CD1D CD1d molecule [Homo sapiens (human)] - Gene

Summary

Official Symbol: CD1Dprovided by HGNC
Official Full Name: CD1d moleculeprovided by HGNC
Primary source: HGNC:HGNC:1637
See related: Ensembl:ENSG00000158473 IMGT/GENE-DB:CD1D; MIM:188410; AllianceGenome:HGNC:1637
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: R3; CD1A; R3G1
Summary: 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]
Expression: Broad expression in appendix (RPKM 5.0), spleen (RPKM 5.0) and 17 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q23.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (158178030..158186427)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (157297517..157323522)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (158147820..158156217)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Varicella Zoster Virus Downregulates Expression of the Nonclassical Antigen Presentation Molecule CD1d.
Title: Varicella Zoster Virus Downregulates Expression of the Nonclassical Antigen Presentation Molecule CD1d.
Cancer-associated fibroblasts express CD1d and activate invariant natural killer T cells under cellular stress.
Title: Cancer-associated fibroblasts express CD1d and activate invariant natural killer T cells under cellular stress.
Epigenetic control of CD1D expression as a mechanism of resistance to immune checkpoint therapy in poorly immunogenic melanomas.
Title: Epigenetic control of CD1D expression as a mechanism of resistance to immune checkpoint therapy in poorly immunogenic melanomas.
CD1d expression in glioblastoma is a promising target for NKT cell-based cancer immunotherapy.
Title: CD1d expression in glioblastoma is a promising target for NKT cell-based cancer immunotherapy.
Low oxygen saturation during sleep reduces CD1D and RAB20 expressions that are reversed by CPAP therapy.
Title: Low oxygen saturation during sleep reduces CD1D and RAB20 expressions that are reversed by CPAP therapy.
Structural Dynamics of the Lipid Antigen-Binding Site of CD1d Protein.
Title: Structural Dynamics of the Lipid Antigen-Binding Site of CD1d Protein.
Invariant NKT Cells From Donor Lymphocyte Infusions (DLI-iNKTs) Promote ex vivo Lysis of Leukemic Blasts in a CD1d-Dependent Manner.
Title: Invariant NKT Cells From Donor Lymphocyte Infusions (DLI-iNKTs) Promote ex vivo Lysis of Leukemic Blasts in a CD1d-Dependent Manner.
Expression of CD1d by astrocytes corresponds with relative activity in multiple sclerosis lesions.
Title: Expression of CD1d by astrocytes corresponds with relative activity in multiple sclerosis lesions.
Increased cytoplasmatic expression of cancer immune surveillance receptor CD1d in anaplastic thyroid carcinomas.
Title: Increased cytoplasmatic expression of cancer immune surveillance receptor CD1d in anaplastic thyroid carcinomas.
Role of CD1d- and MR1-Restricted T Cells in Asthma.
Title: Role of CD1d- and MR1-Restricted T Cells in Asthma.

Submit: New GeneRIF Correction See all GeneRIFs (145)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	CD1d surface expression on human cell lines is downregulated after infection with M-tropic HIV, T-tropic HIV, or after exposure to HIV gp120 in vitro	PubMed
Nef	nef	HIV-1 Nef downregulates the expression of the non-classical MHC-I like CD1d molecule by increasing internalization of CD1d molecules from the cell surface and retaining CD1d in the trans-Golgi-network (TGN)	PubMed
	nef	HIV-1 Vpu and Nef cooperatively inhibit CD1d-mediated lipid antigen presentation in HIV-1-infected DCs	PubMed
	nef	Nef-induced downregulation of CD1d is observed when cells are co-expressing Nef and CD1d, and six amino acids (300-305) in the cytoplasmic tail of CD1d are required for the downregulation by Nef	PubMed
	nef	HIV-1 Nef-mediated downregulation of CD1d requires a tyrosine-based motif in the CD1d cytoplasmic tail and four Nef amino acid motifs (EEEE65, PxxP75, DD165, and LL175), which are known to be involved in the downregulation of MHC-I and CD4	PubMed
Vpr	vpr	HIV-1 Vpr downregulates the expression of CD1D in human monocyte-derived dendritic cells	PubMed
Vpu	vpu	The conserved APW motif in the alpha-helix II domain at the C-terminal region of HIV-1 Vpu is involved in CD1d downregulation	PubMed
	vpu	HIV-1 Vpu proteins from group M, O, and P, and SIV Vpu proteins efficiently downregulate CD1d surface levels	PubMed
	vpu	HIV-1 Vpu downregulates CD1d from the cell surface by inhibiting CD1d recycling from early endosomal compartments to the cell surface	PubMed
	vpu	HIV-1 Vpu proteins from Cameroonian group N viruses are largely unable to downregulate CD1D	PubMed
	vpu	HIV-1 Vpu and Nef cooperatively inhibit CD1d-mediated lipid antigen presentation in HIV-1-infected DCs	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC150819P1 (e-PCR)
- UniSTS:271106

PMC150819P2 (e-PCR)
- UniSTS:271107

PMC150819P3 (e-PCR)
- UniSTS:271108

PMC150819P4 (e-PCR)
- UniSTS:271109

PMC150819P5 (e-PCR)
- UniSTS:271110

PMC150819P6 (e-PCR)
- UniSTS:271111

D1S3312 (e-PCR)
- UniSTS:70497

SHGC-82759 (e-PCR)
- UniSTS:100755

RH66323 (e-PCR)
- UniSTS:24022

A004X45 (e-PCR)
- UniSTS:7416

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables beta-2-microglobulin binding	TAS Traceable Author Statement more info	PubMed
enables cell adhesion molecule binding	IPI Inferred from Physical Interaction more info	PubMed
enables endogenous lipid antigen binding	IBA Inferred from Biological aspect of Ancestor more info
enables exogenous lipid antigen binding	IBA Inferred from Biological aspect of Ancestor more info
enables exogenous lipid antigen binding	IDA Inferred from Direct Assay more info	PubMed
enables lipid antigen binding	IDA Inferred from Direct Assay more info	PubMed
enables lipopeptide binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in T cell selection	TAS Traceable Author Statement more info	PubMed
involved_in antigen processing and presentation, endogenous lipid antigen via MHC class Ib	IBA Inferred from Biological aspect of Ancestor more info
involved_in antigen processing and presentation, endogenous lipid antigen via MHC class Ib	IDA Inferred from Direct Assay more info	PubMed
involved_in antigen processing and presentation, exogenous lipid antigen via MHC class Ib	IBA Inferred from Biological aspect of Ancestor more info
involved_in detection of bacterium	TAS Traceable Author Statement more info	PubMed
involved_in heterotypic cell-cell adhesion	TAS Traceable Author Statement more info	PubMed
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of T cell mediated cytotoxicity	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of T cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of innate immune response	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in basolateral plasma membrane	IEA Inferred from Electronic Annotation more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: antigen-presenting glycoprotein CD1d

Names: CD1D antigen, d polypeptide; HMC class I antigen-like glycoprotein CD1D; T-cell surface glycoprotein CD1d; differentiation antigen CD1-alpha-3; thymocyte antigen CD1D

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001319145.2 → NP_001306074.1 antigen-presenting glycoprotein CD1d isoform 2 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon and has a shorter 3' UTR compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AL138899

Consensus CDS

CCDS91074.1

UniProtKB/TrEMBL

A0A669KB34

Related

ENSP00000501066.1, ENST00000673623.2

Conserved Domains (1) summary

pfam16497
Location:20 → 198

MHC_I_3; MHC-I family domain
NM_001371761.1 → NP_001358690.1 antigen-presenting glycoprotein CD1d isoform 3

Status: REVIEWED

Source sequence(s)

AL138899

Consensus CDS

CCDS91075.1

UniProtKB/TrEMBL

A0A669KAZ2

Related

ENSP00000501010.1, ENST00000673701.2

Conserved Domains (2) summary

cd21029
Location:99 → 191

IgC1_CD1; Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains

cl08246
Location:1 → 94

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
NM_001371762.2 → NP_001358691.1 antigen-presenting glycoprotein CD1d isoform 1 precursor

Status: REVIEWED

Source sequence(s)

AL138899

Consensus CDS

CCDS1173.1

UniProtKB/Swiss-Prot

D3DVD5, P15813, Q5W0J3, Q9UMM3, Q9Y5M4

Related

ENSP00000501100.1, ENST00000674085.2

Conserved Domains (2) summary

cd07698
Location:203 → 295

IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain

pfam16497
Location:1 → 198

MHC_I_3; MHC-I family domain
NM_001371763.1 → NP_001358692.1 antigen-presenting glycoprotein CD1d isoform 1 precursor

Status: REVIEWED

Source sequence(s)

AL138899

Consensus CDS

CCDS1173.1

UniProtKB/Swiss-Prot

D3DVD5, P15813, Q5W0J3, Q9UMM3, Q9Y5M4

Related

ENSP00000357153.3, ENST00000368171.5

Conserved Domains (2) summary

cd07698
Location:203 → 295

IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain

pfam16497
Location:1 → 198

MHC_I_3; MHC-I family domain
NM_001766.4 → NP_001757.1 antigen-presenting glycoprotein CD1d isoform 1 precursor

See identical proteins and their annotated locations for NP_001757.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AL138899, BC027926, BX106524

Consensus CDS

CCDS1173.1

UniProtKB/Swiss-Prot

D3DVD5, P15813, Q5W0J3, Q9UMM3, Q9Y5M4

Related

ENSP00000501245.3, ENST00000673723.4

Conserved Domains (2) summary

cd07698
Location:203 → 295

IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain

pfam16497
Location:1 → 198

MHC_I_3; MHC-I family domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

158178030..158186427

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047433945.1 → XP_047289901.1 antigen-presenting glycoprotein CD1d isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

157297517..157323522

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054339553.1 → XP_054195528.1 antigen-presenting glycoprotein CD1d isoform X3

UniProtKB/TrEMBL

A0A669KB34
XM_054339552.1 → XP_054195527.1 antigen-presenting glycoprotein CD1d isoform X2

UniProtKB/Swiss-Prot

D3DVD5, P15813, Q5W0J3, Q9UMM3, Q9Y5M4