CD1A CD1a molecule [Homo sapiens (human)] - Gene

Summary

Official Symbol: CD1Aprovided by HGNC
Official Full Name: CD1a moleculeprovided by HGNC
Primary source: HGNC:HGNC:1634
See related: Ensembl:ENSG00000158477 MIM:188370; AllianceGenome:HGNC:1634
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: R4; T6; CD1; FCB6; HTA1
Summary: 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 localizes to the plasma membrane and to recycling vesicles of the early endocytic system. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
Expression: Biased expression in skin (RPKM 10.0), esophagus (RPKM 4.8) and 4 other tissues See more
Orthologs: all
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Genomic context

Location:: 1q23.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (158248336..158258269)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (157385427..157395365)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (158218126..158228059)

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?

Oral lupus erythematosus: Immunohistochemical evaluation of CD1a, CD21, CD123, and langerin expression in dendritic cells.
Title: Oral lupus erythematosus: Immunohistochemical evaluation of CD1a, CD21, CD123, and langerin expression in dendritic cells.
Keratinocyte-derived small extracellular vesicles supply antigens for CD1a-resticted T cells and promote their type 2 bias in the context of filaggrin insufficiency.
Title: Keratinocyte-derived small extracellular vesicles supply antigens for CD1a-resticted T cells and promote their type 2 bias in the context of filaggrin insufficiency.
Human Skin T Cells Express Conserved T-Cell Receptors that Cross-React with Staphylococcal Superantigens and CD1a.
Title: Human Skin T Cells Express Conserved T-Cell Receptors that Cross-React with Staphylococcal Superantigens and CD1a.
CD1a is not effective in distinguishing calcifying epithelial odontogenic tumors from amyloid-rich central odontogenic fibroma.
Title: CD1a is not effective in distinguishing calcifying epithelial odontogenic tumors from amyloid-rich central odontogenic fibroma.
CD1a and bound lipids drive T-cell responses in human skin disease.
Title: CD1a and bound lipids drive T-cell responses in human skin disease.
CD1a-mediated immunity from a molecular perspective.
Title: CD1a-mediated immunity from a molecular perspective.
Human skin is colonized by T cells that recognize CD1a independently of lipid.
Title: Human skin is colonized by T cells that recognize CD1a independently of lipid.
Animal models for human group 1 CD1 protein function.
Title: Animal models for human group 1 CD1 protein function.
CD1a function in human skin disease.
Title: CD1a function in human skin disease.
rs16840041, rs2269714, and rs2269715 in high linkage disequilibrium and significantly associated with increase in plasma NFL levels
Title: Genome-wide association study identifies CD1A associated with rate of increase in plasma neurofilament light in non-demented elders.

Submit: New GeneRIF Correction See all GeneRIFs (77)

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
Nef	nef	HIV-1 Nef impairs the generation of a CD3epsilon(+)CD5(+) CD1a(+) T cell differentiation precursor stage that initiates a D-J rearrangement of the TCRbeta locus	PubMed
	nef	CD1a molecules are downregulated by and co-localized with Nef in CD1a-transfected cells; this co-localization is dependent upon the CD1a cytoplasmic tail from amino acid position 325 to 327	PubMed
Tat	tat	CD4 and CD1a surface expression are greatly decreased in Tat expression Jurkat cells	PubMed
	tat	Only the wild-type Tat induces CD1A-expressing MDDC maturation and increases the production of cytokines TNF-alpha, IL-12, MIP-1alpha, and MIP-1beta	PubMed
	tat	CD1A-expressing monocyte-derived dendritic cells (MDDC) efficiently uptake wild-type and Cys-22 Tat but not oxidized Tat	PubMed
Vpr	vpr	HIV-1 Vpr upregulates the gene expression of CD1A in human monocyte-derived dendritic cells	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

RH120517 (e-PCR)
- UniSTS:133682

D1S3258 (e-PCR)
- UniSTS:41819

RH11438 (e-PCR)
- UniSTS:48869

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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 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 adaptive immune response	IEA Inferred from Electronic Annotation more info
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, exogenous lipid antigen via MHC class Ib	IBA Inferred from Biological aspect of Ancestor more info
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in immune response	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of T cell mediated cytotoxicity	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
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 membrane raft	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: T-cell surface glycoprotein CD1a

Names: CD1A antigen, a polypeptide; T-cell surface antigen T6/Leu-6; cluster of differentiation 1 A; cortical thymocyte antigen CD1A; differentiation antigen CD1-alpha-3; epidermal dendritic cell marker CD1a; hTa1 thymocyte antigen

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_001320652.2 → NP_001307581.1 T-cell surface glycoprotein CD1a isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AK312945, AW949640, CA432941, DA822513

UniProtKB/TrEMBL

Q8N5T0

Conserved Domains (2) summary

cd07698
Location:191 → 284

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

cl08246
Location:12 → 185

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
NM_001763.3 → NP_001754.2 T-cell surface glycoprotein CD1a isoform 1 precursor

See identical proteins and their annotated locations for NP_001754.2

Status: REVIEWED

Description

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

Source sequence(s)

CA432941, DB108750, M28825

Consensus CDS

CCDS1174.1

UniProtKB/Swiss-Prot

D3DVD7, P06126, Q13962, Q5TDJ8, Q9UMM4, Q9Y5M5

UniProtKB/TrEMBL

Q8N5T0

Related

ENSP00000289429.5, ENST00000289429.6

Conserved Domains (2) summary

cd07698
Location:202 → 295

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

cl08246
Location:19 → 196

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

158248336..158258269

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024450738.2 → XP_024306506.1 T-cell surface glycoprotein CD1a isoform X1

Conserved Domains (2) summary

cd07698
Location:46 → 139

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

cl08246
Location:2 → 40

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2