This gene encodes a divergent 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 CD... See more...

Aliases for CD1D Gene

Aliases for CD1D Gene

  • CD1d Molecule 2 3 5
  • Antigen-Presenting Glycoprotein CD1d 3 4
  • CD1D Antigen, D Polypeptide 2 3
  • CD1d Antigen 2 4
  • R3G1 3 4
  • HMC Class I Antigen-Like Glycoprotein CD1D 3
  • Differentiation Antigen CD1-Alpha-3 3
  • T-Cell Surface Glycoprotein CD1d 3
  • Thymocyte Antigen CD1D 3
  • CD1A 3
  • R3 3

External Ids for CD1D Gene

Previous GeneCards Identifiers for CD1D Gene

  • GC01P155941
  • GC01P153882
  • GC01P154927
  • GC01P155366
  • GC01P154962
  • GC01P156416
  • GC01P158149
  • GC01P129508

Summaries for CD1D Gene

Entrez Gene Summary for CD1D Gene

  • This gene encodes a divergent 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 localizes to late endosomes and lysosomes via a tyrosine-based motif in the cytoplasmic tail. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

GeneCards Summary for CD1D Gene

CD1D (CD1d Molecule) is a Protein Coding gene. Diseases associated with CD1D include Mycobacterium Malmoense and Glottis Neoplasm. Among its related pathways are Hematopoietic cell lineage and Class I MHC mediated antigen processing and presentation. Gene Ontology (GO) annotations related to this gene include cell adhesion molecule binding. An important paralog of this gene is CD1E.

UniProtKB/Swiss-Prot Summary for CD1D Gene

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

Gene Wiki entry for CD1D Gene

Additional gene information for CD1D Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CD1D Gene

Genomics for CD1D Gene

GeneHancer (GH) Regulatory Elements for CD1D Gene

Promoters and enhancers for CD1D Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J158176 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 505.1 -0.3 -283 1.7 SP2 ZBTB17 JUND ZNF335 IKZF3 PKNOX1 ZNF189 ZFP91 SCRT1 ZBTB40 CD1D ELL2P1 ENSG00000176320 lnc-CD1D-1
GH01J158179 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 500.7 +2.9 2862 4.2 EP300 ZIC2 ZBTB10 ZNF423 ZBTB26 TRIM28 ZNF341 POLR2A EZH2 HDAC2 CD1D ENSG00000176320 ELL2P1 lnc-CD1B-6
GH01J158148 Promoter/Enhancer 1.5 Ensembl ENCODE CraniofacialAtlas 11.4 -28.6 -28558 2.6 ZNF217 NRF1 MYC USF1 SIX5 ZBTB11 HINFP HDAC2 CTBP1 NR2F2 LINC01704 lnc-CD1D-2 piR-31926-003 CD1D ELL2P1 LOC105371460
GH01J158144 Enhancer 0.9 FANTOM5 ENCODE 11.1 -31.6 -31573 3.4 FOSL1 FOS NCOR1 CEBPB PBX2 JUN NFE2 IRF1 JUND PKNOX1 piR-31926-003 CD1D ELL2P1 KIRREL1 OR10R2 OR10X1 LINC01704 LOC105371460
GH01J158188 Enhancer 0.4 dbSUPER 18 +11.2 11206 1.4 ATF2 JUND ATF7 lnc-CD1B-6 CD1D ELL2P1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CD1D on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CD1D

Top Transcription factor binding sites by QIAGEN in the CD1D gene promoter:
  • AML1a
  • AREB6
  • E47
  • FOXD3
  • HOXA5
  • POU2F1
  • POU2F1a
  • PPAR-gamma1
  • STAT3

Genomic Locations for CD1D Gene

Genomic Locations for CD1D Gene
chr1:158,178,038-158,186,427
(GRCh38/hg38)
Size:
8,390 bases
Orientation:
Plus strand
chr1:158,149,737-158,156,217
(GRCh37/hg19)
Size:
6,481 bases
Orientation:
Plus strand

Genomic View for CD1D Gene

Genes around CD1D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CD1D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CD1D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CD1D Gene

Proteins for CD1D Gene

  • Protein details for CD1D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P15813-CD1D_HUMAN
    Recommended name:
    Antigen-presenting glycoprotein CD1d
    Protein Accession:
    P15813
    Secondary Accessions:
    • D3DVD5
    • Q5W0J3
    • Q9UMM3
    • Q9Y5M4

    Protein attributes for CD1D Gene

    Size:
    335 amino acids
    Molecular mass:
    37717 Da
    Quaternary structure:
    • Heterodimer with B2M (beta-2-microglobulin). Interacts with MHC II.
    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, before trafficking back to the cell surface.

    Three dimensional structures from OCA and Proteopedia for CD1D Gene

neXtProt entry for CD1D Gene

Post-translational modifications for CD1D Gene

  • Glycosylation at Asn38, Asn60, Asn126, and Asn181
  • Modification sites at PhosphoSitePlus

Other Protein References for CD1D Gene

Antibody Products

  • Abcam antibodies for CD1D
  • Boster Bio Antibodies for CD1D

Protein Products

  • Abcam proteins for CD1D

No data available for DME Specific Peptides for CD1D Gene

Domains & Families for CD1D Gene

Gene Families for CD1D Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • CD markers
  • Predicted membrane proteins

Protein Domains for CD1D Gene

Suggested Antigen Peptide Sequences for CD1D Gene

GenScript: Design optimal peptide antigens:
  • R3G1 (CD1D_HUMAN)
genes like me logo Genes that share domains with CD1D: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CD1D Gene

Function for CD1D Gene

Molecular function for CD1D Gene

UniProtKB/Swiss-Prot Function:
Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell receptors on natural killer T-cells.
GENATLAS Biochemistry:
cell differentiation antigen CD1D,49kDa,cell surface molecule,B2M associated,identified by monoclonal antibody NOR3.2 expressed on a cortical thymocyte cell line (see CD1@)

Gene Ontology (GO) - Molecular Function for CD1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 30126976
GO:0030881 beta-2-microglobulin binding TAS 14500461
GO:0030882 lipid antigen binding IDA 19124746
GO:0030883 endogenous lipid antigen binding IBA 21873635
GO:0030884 exogenous lipid antigen binding IDA 10523605
genes like me logo Genes that share ontologies with CD1D: view
genes like me logo Genes that share phenotypes with CD1D: view

Animal Models for CD1D Gene

MGI Knock Outs for CD1D:

Clone Products

  • Addgene plasmids for CD1D

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CD1D Gene

Localization for CD1D Gene

Subcellular locations from UniProtKB/Swiss-Prot for CD1D Gene

Cell membrane; Single-pass type I membrane protein. Basolateral cell membrane; Single-pass type I membrane protein. Endosome membrane; Single-pass type I membrane protein. Lysosome membrane; Single-pass type I membrane protein. Endoplasmic reticulum membrane; Single-pass type I membrane protein. Note=Subject to intracellular trafficking between the cell membrane, endosomes and lysosomes. {ECO:0000269 PubMed:9973405}.

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 CD1D gene
Compartment Confidence
plasma membrane 5
extracellular 4
endoplasmic reticulum 4
endosome 4
lysosome 4
nucleus 3
cytoskeleton 2
mitochondrion 2
cytosol 2
golgi apparatus 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CD1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA 21873635
GO:0005737 cytoplasm IDA 19124746
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane IEA --
GO:0005768 endosome IEA --
genes like me logo Genes that share ontologies with CD1D: view

Pathways & Interactions for CD1D Gene

genes like me logo Genes that share pathways with CD1D: view

Gene Ontology (GO) - Biological Process for CD1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001916 positive regulation of T cell mediated cytotoxicity IBA 21873635
GO:0002376 immune system process IEA --
GO:0006955 immune response IBA 21873635
GO:0016045 detection of bacterium TAS 14500461
GO:0034113 heterotypic cell-cell adhesion TAS 19124746
genes like me logo Genes that share ontologies with CD1D: view

No data available for SIGNOR curated interactions for CD1D Gene

Drugs & Compounds for CD1D Gene

(7) Drugs for CD1D Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
cis-tetracosenoyl sulfatide Experimental Pharma Target 0
Phytosphingosine Experimental Pharma 0
Sphingosine Experimental Pharma 0
sphinganine Pharma 0
Sphingosine-1-phosphate Pharma Full agonist, Agonist endogenous second messenger and ligand for S1PR1, Endogenous agonist at S1P1-5 0

(519) Additional Compounds for CD1D Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
3-Dehydrosphinganine
  • 3-dehydro-D-Sphinganine
  • 3-Ketodihydrosphingosine
  • 3-Ketosphinganine
  • (2S)-2-amino-1-Hydroxyoctadecan-3-one
  • 1-Hydroxy-2-amino-3-oxo-octadecane
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 CD1D: view

Transcripts for CD1D Gene

mRNA/cDNA for CD1D Gene

5 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

  • Addgene plasmids for CD1D

Alternative Splicing Database (ASD) splice patterns (SP) for CD1D Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c · 2d ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b · 5c · 5d ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b
SP1: - -
SP2: - -
SP3: - -
SP4: - -
SP5: - - -
SP6:
SP7: - -

Relevant External Links for CD1D Gene

GeneLoc Exon Structure for
CD1D

Expression for CD1D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CD1D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CD1D Gene

This gene is overexpressed in Whole Blood (x9.9), Spleen (x8.6), Small Intestine - Terminal Ileum (x5.5), and Liver (x4.9).

Protein differential expression in normal tissues from HIPED for CD1D Gene

This gene is overexpressed in Lung (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CD1D Gene



Protein tissue co-expression partners for CD1D Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CD1D

SOURCE GeneReport for Unigene cluster for CD1D Gene:

Hs.1799

mRNA Expression by UniProt/SwissProt for CD1D Gene:

P15813-CD1D_HUMAN
Tissue specificity: Expressed on cortical thymocytes, on certain T-cell leukemias, and in various other tissues.

Evidence on tissue expression from TISSUES for CD1D Gene

  • Pancreas(4.2)
  • Blood(3.4)
  • Spleen(3.2)
  • Lymph node(3.1)
  • Liver(2.3)
  • Intestine(2.1)
  • Lung(2.1)
genes like me logo Genes that share expression patterns with CD1D: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CD1D Gene

Orthologs for CD1D Gene

This gene was present in the common ancestor of chordates.

Orthologs for CD1D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CD1D 31 30
  • 98.91 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LOC788175 30
  • 80.33 (n)
-- 31
  • 65 (a)
OneToMany
-- 31
  • 62 (a)
OneToMany
-- 31
  • 62 (a)
OneToMany
CD1D 31
  • 45 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Cd1d1 17 31 30
  • 75.47 (n)
Cd1d2 31
  • 61 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Cd1d1 30
  • 74.87 (n)
dog
(Canis familiaris)
Mammalia CD1D 31
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves CD1A1 31
  • 24 (a)
ManyToMany
CD1.2 31
  • 22 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 26 (a)
OneToMany
Species where no ortholog for CD1D 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for CD1D Gene

ENSEMBL:
Gene Tree for CD1D (if available)
TreeFam:
Gene Tree for CD1D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CD1D: view image

Paralogs for CD1D Gene

(4) SIMAP similar genes for CD1D Gene using alignment to 1 proteins:

  • CD1D_HUMAN
genes like me logo Genes that share paralogs with CD1D: view

Variants for CD1D Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CD1D Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
724721 Likely Benign: not provided 158,181,538(+) T/C MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT
775613 Benign: not provided 158,181,583(+) A/T MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT
rs62621276 - p.Thr64Ser

Additional dbSNP identifiers (rs#s) for CD1D Gene

Structural Variations from Database of Genomic Variants (DGV) for CD1D Gene

Variant ID Type Subtype PubMed ID
esv3578208 CNV loss 25503493
nsv999542 CNV loss 25217958

Variation tolerance for CD1D Gene

Residual Variation Intolerance Score: 83.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.67; 31.99% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CD1D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CD1D

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CD1D Gene

Disorders for CD1D Gene

MalaCards: The human disease database

(36) MalaCards diseases for CD1D Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
mycobacterium malmoense
  • m. malmoense
glottis neoplasm
  • neoplasm of glottis
langerhans cell sarcoma
  • malignant langerhans cell sarcoma
non-langerhans-cell histiocytosis
  • histiocytosis, non-langerhans-cell
allergic contact dermatitis
  • contact dermatitis, allergic
- elite association - COSMIC cancer census association via MalaCards
Search CD1D in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CD1D

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CD1D: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CD1D Gene

Publications for CD1D Gene

  1. CD1d-lipid-antigen recognition by the semi-invariant NKT T-cell receptor. (PMID: 17581592) Borg NA … Rossjohn J (Nature 2007) 3 4 23 54
  2. Susceptibility to Guillain-Barré syndrome is associated to polymorphisms of CD1 genes. (PMID: 16820217) Caporale CM … Uncini A (Journal of neuroimmunology 2006) 3 23 41 54
  3. Regulation of intracellular trafficking of human CD1d by association with MHC class II molecules. (PMID: 11927549) Kang SJ … Cresswell P (The EMBO journal 2002) 3 4 23 54
  4. Isolation and characterization of a cDNA and gene coding for a fourth CD1 molecule. (PMID: 2463622) Balk SP … Terhorst C (Proceedings of the National Academy of Sciences of the United States of America 1989) 2 3 4 54
  5. Uncoupling between CD1d upregulation induced by retinoic acid and conduritol-B-epoxide and iNKT cell responsiveness. (PMID: 19651460) Balreira A … Arosa FA (Immunobiology 2010) 3 23 54

Products for CD1D Gene

  • Addgene plasmids for CD1D

Sources for CD1D Gene