CLEC4A C-type lectin domain family 4 member A [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLEC4Aprovided by HGNC
Official Full Name: C-type lectin domain family 4 member Aprovided by HGNC
Primary source: HGNC:HGNC:13257
See related: Ensembl:ENSG00000111729 MIM:605306; AllianceGenome:HGNC:13257
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: DCIR; LLIR; CD367; DDB27; hDCIR; CLECSF6; HDCGC13P
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 inflammatory and immune response. Multiple transcript variants encoding distinct isoforms have been identified for this gene. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region. [provided by RefSeq, Jul 2008]
Expression: Broad expression in appendix (RPKM 5.2), bone marrow (RPKM 2.2) and 20 other tissues See more
Orthologs: all
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Genomic context

Location:: 12p13.31

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (8102907..8138607)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (8116443..8152211)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (8276213..8291203)

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 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 C-type lectin DCIR contributes to the immune response and pathogenesis of colorectal cancer.
Title: The C-type lectin DCIR contributes to the immune response and pathogenesis of colorectal cancer.
DCIR suppresses osteoclastic proliferation and resorption by downregulating M-CSF and RANKL signaling.
Title: DCIR suppresses osteoclastic proliferation and resorption by downregulating M-CSF and RANKL signaling.
Differential expression of immune-regulatory proteins C5AR1, CLEC4A and NLRP3 on peripheral blood mononuclear cells in early-stage non-small cell lung cancer patients.
Title: Differential expression of immune-regulatory proteins C5AR1, CLEC4A and NLRP3 on peripheral blood mononuclear cells in early-stage non-small cell lung cancer patients.
DCIR and its ligand asialo-biantennary N-glycan regulate DC function and osteoclastogenesis.
Title: DCIR and its ligand asialo-biantennary N-glycan regulate DC function and osteoclastogenesis.
Pivotal role of the carbohydrate recognition domain in self-interaction of CLEC4A to elicit the ITIM-mediated inhibitory function in murine conventional dendritic cells in vitro.
Title: Pivotal role of the carbohydrate recognition domain in self-interaction of CLEC4A to elicit the ITIM-mediated inhibitory function in murine conventional dendritic cells in vitro.
Authors have determined the structure, tissue distribution, and molecular function of the cartilage-specific lectin CLEC3A and show that CLEC3A binds to plasminogen and participates in tPA-mediated plasminogen activation.
Title: The cartilage-specific lectin C-type lectin domain family 3 member A (CLEC3A) enhances tissue plasminogen activator-mediated plasminogen activation.
DCIR SNP rs2377422 is a novel genetic susceptibility factor for both SLE and primary SS.
Title: Contribution of dendritic cell immunoreceptor (DCIR) polymorphisms in susceptibility of systemic lupus erythematosus and primary Sjogren's syndrome.
this study shows that sulfo-Lewis(a) is a high affinity ligand for DCIR and that DCIR interacts with ligands from both pathogenic and endogenous origin of which most are shared by DC-SIGN.
Title: DCIR interacts with ligands from both endogenous and pathogenic origin.
No association was found between our inflammatory bowel disease cohort and the candidate single nucleotide polymorphisms for DCIR (CD/HC: P=0.22 and UC/HC: P=0.41)
Title: Single nucleotide polymorphisms in C-type lectin genes, clustered in the IBD2 and IBD6 susceptibility loci, may play a role in the pathogenesis of inflammatory bowel diseases.
Data provide evidence for association between DCIR rs2377422 and RA in non-Caucasian populations and confirm the influence of DCIR polymorphisms on RA susceptibility, especially on ACPA-negative RA.
Title: A replication study confirms the association of dendritic cell immunoreceptor (DCIR) polymorphisms with ACPA - negative RA in a large Asian cohort.

Submit: New GeneRIF Correction See all GeneRIFs (19)

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 Env gp120/41 (JRFL Env in the contaxt of HIV-Gag-GFP VLP) binds to CLEC4A (DCIR) on the surface of basophils	PubMed
	env	DCIR is less efficient than DC-SIGN in capturing a wide range of HIV-1 isolates and transferring them to target cells, and exhibits a distinct binding affinity to gp120 compared to that of DC-SIGN to gp120	PubMed
	env	HIV-1 gp140 trimers bind to dendritic cell immunoreceptor (DCIR) more strongly than HIV-1 gp120 proteins	PubMed
Envelope surface glycoprotein gp160, precursor	env	HIV-1 gp140 trimers bind to dendritic cell immunoreceptor (DCIR) more strongly than HIV-1 gp120 proteins	PubMed
	env	Soluble DCIR has a lesser binding affinity to HIV-1 gp140 than soluble DC-SIGN	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

NoName (e-PCR)
- UniSTS:486216

CLECSF6_3585 (e-PCR)
- UniSTS:468340

G41279 (e-PCR)
- UniSTS:18361

NoName (e-PCR)
- UniSTS:482002

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables D-mannose binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables carbohydrate binding	IBA Inferred from Biological aspect of Ancestor more info
enables carbohydrate binding	IDA Inferred from Direct Assay more info	PubMed
enables pattern recognition receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables transmembrane signaling receptor activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in CD8-positive, alpha-beta T cell activation	IDA Inferred from Direct Assay more info	PubMed
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
involved_in antigen processing and presentation of exogenous peptide antigen via MHC class I	IDA Inferred from Direct Assay more info	PubMed
involved_in cell adhesion	TAS Traceable Author Statement more info	PubMed
involved_in cell surface receptor signaling pathway	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of cytokine production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of tumor necrosis factor production	IDA Inferred from Direct Assay more info	PubMed
involved_in plasmacytoid dendritic cell antigen processing and presentation	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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

Names: C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 6; C-type lectin DDB27; C-type lectin superfamily member 6; dendritic cell immunoreceptor; lectin-like immunoreceptor

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_016184.4 → NP_057268.1 C-type lectin domain family 4 member A isoform 1

See identical proteins and their annotated locations for NP_057268.1

Status: REVIEWED

Description

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

Source sequence(s)

AC006511, AF067800, AI400631, AJ133532

Consensus CDS

CCDS8590.1

UniProtKB/Swiss-Prot

Q17R69, Q8WXW9, Q9H2Z9, Q9NS33, Q9UI34, Q9UMR7

Related

ENSP00000229332.5, ENST00000229332.12

Conserved Domains (1) summary

cd03590
Location:106 → 232

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_194447.3 → NP_919429.2 C-type lectin domain family 4 member A isoform 3

See identical proteins and their annotated locations for NP_919429.2

Status: REVIEWED

Description

Transcript Variant: This variant (3), also known as LLIRv1, lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (3), that is missing the transmembrane domain compared to isoform 1.

Source sequence(s)

AC006511, AF067800, AI400631, AJ133532

Consensus CDS

CCDS41745.1

UniProtKB/Swiss-Prot

Q9UMR7

Related

ENSP00000353690.3, ENST00000360500.5

Conserved Domains (1) summary

cd03590
Location:67 → 193

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_194448.3 → NP_919430.1 C-type lectin domain family 4 member A isoform 4

See identical proteins and their annotated locations for NP_919430.1

Status: REVIEWED

Description

Transcript Variant: This variant (4), also known as LLIRv2, lacks an in-frame segment of the coding region, compared to variant 1. It encodes the shortest isoform (4), that is missing a region thought to be responsible for oligomerization, compared to isoform 1.

Source sequence(s)

AC006511, AF067800, AI400631, AJ133532

Consensus CDS

CCDS8591.1

UniProtKB/Swiss-Prot

Q9UMR7

Related

ENSP00000344646.3, ENST00000345999.9

Conserved Domains (1) summary

cd03590
Location:34 → 160

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_194450.3 → NP_919432.1 C-type lectin domain family 4 member A isoform 2

See identical proteins and their annotated locations for NP_919432.1

Status: REVIEWED

Description

Transcript Variant: This variant (2), also known as C-type lectin DDB27 short form, lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (2), that is missing the transmembrane domain compared to isoform 1.

Source sequence(s)

AC006511, AF067800, AI400631, AJ133532

Consensus CDS

CCDS8592.1

UniProtKB/Swiss-Prot

Q9UMR7

Related

ENSP00000247243.5, ENST00000352620.9

Conserved Domains (1) summary

cd03590
Location:73 → 199

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

8102907..8138607

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017019382.3 → XP_016874871.1 C-type lectin domain family 4 member A isoform X2

Conserved Domains (1) summary

cd03590
Location:11 → 137

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)
XM_011520684.3 → XP_011518986.1 C-type lectin domain family 4 member A isoform X1

Conserved Domains (1) summary

cd03590
Location:69 → 195

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

8116443..8152211

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054372159.1 → XP_054228134.1 C-type lectin domain family 4 member A isoform X2
XM_054372158.1 → XP_054228133.1 C-type lectin domain family 4 member A isoform X1