for PCDHAC1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHAC1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDHAC1 33
  • 99.55 (n)
(Mus musculus)
Mammalia Pcdhac1 33 16
  • 85.43 (n)
(Rattus norvegicus)
Mammalia Pcdhac1 33
  • 85.05 (n)
(Ornithorhynchus anatinus)
Mammalia PCDHAC1 34
  • 46 (a)
(Bos Taurus)
Mammalia PCDHAC1 34
  • 40 (a)
(Gallus gallus)
Aves CCNRC01 33
  • 63.72 (n)
(Anolis carolinensis)
Reptilia PCDHAC1 34
  • 56 (a)
(Danio rerio)
Actinopterygii PCDHAC1 34
  • 34 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 30 (a)
CSA.7308 34
  • 20 (a)
Species where no ortholog for PCDHAC1 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)
  • dog (Canis familiaris)
  • 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)
  • oppossum (Monodelphis domestica)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PCDHAC1 Gene

Gene Tree for PCDHAC1 (if available)
Gene Tree for PCDHAC1 (if available)

Paralogs for PCDHAC1 Gene

Variants for PCDHAC1 Gene

Sequence variations from dbSNP and Humsavar for PCDHAC1 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs150254638 uncertain-significance, Hirschsprung disease 1 140,978,974(+) G/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs386352346 uncertain-significance, not provided 140,929,288(+) G/A coding_sequence_variant, missense_variant
rs1000122176 -- 140,965,777(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000222500 -- 140,957,863(+) T/G genic_downstream_transcript_variant, intron_variant
rs1000356638 -- 140,999,029(+) C/T genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHAC1 Gene

Variant ID Type Subtype PubMed ID
esv2505753 CNV deletion 19546169
esv2759382 CNV gain 17122850
nsv1031849 CNV loss 25217958
nsv599904 CNV loss 21841781

Variation tolerance for PCDHAC1 Gene

Residual Variation Intolerance Score: 72.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.13; 61.32% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHAC1 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 PCDHAC1 Gene

Disorders for PCDHAC1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PCDHAC1 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
protocadherin-alpha gene cluster
  • pcdha@
spherocytosis, type 5
  • sph5
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDHAC1

genes like me logo Genes that share disorders with PCDHAC1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDHAC1 Gene

Publications for PCDHAC1 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 58
  2. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  3. Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. (PMID: 22589738) Fox CS … Borecki IB (PLoS genetics 2012) 3 58
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 58
  5. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PMID: 11230163) Wu Q … Maniatis T (Genome research 2001) 3 58

Products for PCDHAC1 Gene

Sources for PCDHAC1 Gene

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