CD1E CD1e molecule [Homo sapiens (human)] - Gene

Summary

Official Symbol: CD1Eprovided by HGNC
Official Full Name: CD1e moleculeprovided by HGNC
Primary source: HGNC:HGNC:1638
See related: Ensembl:ENSG00000158488 MIM:188411; AllianceGenome:HGNC:1638
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: R2; CD1A
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 within Golgi compartments, endosomes, and lysosomes, and is cleaved into a stable soluble form. The soluble form is required for the intracellular processing of some glycolipids into a form that can be presented by other CD1 family members. Many alternatively spliced transcript variants encoding different isoforms have been described. Additional transcript variants have been found; however, their biological validity has not been determined. [provided by RefSeq, Jun 2010]
Expression: Broad expression in skin (RPKM 3.1), esophagus (RPKM 2.3) and 18 other tissues See more
Orthologs: all
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Genomic context

Location:: 1q23.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (158353894..158357553)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (157490987..157494646)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (158323684..158327343)

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?

CD1 gene polymorphism and susceptibility to celiac disease: Association of CD1E*02/02 in Moroccans.
Title: CD1 gene polymorphism and susceptibility to celiac disease: Association of CD1E*02/02 in Moroccans.
Single nucleotide polymorphisms in exon 2 of CD1A (*01/*02) and CD1E (*01/*02) cannot be recognized as a susceptibility or disease-causative factor for Guillain-Barre syndrome in the Bangladeshi population
Title: CD1A and CD1E gene polymorphisms are not associated with susceptibility to Guillain-Barré syndrome in the Bangladeshi population.
There was no association between polymorphisms of CD1E genes and the susceptibilities to Guillain-Barre syndrome.
Title: Polymorphisms in exon 2 of CD1 genes are associated with susceptibility to Guillain-Barré syndrome.
for isoforms CD1b through CD1e, our simulations show the near-complete collapse of the hydrophobic cavities in the absence of the antigen. This event results from the spontaneous closure of the binding domain entrance, flanked by two alpha-helices.
Title: Dynamics of the antigen-binding grooves in CD1 proteins: reversible hydrophobic collapse in the lipid-free state.
The interaction of LAPTM5 with CD1e and their colocalization in antigen processing compartments both suggest that LAPTM5 might influence the role of CD1e in the presentation of lipid antigens.
Title: Lysosomal-associated transmembrane protein 5 (LAPTM5) is a molecular partner of CD1e.
Deciphering the role of CD1e protein in mycobacterial phosphatidyl-myo-inositol mannosides (PIM) processing for presentation by CD1b to T lymphocytes
Title: Deciphering the role of CD1e protein in mycobacterial phosphatidyl-myo-inositol mannosides (PIM) processing for presentation by CD1b to T lymphocytes.
in the late endosomes/lysosomes of dendritic cells, the acid pH promotes the binding of lipid antigens to CD1e through increased hydrophobic and ionic interactions
Title: Increased flexibility and liposome-binding capacity of CD1e at endosomal pH.
allelic variation in CD1E does not play a major role in determining multifocal motor neuropathy susceptibility.
Title: Multifocal motor neuropathy is not associated with genetic variation in PTPN22, BANK1, Blk, FCGR2B, CD1A/E, and TAG-1 genes.
In Guillain-Barre syndrome, an initially positive association study with polymorphism of CD1A and CD1E genes was not confirmed
Title: Polymorphism of CD1 and SH2D2A genes in inflammatory neuropathies.
CD1e may positively or negatively affect lipid presentation by CD1b, CD1c, and CD1d.
Title: Fine tuning by human CD1e of lipid-specific immune responses.

Submit: New GeneRIF Correction See all GeneRIFs (21)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AL009528 (e-PCR)
- UniSTS:50199

RH70821 (e-PCR)
- UniSTS:871

NoName (e-PCR)
- UniSTS:480918

RH46983 (e-PCR)
- UniSTS:75472

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

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 Golgi apparatus	IDA Inferred from Direct Assay more info
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in early endosome	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 late endosome	IEA Inferred from Electronic Annotation more info
located_in lysosomal lumen	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: T-cell surface glycoprotein CD1e, membrane-associated

Names: CD1E antigen, e polypeptide; R2G1; differentiation antigen CD1-alpha-3; hCD1e; leukocyte differentiation antigen; thymocyte antigen CD1E

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_001042583.3 → NP_001036048.1 T-cell surface glycoprotein CD1e, membrane-associated isoform b precursor

See identical proteins and their annotated locations for NP_001036048.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform b, also known as 2).

Source sequence(s)

AJ289112, AL121986, BC131693, DC406237

Consensus CDS

CCDS41418.1

UniProtKB/TrEMBL

A2RRL5

Related

ENSP00000357142.3, ENST00000368160.7

Conserved Domains (2) summary

cd07698
Location:209 → 301

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

cl08246
Location:30 → 204

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
NM_001042584.3 → NP_001036049.1 T-cell surface glycoprotein CD1e, membrane-associated isoform c precursor

See identical proteins and their annotated locations for NP_001036049.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 3' coding region, compared to variant 1, that results in a frameshift. It encodes an isoform (c, also known as 3), which has a shorter and distinct C-terminus compared to isoform a.

Source sequence(s)

AJ289113, AL121986, BC131693, DC406237

Consensus CDS

CCDS41421.1

UniProtKB/TrEMBL

A2RRL5

Related

ENSP00000357143.3, ENST00000368161.7

Conserved Domains (2) summary

cl08246
Location:30 → 204

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

cl11960
Location:209 → 269

Ig; Immunoglobulin domain
NM_001042585.3 → NP_001036050.1 T-cell surface glycoprotein CD1e, membrane-associated isoform d precursor

See identical proteins and their annotated locations for NP_001036050.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses two alternate in-frame splice sites in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform d, also known as 4), compared to isoform a.

Source sequence(s)

AJ289114, AL121986, BC131693, DC406237

Consensus CDS

CCDS41419.1

UniProtKB/TrEMBL

A2RRL5

Related

ENSP00000357145.3, ENST00000368163.7

Conserved Domains (2) summary

cl08246
Location:30 → 204

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

cl11960
Location:209 → 248

Ig; Immunoglobulin domain
NM_001042586.3 → NP_001036051.1 T-cell surface glycoprotein CD1e, membrane-associated isoform e precursor

See identical proteins and their annotated locations for NP_001036051.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) is missing two coding exons and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform e, also known as 9) compared to isoform a.

Source sequence(s)

AJ289119, AL121986, DC406237

Consensus CDS

CCDS41420.1

UniProtKB/Swiss-Prot

P15812

Related

ENSP00000357148.3, ENST00000368166.7

Conserved Domains (1) summary

cd07698
Location:20 → 112

IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
NM_001042587.3 → NP_001036052.1 T-cell surface glycoprotein CD1e, membrane-associated isoform f precursor

See identical proteins and their annotated locations for NP_001036052.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) is missing two coding exons and uses an alternate splice site in the 3' coding region, which results in a translational frameshift, compared to variant 1. It encodes a protein (isoform f, also known as 10) that is shorter and has a distinct C-terminus compared to isoform a.

Source sequence(s)

AJ289120, AL121986, DC406237

Consensus CDS

CCDS41422.1

UniProtKB/Swiss-Prot

P15812

Related

ENSP00000357146.3, ENST00000368164.7

Conserved Domains (1) summary

cl11960
Location:20 → 80

Ig; Immunoglobulin domain
NM_001185107.2 → NP_001172036.1 T-cell surface glycoprotein CD1e, membrane-associated isoform g precursor

See identical proteins and their annotated locations for NP_001172036.1

Status: REVIEWED

Description

Transcript Variant: This variant (7) is missing a coding exon, compared to variant 1. It encodes a protein (isoform g, also known as 5) that is shorter when it is compared to isoform a.

Source sequence(s)

AJ289115, AL121986, BC131693, DC406237

Consensus CDS

CCDS53385.1

UniProtKB/Swiss-Prot

P15812

UniProtKB/TrEMBL

A2RRL5

Related

ENSP00000357147.3, ENST00000368165.7

Conserved Domains (2) summary

cd07698
Location:120 → 211

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

cl08246
Location:30 → 142

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
NM_001185108.2 → NP_001172037.1 T-cell surface glycoprotein CD1e, membrane-associated isoform i precursor

See identical proteins and their annotated locations for NP_001172037.1

Status: REVIEWED

Description

Transcript Variant: This variant (9) is missing a coding exon and uses two alternate in-frame splice sites in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform i, also known as 7), compared to isoform a.

Source sequence(s)

AJ289117, AL121986, BC131693, DC406237

Consensus CDS

CCDS53384.1

UniProtKB/Swiss-Prot

P15812

UniProtKB/TrEMBL

A2RRL5

Related

ENSP00000357137.3, ENST00000368155.7

Conserved Domains (2) summary

cl08246
Location:30 → 142

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

cl11960
Location:137 → 158

Ig; Immunoglobulin domain
NM_001185110.2 → NP_001172039.1 T-cell surface glycoprotein CD1e, membrane-associated isoform l precursor

See identical proteins and their annotated locations for NP_001172039.1

Status: REVIEWED

Description

Transcript Variant: This variant (12) is missing two coding exons and uses two alternate in-frame splice sites in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform l, also known as 12), compared to isoform a.

Source sequence(s)

AJ289122, AL121986, DC406237

Consensus CDS

CCDS53389.1

UniProtKB/Swiss-Prot

P15812

Related

ENSP00000357139.1, ENST00000368157.5

Conserved Domains (1) summary

cl11960
Location:20 → 59

Ig; Immunoglobulin domain
NM_001185112.2 → NP_001172041.1 T-cell surface glycoprotein CD1e, membrane-associated isoform j precursor

See identical proteins and their annotated locations for NP_001172041.1

Status: REVIEWED

Description

Transcript Variant: This variant (10) is missing two coding exons, compared to variant 1, resulting in a shorter protein (isoform j, also known as 10), compared to isoform a.

Source sequence(s)

AJ289118, AL121986, DC406237

Consensus CDS

CCDS53390.1

UniProtKB/Swiss-Prot

P15812

Related

ENSP00000416228.2, ENST00000452291.6

Conserved Domains (1) summary

cd07698
Location:20 → 112

IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
NM_001185113.2 → NP_001172042.1 T-cell surface glycoprotein CD1e, membrane-associated isoform k precursor

See identical proteins and their annotated locations for NP_001172042.1

Status: REVIEWED

Description

Transcript Variant: This variant (11) is missing two coding exons and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform k, also known as 11), compared to isoform a.

Source sequence(s)

AJ289121, AL121986, DC406237

Consensus CDS

CCDS53388.1

UniProtKB/Swiss-Prot

P15812

Related

ENSP00000357136.1, ENST00000368154.5

Conserved Domains (1) summary

cl11960
Location:20 → 59

Ig; Immunoglobulin domain
NM_001185114.2 → NP_001172043.1 T-cell surface glycoprotein CD1e, membrane-associated isoform m precursor

Status: REVIEWED

Description

Transcript Variant: This variant (13) is missing one coding exon and uses two alternate in-frame splice sites in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform m), compared to isoform a.

Source sequence(s)

AK311643, AL121986

Consensus CDS

CCDS53387.1

UniProtKB/Swiss-Prot

P15812

Related

ENSP00000402906.2, ENST00000444681.6

Conserved Domains (2) summary

cd07698
Location:110 → 202

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

cl08246
Location:21 → 105

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
NM_001185115.2 → NP_001172044.1 T-cell surface glycoprotein CD1e, membrane-associated isoform h precursor

See identical proteins and their annotated locations for NP_001172044.1

Status: REVIEWED

Description

Transcript Variant: This variant (8) is missing a coding exon and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform h, also known as 6), compared to isoform a.

Source sequence(s)

AJ289116, AL121986, BC131693, DC406237

Consensus CDS

CCDS53386.1

UniProtKB/Swiss-Prot

P15812

UniProtKB/TrEMBL

A2RRL5

Related

ENSP00000357138.1, ENST00000368156.5

Conserved Domains (2) summary

cd07698
Location:120 → 211

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

cl08246
Location:30 → 142

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
NM_030893.4 → NP_112155.2 T-cell surface glycoprotein CD1e, membrane-associated isoform a precursor

See identical proteins and their annotated locations for NP_112155.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform a, also known as 1).

Source sequence(s)

AJ289111, AL121986, BC131693, DC406237

Consensus CDS

CCDS41417.1

UniProtKB/Swiss-Prot

B4DZV3, E7EP01, P15812, Q5TDJ9, Q5TDK3, Q5TDK4, Q5TDK5, Q5TDK6, Q5TDK8, Q5TDL1, Q712E4, Q712E5, Q712E6, Q712E7, Q712E8, Q712E9, Q712F0, Q712F1, Q712F2, Q712F3, Q712F4, Q712F5, Q96TD0, Q96TD1, Q9UMM1, Q9Y5M3

UniProtKB/TrEMBL

A2RRL5

Related

ENSP00000357149.3, ENST00000368167.8

Conserved Domains (2) summary

cd07698
Location:209 → 301

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

cl08246
Location:30 → 204

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

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

158353894..158357553

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011510133.4 → XP_011508435.1 T-cell surface glycoprotein CD1e, membrane-associated isoform X1

UniProtKB/TrEMBL

A2RRL5

Conserved Domains (2) summary

cl08246
Location:30 → 204

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

cl11960
Location:209 → 248

Ig; Immunoglobulin domain
XM_047434051.1 → XP_047290007.1 T-cell surface glycoprotein CD1e, membrane-associated isoform X3
XM_047434050.1 → XP_047290006.1 T-cell surface glycoprotein CD1e, membrane-associated isoform X2
XM_047434054.1 → XP_047290010.1 T-cell surface glycoprotein CD1e, membrane-associated isoform X4
XM_047434055.1 → XP_047290011.1 T-cell surface glycoprotein CD1e, membrane-associated isoform X5

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

157490987..157494646

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054339566.1 → XP_054195541.1 T-cell surface glycoprotein CD1e, membrane-associated isoform X1
XM_054339568.1 → XP_054195543.1 T-cell surface glycoprotein CD1e, membrane-associated isoform X3
XM_054339567.1 → XP_054195542.1 T-cell surface glycoprotein CD1e, membrane-associated isoform X2
XM_054339569.1 → XP_054195544.1 T-cell surface glycoprotein CD1e, membrane-associated isoform X4
XM_054339570.1 → XP_054195545.1 T-cell surface glycoprotein CD1e, membrane-associated isoform X5