CLEC4D C-type lectin domain family 4 member D [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLEC4Dprovided by HGNC
Official Full Name: C-type lectin domain family 4 member Dprovided by HGNC
Primary source: HGNC:HGNC:14554
See related: Ensembl:ENSG00000166527 MIM:609964; AllianceGenome:HGNC:14554
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: MCL; MPCL; CD368; CLEC6; CLEC-6; CLECSF8; Dectin-3
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. 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: Biased expression in bone marrow (RPKM 17.6), appendix (RPKM 4.0) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 12p13.31

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (8513503..8531696)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (8496932..8515063)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (8666099..8674962)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

C-type lectin receptor Dectin3 deficiency balances the accumulation and function of FoxO1-mediated LOX-1(+) M-MDSCs in relieving lupus-like symptoms.
Title: C-type lectin receptor Dectin3 deficiency balances the accumulation and function of FoxO1-mediated LOX-1(+) M-MDSCs in relieving lupus-like symptoms.
The Mincle/Syk/NF-kappaB Signaling Circuit Is Essential for Maintaining the Protumoral Activities of Tumor-Associated Macrophages.
Title: The Mincle/Syk/NF-κB Signaling Circuit Is Essential for Maintaining the Protumoral Activities of Tumor-Associated Macrophages.
The Syk-Coupled C-Type Lectin Receptors Dectin-2 and Dectin-3 Are Involved in Paracoccidioides brasiliensis Recognition by Human Plasmacytoid Dendritic Cells.
Title: The Syk-Coupled C-Type Lectin Receptors Dectin-2 and Dectin-3 Are Involved in Paracoccidioides brasiliensis Recognition by Human Plasmacytoid Dendritic Cells.
Results show the molecular mechanism of glycolipid recognition through C-type lectin receptors, which may provide clues to rational design for effective adjuvants.
Title: Structural analysis for glycolipid recognition by the C-type lectins Mincle and MCL.
CLECSF8 functions as an activation receptor on myeloid cells and associates with a novel adaptor molecule
Title: The C-type lectin receptor CLECSF8 (CLEC4D) is expressed by myeloid cells and triggers cellular activation through Syk kinase.
Cross-linking of the receptor leads to a rapid internalization suggesting that CLECSF8 constitutes and endocytic receptor.
Title: The human C-type lectin CLECSF8 is a novel monocyte/macrophage endocytic receptor.

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Phenotypes

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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

MARC_4325-4326:991938466:1 (e-PCR)
- UniSTS:231081

MARC_4325-4326:996679570:1 (e-PCR)
- UniSTS:231081

MARC_3557-3558:966881413:1 (e-PCR)
- UniSTS:269274

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables D-mannose binding	IDA Inferred from Direct Assay more info	PubMed
enables carbohydrate binding	IBA Inferred from Biological aspect of Ancestor more info
enables immunoglobulin receptor binding	IEA Inferred from Electronic Annotation 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 pattern recognition receptor activity	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 Fc-gamma receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in T cell differentiation involved in immune response	IEA Inferred from Electronic Annotation more info
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 antifungal innate immune response	IDA Inferred from Direct Assay more info	PubMed
involved_in defense response to bacterium	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of canonical NF-kappaB signal transduction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of myeloid dendritic cell activation	ISS Inferred from Sequence or Structural Similarity 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
is_active_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in specific 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 D

Names: C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 8; C-type lectin receptor; C-type lectin superfamily member 8; C-type lectin-like receptor 6; DC-associated C-type lectin 3; Dectin 3; dendritic cell-associated C-type lectin 3; macrophage C-type 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_080387.5 → NP_525126.2 C-type lectin domain family 4 member D

See identical proteins and their annotated locations for NP_525126.2

Status: REVIEWED

Source sequence(s)

AC092746, BC032313, BI909298

Consensus CDS

CCDS8593.1

UniProtKB/Swiss-Prot

Q8N5J5, Q8WXI8

Related

ENSP00000299665.2, ENST00000299665.3

Conserved Domains (1) summary

cd03590
Location:84 → 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)

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

8513503..8531696

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047428772.1 → XP_047284728.1 C-type lectin domain family 4 member D isoform X3
XM_047428771.1 → XP_047284727.1 C-type lectin domain family 4 member D isoform X2
XM_011520632.3 → XP_011518934.1 C-type lectin domain family 4 member D isoform X1

See identical proteins and their annotated locations for XP_011518934.1

UniProtKB/Swiss-Prot

Q8N5J5, Q8WXI8

Conserved Domains (1) summary

cd03590
Location:84 → 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

8496932..8515063

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054371926.1 → XP_054227901.1 C-type lectin domain family 4 member D isoform X1

UniProtKB/Swiss-Prot

Q8N5J5, Q8WXI8
XM_054371928.1 → XP_054227903.1 C-type lectin domain family 4 member D isoform X3
XM_054371927.1 → XP_054227902.1 C-type lectin domain family 4 member D isoform X2