CLEC4C C-type lectin domain family 4 member C [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLEC4Cprovided by HGNC
Official Full Name: C-type lectin domain family 4 member Cprovided by HGNC
Primary source: HGNC:HGNC:13258
See related: Ensembl:ENSG00000198178 MIM:606677; AllianceGenome:HGNC:13258
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: DLEC; HECL; BDCA2; CD303; BDCA-2; CLECSF7; CLECSF11; PRO34150
Summary: This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signalling, glycoprotein turnover, and roles in inflammation and immune response. The encoded type 2 transmembrane protein may play a role in dendritic cell function. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
Expression: Biased expression in lymph node (RPKM 1.5), spleen (RPKM 0.9) and 6 other tissues See more
Orthologs: all
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Genomic context

Location:: 12p13.31

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (7729383..7749541, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (7744033..7766234, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (7881979..7902137, complement)

Chromosome 12 - NC_000012.12 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?

The differentiation of new human CD303(+) Plasmacytoid dendritic cell subpopulations expressing CD205 and/or CD103 regulated by Non-Small-Cell lung cancer cells.
Title: The differentiation of new human CD303(+) Plasmacytoid dendritic cell subpopulations expressing CD205 and/or CD103 regulated by Non-Small-Cell lung cancer cells.
Zika Virus Inhibits IFN-alpha Response by Human Plasmacytoid Dendritic Cells and Induces NS1-Dependent Triggering of CD303 (BDCA-2) Signaling.
Title: Zika Virus Inhibits IFN-α Response by Human Plasmacytoid Dendritic Cells and Induces NS1-Dependent Triggering of CD303 (BDCA-2) Signaling.
Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation.
Title: Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation.
24F4A (BIIB059) is an antibody targeting BDCA2.
Title: Effect of in vivo Hydroxychloroquine and ex vivo Anti-BDCA2 mAb Treatment on pDC IFNα Production From Patients Affected With Cutaneous Lupus Erythematosus.
Identification of serum glycoprotein ligands for the immunomodulatory receptor blood dendritic cell antigen 2.
Title: Identification of serum glycoprotein ligands for the immunomodulatory receptor blood dendritic cell antigen 2.
decrease in the surface expression of CLEC4C and the endoplasmic reticulum localization of the mutant construct were observed
Title: CLEC4C p.K210del variant causes impaired cell surface transport in plasmacytoid dendritic cells of amyotrophic lateral sclerosis.
Human BDCA2+CD123+CD56+ dendritic cells (DCs) related to blastic plasmacytoid dendritic cell neoplasm represent a unique myeloid DC subset.
Title: Human BDCA2+CD123+CD56+ dendritic cells (DCs) related to blastic plasmacytoid dendritic cell neoplasm represent a unique myeloid DC subset.
BDCA-2 binds selectively to glycans containing the epitope Galbeta1-3/4GlcNAcbeta1-2Man.
Title: A Novel Mechanism for Binding of Galactose-terminated Glycans by the C-type Carbohydrate Recognition Domain in Blood Dendritic Cell Antigen 2.
We show the crystal structures of a carbohydrate recognition domain (CRD) of human C-type lectin receptor blood dendritic cell antigen-2 (BDCA2).
Title: Crystal structures of carbohydrate recognition domain of blood dendritic cell antigen-2 (BDCA2) reveal a common domain-swapped dimer.
Reduction in Treg numbers following Ag delivery to BDCA2 restored both CD4(+) T cell activation and Ab responses, demonstrating that Tregs were required for the observed tolerance.
Title: Targeting antigens through blood dendritic cell antigen 2 on plasmacytoid dendritic cells promotes immunologic tolerance.

Submit: New GeneRIF Correction See all GeneRIFs (20)

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	HIV-1 gp120-mediated inhibition of IFN-alpha production involves CD4 and BDCA2 in plasmacytoid dendritic cells	PubMed
	env	HIV-1 gp120 monomers and trimers bind to BDCA2 in transfected cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:489987

D11S2921 (e-PCR)
- UniSTS:152074

NoName (e-PCR)
- UniSTS:481817

PMC156606P1 (e-PCR)
- UniSTS:271408

NoName (e-PCR)
- UniSTS:482097

D1S1423 (e-PCR)
- UniSTS:149619

Clone Names

MGC125789, MGC125791, MGC125792, MGC125793

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables carbohydrate binding	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables pattern recognition receptor activity	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 antifungal innate immune response	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in ficolin-1-rich granule membrane	TAS Traceable Author Statement more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in secretory granule membrane	TAS Traceable Author Statement more info
located_in tertiary granule membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: C-type lectin domain family 4 member C

Names: C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 11; C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 7; C-type lectin superfamily member 7; blood dendritic cell antigen 2 protein; dendritic cell lectin b; dendritic lectin

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_001371390.1 → NP_001358319.1 C-type lectin domain family 4 member C isoform 1

Status: REVIEWED

Source sequence(s)

AC006517, AY358223

Consensus CDS

CCDS8583.1

UniProtKB/Swiss-Prot

D3DUU3, Q3T1C3, Q6UXS8, Q8WTT0, Q8WXX8

UniProtKB/TrEMBL

B3KV04

Related

ENSP00000353500.3, ENST00000360345.8

Conserved Domains (1) summary

cd03590
Location:83 → 208

CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
NM_001371391.1 → NP_001358320.1 C-type lectin domain family 4 member C isoform 3

Status: REVIEWED

Source sequence(s)

AC006517

UniProtKB/TrEMBL

B3KV04

Conserved Domains (1) summary

cd03590
Location:46 → 171

CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
NM_130441.3 → NP_569708.1 C-type lectin domain family 4 member C isoform 1

See identical proteins and their annotated locations for NP_569708.1

Status: REVIEWED

Description

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

Source sequence(s)

AC006517, AF293615

Consensus CDS

CCDS8583.1

UniProtKB/Swiss-Prot

D3DUU3, Q3T1C3, Q6UXS8, Q8WTT0, Q8WXX8

UniProtKB/TrEMBL

B3KV04

Related

ENSP00000440428.1, ENST00000542353.5

Conserved Domains (1) summary

cd03590
Location:83 → 208

CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
NM_203503.2 → NP_987099.1 C-type lectin domain family 4 member C isoform 2

See identical proteins and their annotated locations for NP_987099.1

Status: REVIEWED

Description

Transcript Variant: This variant (2), also known as DLEC-beta, lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (2), compared to isoform 1.

Source sequence(s)

AC006517, AF293615, AF325460

Consensus CDS

CCDS8584.1

UniProtKB/TrEMBL

B3KV04

Related

ENSP00000445338.1, ENST00000540085.5

Conserved Domains (1) summary

cd03590
Location:52 → 177

CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)

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_000012.12 Reference GRCh38.p14 Primary Assembly

Range

7729383..7749541 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024448873.2 → XP_024304641.1 C-type lectin domain family 4 member C isoform X1

UniProtKB/Swiss-Prot

D3DUU3, Q3T1C3, Q6UXS8, Q8WTT0, Q8WXX8

UniProtKB/TrEMBL

B3KV04

Conserved Domains (1) summary

cd03590
Location:83 → 208

CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

7744033..7766234 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054371339.1 → XP_054227314.1 C-type lectin domain family 4 member C isoform X2

UniProtKB/TrEMBL

B3KV04
XM_054371337.1 → XP_054227312.1 C-type lectin domain family 4 member C isoform X1

UniProtKB/Swiss-Prot

D3DUU3, Q3T1C3, Q6UXS8, Q8WTT0, Q8WXX8

UniProtKB/TrEMBL

B3KV04
XM_054371338.1 → XP_054227313.1 C-type lectin domain family 4 member C isoform X1

UniProtKB/Swiss-Prot

D3DUU3, Q3T1C3, Q6UXS8, Q8WTT0, Q8WXX8

UniProtKB/TrEMBL

B3KV04