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Aliases for CD1C Gene

Aliases for CD1C Gene

  • CD1c Molecule 2 3 5
  • CD1C Antigen, C Polypeptide 2 3
  • CD1c Antigen 2 4
  • Differentiation Antigen CD1-Alpha-3 3
  • Cortical Thymocyte Antigen CD1C 3
  • BDCA1 3
  • CD1A 3
  • CD1 3
  • R7 3

External Ids for CD1C Gene

Previous HGNC Symbols for CD1C Gene

  • CD1

Previous GeneCards Identifiers for CD1C Gene

  • GC01P156052
  • GC01P153993
  • GC01P155037
  • GC01P155476
  • GC01P155072
  • GC01P156526
  • GC01P158259
  • GC01P129617

Summaries for CD1C Gene

Entrez Gene Summary for CD1C Gene

  • This gene encodes a member of the CD1 family of transmembrane glycoproteins, which are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. The CD1 proteins mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. The protein encoded by this gene is broadly distributed throughout the endocytic system via a tyrosine-based motif in the cytoplasmic tail. Alternatively spliced transcript variants of this gene have been observed, but their full-length nature is not known. [provided by RefSeq, Jul 2008]

GeneCards Summary for CD1C Gene

CD1C (CD1c Molecule) is a Protein Coding gene. Diseases associated with CD1C include mycobacterium malmoense. Among its related pathways are Hematopoietic cell lineage and B Cell Development Pathways. GO annotations related to this gene include beta-2-microglobulin binding and lipopeptide binding. An important paralog of this gene is CD1B.

UniProtKB/Swiss-Prot for CD1C Gene

  • Antigen-presenting protein that binds self and non-self lipid and glycolipid antigens and presents them to T-cell receptors on natural killer T-cells.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CD1C Gene

Genomics for CD1C Gene

Regulatory Elements for CD1C Gene

Enhancers for CD1C Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around CD1C on UCSC Golden Path with GeneCards custom track

Genomic Location for CD1C Gene

Chromosome:
1
Start:
158,289,773 bp from pter
End:
158,294,774 bp from pter
Size:
5,002 bases
Orientation:
Plus strand

Genomic View for CD1C Gene

Genes around CD1C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CD1C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CD1C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CD1C Gene

Proteins for CD1C Gene

  • Protein details for CD1C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P29017-CD1C_HUMAN
    Recommended name:
    T-cell surface glycoprotein CD1c
    Protein Accession:
    P29017
    Secondary Accessions:
    • Q5TDJ7
    • Q6IAS4
    • Q9UMM0
    • Q9UN96

    Protein attributes for CD1C Gene

    Size:
    333 amino acids
    Molecular mass:
    37654 Da
    Quaternary structure:
    • Heterodimer with B2M (beta-2-microglobulin).
    Miscellaneous:
    • During protein synthesis and maturation, CD1 family members bind endogenous lipids that are replaced by lipid or glycolipid antigens when the proteins are internalized and pass through endosomes or lysosomes, before trafficking back to the cell surface.

    Three dimensional structures from OCA and Proteopedia for CD1C Gene

neXtProt entry for CD1C Gene

Proteomics data for CD1C Gene at MOPED

Post-translational modifications for CD1C Gene

  • Ubiquitination at Lys 197
  • Glycosylation at Asn 38, Asn 70, Asn 75, Asn 78, and Asn 146
  • Modification sites at PhosphoSitePlus

Other Protein References for CD1C Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CD1C Gene

Domains & Families for CD1C Gene

Gene Families for CD1C Gene

Graphical View of Domain Structure for InterPro Entry

P29017

UniProtKB/Swiss-Prot:

CD1C_HUMAN :
  • Contains 1 Ig-like (immunoglobulin-like) domain.
Domain:
  • Contains 1 Ig-like (immunoglobulin-like) domain.
genes like me logo Genes that share domains with CD1C: view

Function for CD1C Gene

Molecular function for CD1C Gene

GENATLAS Biochemistry:
cell differentiation antigen CD1C,43kDa,membrane glycoprotein,B2M associated,identified by monoclonal antibodies L161,7C6,PHM3 (see CD1@)
UniProtKB/Swiss-Prot Function:
Antigen-presenting protein that binds self and non-self lipid and glycolipid antigens and presents them to T-cell receptors on natural killer T-cells.

Gene Ontology (GO) - Molecular Function for CD1C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030881 beta-2-microglobulin binding IBA --
GO:0071723 lipopeptide binding IDA 21167756
genes like me logo Genes that share ontologies with CD1C: view
genes like me logo Genes that share phenotypes with CD1C: view

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CD1C Gene

Localization for CD1C Gene

Subcellular locations from UniProtKB/Swiss-Prot for CD1C Gene

Cell membrane; Single-pass type I membrane protein. Endosome membrane; Single-pass type I membrane protein. Lysosome. Note=Subject to intracellular trafficking between the cell membrane and endosomes. {ECO:0000269 PubMed:10890914, ECO:0000269 PubMed:3097645}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CD1C Gene COMPARTMENTS Subcellular localization image for CD1C gene
Compartment Confidence
plasma membrane 5
endosome 4
lysosome 4
vacuole 4
extracellular 3
cytosol 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for CD1C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005887 integral component of plasma membrane TAS 1702817
GO:0010008 endosome membrane IEA --
genes like me logo Genes that share ontologies with CD1C: view

Pathways & Interactions for CD1C Gene

genes like me logo Genes that share pathways with CD1C: view

Interacting Proteins for CD1C Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000357152%0d%0a9606.ENSP00000452780%0d%0a
Selected Interacting proteins: ENSP00000357152 for CD1C Gene via STRING

Symbol External ID(s) Details
B2M

Gene Ontology (GO) - Biological Process for CD1C Gene

None

No data available for SIGNOR curated interactions for CD1C Gene

Drugs & Compounds for CD1C Gene

(3) Drugs for CD1C Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Sphingosine Experimental Pharma 0
sphinganine Pharma 0
Sphingosine-1-phosphate Pharma Full agonist, Agonist Endogenous agonist at S1P1-5 0

(464) Additional Compounds for CD1C Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
3-Dehydrosphinganine
  • (2S)-2-amino-1-hydroxyoctadecan-3-one
  • 1-Hydroxy-2-amino-3-oxo-octadecane
  • 2-Amino-1-hydroxy-3-Octadecanone
  • 3-Dehydro-D-sphinganine
  • 3-Dehydrosphinganine
16105-69-4
3-O-Sulfogalactosylceramide (d18:1/12:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
852100-88-0
3-O-Sulfogalactosylceramide (d18:1/14:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
3-O-Sulfogalactosylceramide (d18:1/16:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
862509-48-6
3-O-Sulfogalactosylceramide (d18:1/18:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
244215-65-4
genes like me logo Genes that share compounds with CD1C: view

Transcripts for CD1C Gene

mRNA/cDNA for CD1C Gene

Unigene Clusters for CD1C Gene

CD1c molecule:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CD1C Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7
SP1: - -
SP2: -
SP3:

Relevant External Links for CD1C Gene

GeneLoc Exon Structure for
CD1C
ECgene alternative splicing isoforms for
CD1C

Expression for CD1C Gene

mRNA expression in normal human tissues for CD1C Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CD1C Gene

This gene is overexpressed in Spleen (x16.2), Small Intestine - Terminal Ileum (x5.4), and Whole Blood (x5.3).

Protein differential expression in normal tissues from HIPED for CD1C Gene

This gene is overexpressed in Tlymphocyte (26.3), Oral epithelium (21.3), Lymph node (11.7), and Blymphocyte (9.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for CD1C Gene



SOURCE GeneReport for Unigene cluster for CD1C Gene Hs.132448

mRNA Expression by UniProt/SwissProt for CD1C Gene

P29017-CD1C_HUMAN
Tissue specificity: Expressed on cortical thymocytes, on certain T-cell leukemias, and in various other tissues.
genes like me logo Genes that share expression patterns with CD1C: view

Primer Products

In Situ Assay Products

No data available for Protein tissue co-expression partners for CD1C Gene

Orthologs for CD1C Gene

This gene was present in the common ancestor of chordates.

Orthologs for CD1C Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia CD1C 35
  • 73.41 (n)
  • 67.07 (a)
CD1D 36
  • 66 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia CD1C 35
  • 98.7 (n)
  • 98.5 (a)
CD1C 36
  • 98 (a)
OneToOne
chicken
(Gallus gallus)
Aves CD1.2 36
  • 22 (a)
ManyToMany
CD1A1 36
  • 24 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 27 (a)
OneToMany
Species with no ortholog for CD1C:
  • 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)
  • cow (Bos Taurus)
  • 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)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for CD1C Gene

ENSEMBL:
Gene Tree for CD1C (if available)
TreeFam:
Gene Tree for CD1C (if available)

Paralogs for CD1C Gene

Paralogs for CD1C Gene

(15) SIMAP similar genes for CD1C Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with CD1C: view

Variants for CD1C Gene

Sequence variations from dbSNP and Humsavar for CD1C Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs3138100 - 158,291,281(+) GCATA(A/C)CTGGT reference, missense
rs3138105 - 158,293,221(+) CCACT(C/T)TTCCA intron-variant, reference, missense
rs728212 -- 158,291,600(+) TCTTG(A/T)GCTTT intron-variant
rs3138099 -- 158,291,225(+) CTGGA(C/T)GAGTT reference, synonymous-codon
rs3138101 -- 158,291,870(+) GGCCA(C/T)TTTTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CD1C Gene

Variant ID Type Subtype PubMed ID
dgv393n71 CNV Gain 21882294
nsv831692 CNV Gain 17160897

Variation tolerance for CD1C Gene

Residual Variation Intolerance Score: 32.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.83; 34.33% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CD1C Gene

HapMap Linkage Disequilibrium report
CD1C

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CD1C Gene

Disorders for CD1C Gene

MalaCards: The human disease database

(1) MalaCards diseases for CD1C Gene - From: GeneCards

Disorder Aliases PubMed IDs
mycobacterium malmoense
  • m. malmoense
- elite association - COSMIC cancer census association via MalaCards
Search CD1C in MalaCards View complete list of genes associated with diseases

Relevant External Links for CD1C

Genetic Association Database (GAD)
CD1C
Human Genome Epidemiology (HuGE) Navigator
CD1C
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CD1C
genes like me logo Genes that share disorders with CD1C: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CD1C Gene

Publications for CD1C Gene

  1. Structure and expression of the human thymocyte antigens CD1a, CD1b, and CD1c. (PMID: 2447586) Martin L.H. … Milstein C. (Proc. Natl. Acad. Sci. U.S.A. 1987) 2 3 4 67
  2. IgG regulates the CD1 expression profile and lipid antigen-presenting function in human dendritic cells via FcgammaRIIa. (PMID: 18337560) Smed-SAPrensen A. … Sandberg J.K. (Blood 2008) 3 23
  3. CD1a and CD1c activate intrathyroidal T cells during Graves' disease and Hashimoto's thyroiditis. (PMID: 15749918) Roura-Mir C. … Moody D.B. (J. Immunol. 2005) 3 23
  4. Direct measurement of antigen binding properties of CD1 proteins using fluorescent lipid probes. (PMID: 14551186) Im J.S. … Porcelli S.A. (J. Biol. Chem. 2004) 3 23
  5. CD1-dependent dendritic cell instruction. (PMID: 12415264) Vincent M.S. … Brenner M.B. (Nat. Immunol. 2002) 3 23

Products for CD1C Gene

Sources for CD1C Gene

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