CLEC6A C-type lectin domain containing 6A [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLEC6Aprovided by HGNC
Official Full Name: C-type lectin domain containing 6Aprovided by HGNC
Primary source: HGNC:HGNC:14556
See related: Ensembl:ENSG00000205846 MIM:613579; AllianceGenome:HGNC:14556
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: CLEC4N; CLECSF10; dectin-2; hDECTIN-2
Summary: The protein encoded by this gene is a type II membrane receptor with an extracellular C-type lectin-like domain fold. The extracellular portion binds structures with a high mannose content and has been shown to recognize several pathogens, including C. elegans, S. cerevisiae, M. tuberculosis, C. neoformans, and house dust mite. When stimulated, the encoded protein initiates signalling through the CARD9-Bcl10-Malt1 pathway, leading to the induction of cytokines. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]
Expression: Low expression observed in reference dataset See more
Orthologs: all
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Genomic context

Location:: 12p13.31

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (8455962..8478330)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (8439728..8461787)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (8608558..8630926)

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?

The ligation between ERMAP, galectin-9 and dectin-2 promotes Kupffer cell phagocytosis and antitumor immunity.
Title: The ligation between ERMAP, galectin-9 and dectin-2 promotes Kupffer cell phagocytosis and antitumor immunity.
SOCS3 Regulates Dectin-2-Induced Inflammation in PBMCs of Diabetic Patients.
Title: SOCS3 Regulates Dectin-2-Induced Inflammation in PBMCs of Diabetic Patients.
Human thioredoxin, a damage-associated molecular pattern and Malassezia-crossreactive autoallergen, modulates immune responses via the C-type lectin receptors Dectin-1 and Dectin-2.
Title: Human thioredoxin, a damage-associated molecular pattern and Malassezia-crossreactive autoallergen, modulates immune responses via the C-type lectin receptors Dectin-1 and Dectin-2.
Deletion of haematopoietic Dectin-2 did not influence atherosclerosis development under hyperglycaemic conditions, despite some minor effects on inflammation.
Title: Deletion of haematopoietic Dectin-2 or CARD9 does not protect from atherosclerosis development under hyperglycaemic conditions.
dimannoside caps and multivalent interaction are required for ligand binding to and signaling via Dectin-2.
Title: Deciphering the molecular basis of mycobacteria and lipoglycan recognition by the C-type lectin Dectin-2.
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.
Dectin-1/Dectin-2-induced autocrine PGE2 signaling licenses dendritic cells to prime Th2 responses.
Title: Dectin-1/2-induced autocrine PGE2 signaling licenses dendritic cells to prime Th2 responses.
functions in Kupffer cells to mediate the uptake and clearance of cancer cells
Title: The innate immune receptor Dectin-2 mediates the phagocytosis of cancer cells by Kupffer cells for the suppression of liver metastasis.
Data suggest that the specificity and geometry of dectin-2/CLEC6A carbohydrate-binding site provide molecular mechanism for binding of dectin-2 to fungal mannans and also to bacterial lipopolysaccharides, capsular polysaccharides, and lipoarabinomannans that contain mannose-alpha-1--2-mannose disaccharide unit. (CLEC6A = C-type lectin domain containing 6A)
Title: Mechanism of pathogen recognition by human dectin-2.
these data indicate that mannosylated O-antigens from several Gram-negative bacteria augment TLR4 responses through interaction with Dectin-2.
Title: Dectin-2 Recognizes Mannosylated O-antigens of Human Opportunistic Pathogens and Augments Lipopolysaccharide Activation of Myeloid Cells.

Submit: New GeneRIF Correction See all GeneRIFs (16)

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)

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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 carbohydrate binding	ISS Inferred from Sequence or Structural Similarity more info
enables mannose binding	IDA Inferred from Direct Assay more info	PubMed
enables pattern recognition receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables pattern recognition receptor activity	ISS Inferred from Sequence or Structural Similarity more info
enables phospholipase binding	ISS Inferred from Sequence or Structural Similarity 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
involved_in antifungal innate immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in defense response to fungus	ISS Inferred from Sequence or Structural Similarity more info
involved_in detection of yeast	ISS Inferred from Sequence or Structural Similarity more info
involved_in innate immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of T-helper 17 type immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of canonical NF-kappaB signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cytokine production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of intracellular signal transduction	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of positive regulation of peptidyl-tyrosine phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to yeast	ISS Inferred from Sequence or Structural Similarity more info
involved_in stimulatory C-type lectin receptor signaling pathway	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
is_active_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: C-type lectin domain family 6 member A

Names: C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 10; C-type lectin superfamily member 10; DC-associated C-type lectin 2; dectin 2; dendritic cell-associated C-type lectin 2

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_001007033.2 → NP_001007034.1 C-type lectin domain family 6 member A isoform 1

See identical proteins and their annotated locations for NP_001007034.1

Status: REVIEWED

Description

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

Source sequence(s)

AC092746, AC092865

Consensus CDS

CCDS31739.1

UniProtKB/Swiss-Prot

A2RUK3, Q6EIG7

Related

ENSP00000371505.3, ENST00000382073.4

Conserved Domains (1) summary

cd03590
Location:79 → 204

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_001317999.2 → NP_001304928.1 C-type lectin domain family 6 member A isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1. This variant is supported by transcripts from the mouse ortholog Clec4n (GeneID 56620) and by PMID:15810886.

Source sequence(s)

AC092746, AC092865

UniProtKB/Swiss-Prot

Q6EIG7

Conserved Domains (1) summary

cd03590
Location:49 → 174

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)