CD1D Gene

HGNC Family	Immunoglobulin superfamily domain containing, CD molecules (CD)
Name	CD1d molecule
Description	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]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n CD1d is a non‐polymorphic, major histocompatibility complex class I–like molecule whose principal function is to bind and present lipid antigens—derived from both self and microbial sources—to invariant natural killer T (iNKT) cells. This glycolipid presentation, exemplified by ligands such as α‐galactosylceramide, initiates rapid iNKT cell activation and cytokine release that bridges innate and adaptive immunity."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "4"}]}, {"type": "t", "text": " Structural studies further reveal that CD1d possesses a uniquely configured binding groove that tightly accommodates glycolipids in a “lock‐and‐key” mode. This precise orientation is critical not only for efficient antigen loading and editing (as shown by analyses in lipid‐transfer protein–deficient systems) but also for the subsequent development and effector function of iNKT cells."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": " In vivo models demonstrate that impaired CD1d‐mediated antigen presentation leads to marked deficiencies in CD1d‐reactive NKT cells, underscoring its role as a linchpin in immune surveillance."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": " Moreover, activation of CD1d‐restricted NKT cells has been implicated in the modulation of inflammatory processes such as atherosclerosis, where enhanced CD1d signaling can exacerbate vascular lesion development."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "8"}]}, {"type": "t", "text": " Collectively, these findings position CD1d as a pivotal mediator in immune regulation, influencing host defense, autoimmunity, tumor immunosurveillance, and inflammation through its specialized role in lipid antigen presentation.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "T Kawano, J Cui, Y Koezuka, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CD1d-restricted and TCR-mediated activation of valpha14 NKT cells by glycosylceramides."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Science (1997)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1126/science.278.5343.1626"}], "href": "https://doi.org/10.1126/science.278.5343.1626"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "9374463"}], "href": "https://pubmed.ncbi.nlm.nih.gov/9374463"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Emmanuel Treiner, Livine Duban, Seiamak Bahram, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Selection of evolutionarily conserved mucosal-associated invariant T cells by MR1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature01433"}], "href": "https://doi.org/10.1038/nature01433"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12634786"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12634786"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Dapeng Zhou, Jochen Mattner, Carlos Cantu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Lysosomal glycosphingolipid recognition by NKT cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Science (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1126/science.1103440"}], "href": "https://doi.org/10.1126/science.1103440"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15539565"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15539565"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Natalie A Borg, Kwok S Wun, Lars Kjer-Nielsen, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CD1d-lipid-antigen recognition by the semi-invariant NKT T-cell receptor."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature05907"}], "href": "https://doi.org/10.1038/nature05907"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17581592"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17581592"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Dapeng Zhou, Carlos Cantu, Yuval Sagiv, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Editing of CD1d-bound lipid antigens by endosomal lipid transfer proteins."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Science (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1126/science.1092009"}], "href": "https://doi.org/10.1126/science.1092009"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "14684827"}], "href": "https://pubmed.ncbi.nlm.nih.gov/14684827"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Michael Koch, Victoria S Stronge, Dawn Shepherd, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The crystal structure of human CD1d with and without alpha-galactosylceramide."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Immunol (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ni1225"}], "href": "https://doi.org/10.1038/ni1225"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16007090"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16007090"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Frederic Geissmann, Thomas O Cameron, Stephane Sidobre, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Intravascular immune surveillance by CXCR6+ NKT cells patrolling liver sinusoids."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "PLoS Biol (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1371/journal.pbio.0030113"}], "href": "https://doi.org/10.1371/journal.pbio.0030113"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15799695"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15799695"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Emmanuel Tupin, Antonino Nicoletti, Rima Elhage, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CD1d-dependent activation of NKT cells aggravates atherosclerosis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Exp Med (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1084/jem.20030997"}], "href": "https://doi.org/10.1084/jem.20030997"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "14744994"}], "href": "https://pubmed.ncbi.nlm.nih.gov/14744994"}]}]}]}
Synonyms	R3, R3G1
Proteins	CD1D_HUMAN
NCBI Gene ID	912
API
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

CD1D has 8,279 functional associations with biological entities spanning 8 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 110 datasets.

Click the + buttons to view associations for CD1D from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

CD1D Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of CD1D gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of CD1D gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of CD1D gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of CD1D gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of CD1D gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of CD1D gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of CD1D gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of CD1D gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of CD1D gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of CD1D gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of CD1D gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with CD1D gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of CD1D gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of CD1D gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of CD1D gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of CD1D gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing CD1D protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing CD1D protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with CD1D protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with CD1D protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of CD1D gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with CD1D gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with CD1D gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with CD1D gene/protein from the curated CTD Gene-Disease Associations dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by CD1D gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with CD1D gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with CD1D gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with CD1D gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with CD1D gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	DrugBank Drug Targets	interacting drugs for CD1D protein from the curated DrugBank Drug Targets dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at CD1D gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of CD1D gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of CD1D gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing CD1D from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with CD1D gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with CD1D gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of CD1D gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with CD1D gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
	GeneSigDB Published Gene Signatures	PubMedIDs of publications reporting gene signatures containing CD1D from the GeneSigDB Published Gene Signatures dataset.
	GEO Signatures of Differentially Expressed Genes for Diseases	disease perturbations changing expression of CD1D gene from the GEO Signatures of Differentially Expressed Genes for Diseases dataset.