CD1C CD1c molecule [Homo sapiens (human)] - Gene

Summary

Official Symbol: CD1Cprovided by HGNC
Official Full Name: CD1c moleculeprovided by HGNC
Primary source: HGNC:HGNC:1636
See related: Ensembl:ENSG00000158481 MIM:188340; AllianceGenome:HGNC:1636
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: R7; CD1; CD1A; BDCA1
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 is broadly distributed throughout the endocytic system via a tyrosine-based motif in the cytoplasmic tail. Alternatively spliced transcript variants of this gene have been observed, but their full-length nature is not known. [provided by RefSeq, Jul 2008]
Expression: Broad expression in lymph node (RPKM 8.6), appendix (RPKM 6.9) and 15 other tissues See more
Orthologs: all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 1q23.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (158289923..158294774)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (157427020..157431871)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (158259713..158264564)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identifying CD1c as a potential biomarker by the comprehensive exploration of tumor mutational burden and immune infiltration in diffuse large B cell lymphoma.
Title: Identifying CD1c as a potential biomarker by the comprehensive exploration of tumor mutational burden and immune infiltration in diffuse large B cell lymphoma.
CD1C is associated with breast cancer prognosis and immune infiltrates.
Title: CD1C is associated with breast cancer prognosis and immune infiltrates.
Rational design of a hydrolysis-resistant mycobacterial phosphoglycolipid antigen presented by CD1c to T cells.
Title: Rational design of a hydrolysis-resistant mycobacterial phosphoglycolipid antigen presented by CD1c to T cells.
Animal models for human group 1 CD1 protein function.
Title: Animal models for human group 1 CD1 protein function.
The expression of histones, small nucleolar RNA H/ACA box (SNORA) and small nucleolar RNA C/D/box (SNORD), and long non-coding RNA (lncRNA) is also substantially upregulated in the DCs from aged. In contrast, the antigen-presenting and energy generating pathways are downregulated
Title: Transcriptional Profiling of Age-Associated Gene Expression Changes in Human Circulatory CD1c+ Myeloid Dendritic Cell Subset.
these results demonstrated the mechanism that suppression of CD1c by BCG infection is mediated by miR-381-3p
Title: MiR-381-3p Regulates the Antigen-Presenting Capability of Dendritic Cells and Represses Antituberculosis Cellular Immune Responses by Targeting CD1c.
We found a significant difference in the density of intraepidermal CD1c+ cells between the examined lesions; the mean CD1c cell count was 7.00/mm(2) for invasive melanomas, 2.94 for in situ melanomas, and 13.35 for dysplastic nevi
Title: Melanomas and Dysplastic Nevi Differ in Epidermal CD1c+ Dendritic Cell Count.
Stressed beta-cells have little effect on human BDCA1-expressed dendritic cells activation and function, while enterovirus-infected beta-cells impact these cells significantly.
Title: Distinct activation of primary human BDCA1(+) dendritic cells upon interaction with stressed or infected β cells.
Circulating atopic dermatitis pre-dendritic CD1c+ cells are premature and bear atopic characteristics even without tissue-specific stimulation, suggesting that their development is not only influenced by the skin microenvironment, but also by the local milieu in the blood.
Title: CD1c+ Blood Dendritic Cells in Atopic Dermatitis are Premature and Can Produce Disease-specific Chemokines.
human CD1c adopts different conformations dependent on ligand occupancy of its groove, with CE and ASG stabilizing CD1c conformations that provide a footprint for binding of CD1c self-reactive T-cell receptors
Title: Cholesteryl esters stabilize human CD1c conformations for recognition by self-reactive T cells.

Submit: New GeneRIF Correction See all GeneRIFs (40)

Phenotypes

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

Protein interactions

Protein	Gene	Interaction	Pubs
Vpu	vpu	HIV-1 Vpu downregulates CD1c in Jurkat cells	PubMed

Go to the HIV-1, Human Interaction Database

General gene information

Go to the top of the page Help

Markers

NoName (e-PCR)
- UniSTS:486912

D1S3359 (e-PCR)
- UniSTS:37643

NoName (e-PCR)
- UniSTS:495206

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables endogenous lipid antigen binding	IBA Inferred from Biological aspect of Ancestor more info
enables endogenous lipid antigen binding	IDA Inferred from Direct Assay more info	PubMed
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 glycolipid binding	IDA Inferred from Direct Assay more info	PubMed
enables lipopeptide binding	IBA Inferred from Biological aspect of Ancestor more info
enables lipopeptide binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in T cell activation involved in immune response	IDA Inferred from Direct Assay more info	PubMed
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 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 endoplasmic reticulum	IDA Inferred from Direct Assay 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 intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

Go to the top of the page Help

Preferred Names: T-cell surface glycoprotein CD1c

Names: CD1C antigen, c polypeptide; cortical thymocyte antigen CD1C; differentiation antigen CD1-alpha-3

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001765.3 → NP_001756.2 T-cell surface glycoprotein CD1c precursor

See identical proteins and their annotated locations for NP_001756.2

Status: REVIEWED

Source sequence(s)

AA824381, AL121986, M28827

Consensus CDS

CCDS1175.1

UniProtKB/Swiss-Prot

P29017, Q5TDJ7, Q6IAS4, Q9UMM0, Q9UN96

Related

ENSP00000357152.3, ENST00000368170.8

Conserved Domains (2) summary

cd07698
Location:204 → 296

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

cl08246
Location:20 → 197

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

158289923..158294774

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005245579.6 → XP_005245636.1 T-cell surface glycoprotein CD1c isoform X1

UniProtKB/TrEMBL

H0Y6Y6

Related

ENSP00000408755.1, ENST00000443761.1

Conserved Domains (2) summary

cd07698
Location:204 → 297

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

cl08246
Location:20 → 197

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