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CD1C Gene(Protein Coding)

CD1c Molecule

GCID:
GC01P158289
GIFtS:
55
Genes Participants
UDN Logo

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
  • T-Cell Surface Glycoprotein CD1c 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 and Foramen Magnum Meningioma. Among its related pathways are Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell and Innate Immune System. 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 CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CD1C Gene

Genomics for CD1C Gene

Products:

  1. Regulatory Element

Regulatory Elements for CD1C Gene

Enhancers for CD1C 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
GH01G158247 1.5 FANTOM5 Ensembl ENCODE dbSUPER 14 -41.1 -41073 2.2 SRF CBFB MAX ZNF507 EED IKZF1 SCRT2 ETV6 RELB MLLT1 CD1C CD1E CD1D CD1B OR10T2 CD1A GC01P158261 GC01P158260
GH01G158324 1.1 FANTOM5 Ensembl dbSUPER 10.6 +34.9 34928 0.6 IKZF1 JUNB RELB IKZF2 TBX21 CD1C CD1A CD1B GC01P158293 GC01P158292
GH01G158154 0.7 Ensembl 9.6 -135.5 -135473 0.6 SCRT1 TEAD4 JUNB ZNF83 EED IKZF1 SCRT2 ETV6 ZNF24 IKZF2 ELL2P1 CD1D CD1A CD1C LINC01704
GH01G158361 0.5 dbSUPER 10.5 +74.3 74299 4.2 ZNF316 FOXA2 MAFG CD1B OR10T2 CD1C OR10K2 OR10X1 CD1E
GH01G158362 0.5 dbSUPER 10.5 +74.1 74107 3.7 ZNF316 FOXA2 MAFG CD1B OR10T2 CD1C OR10K2 OR10X1 CD1E
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CD1C on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the CD1C gene promoter:

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 Structure • Gene Density

RefSeq DNA sequence for CD1C Gene

Proteins for CD1C Gene

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  1. Antibody
  2. Protein
  3. Assay

  • 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

Protein Expression for CD1C Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CD1C Gene

  • Ubiquitination at Lys197
  • Glycosylation at Asn38, Asn70, posLast=7575, posLast=7878, and Asn146
  • Modification sites at PhosphoSitePlus

Other Protein References for CD1C Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for CD1C

No data available for DME Specific Peptides for CD1C Gene

Domains & Families for CD1C Gene

Gene Families for CD1C Gene

HGNC:

Protein Domains for CD1C Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for CD1C Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

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

Function for CD1C Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

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:0008289 lipid binding IEA --
GO:0030881 beta-2-microglobulin binding IBA --
GO:0030883 endogenous lipid antigen binding IDA 21167756
GO:0030884 exogenous lipid antigen binding IDA 21167756
GO:0051861 glycolipid 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

Inhibitory RNA Products

Clone Products

Flow Cytometry 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
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 CD1C gene
Compartment Confidence
plasma membrane 5
lysosome 4
endosome 4
extracellular 3
mitochondrion 1
peroxisome 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for CD1C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IEA --
GO:0005768 endosome IEA --
GO:0005886 plasma membrane TAS --
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

Gene Ontology (GO) - Biological Process for CD1C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002250 adaptive immune response IEA --
GO:0002286 T cell activation involved in immune response IDA 21167756
GO:0002376 immune system process IEA --
GO:0048007 antigen processing and presentation, exogenous lipid antigen via MHC class Ib IBA --
GO:0050776 regulation of immune response TAS --
genes like me logo Genes that share ontologies with CD1C: view

No data available for SIGNOR curated interactions for CD1C Gene

Drugs & Compounds for CD1C Gene

Products:

  1. Drug

(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 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

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for CD1C Gene

(2) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(55) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CD1C Gene

CD1c molecule:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CD1C Gene

mRNA expression in normal human tissues for CD1C Gene
mRNA expression by BioGPS for CD1C GenemRNA expression by GTEx 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, MaxQB, and MOPED for CD1C Gene



NURSA nuclear receptor signaling pathways regulating expression of CD1C Gene:

CD1C

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.

Evidence on tissue expression from TISSUES for CD1C Gene

  • Lymph node(3.4)
  • Spleen(3.4)
  • Blood(2.7)
  • Skin(2.4)
genes like me logo Genes that share expression patterns with CD1C: view

Primer Products

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
 Mammalia CD1C 34 35
  • 98.7 (n)
dog
(Canis familiaris)
 Mammalia CD1C 34
  • 73.41 (n)
CD1D 35
  • 66 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves CD1A1 35
  • 24 (a)
 ManyToMany
CD1.2 35
  • 22 (a)
 ManyToMany
lizard
(Anolis carolinensis)
 Reptilia -- 35
  • 27 (a)
 OneToMany
Species where no ortholog for CD1C 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)
  • 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
rs1000976741 -- 158,291,777(+) GAATG(C/T)TATCC intron-variant
rs1001814127 -- 158,294,709(+) TATGT(C/G)ACTTA intron-variant, downstream-variant-500B, utr-variant-3-prime
rs1002875977 -- 158,288,138(+) CACAA(A/G)ATGAG intron-variant, upstream-variant-2KB
rs1003177926 -- 158,293,628(+) ATTTG(G/T)AATGT intron-variant, utr-variant-3-prime
rs1003183281 -- 158,289,930(+) ATCTT(C/T)TTAGT intron-variant, utr-variant-5-prime

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

Variant ID Type Subtype PubMed ID
nsv831692 CNV gain 17160897
nsv999542 CNV loss 25217958

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

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CD1C

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

Disorders for CD1C Gene

MalaCards: The human disease database

(5) MalaCards diseases for CD1C Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
mycobacterium malmoense
  • m. malmoense
foramen magnum meningioma
  • meningioma of the foramen magnum
immune system organ benign neoplasm
thymus lipoma
  • thymolipoma
skull base meningioma
  • meningioma of the skull base
- 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. CD1c-mediated T-cell recognition of isoprenoid glycolipids in Mycobacterium tuberculosis infection. (PMID: 10786796) Moody D.B. … Porcelli S.A. (Nature 2000) 3 4 22 64
  2. Human CD1b and CD1c isoforms survey different intracellular compartments for the presentation of microbial lipid antigens. (PMID: 10899914) Briken V. … Porcelli S.A. (J. Exp. Med. 2000) 3 4 22 64
  3. 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 64
  4. The 2.5 a structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation. (PMID: 21167756) Scharf L. … Adams E.J. (Immunity 2010) 3 4 64
  5. 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 22 64

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