CLEC10A C-type lectin domain containing 10A [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLEC10Aprovided by HGNC
Official Full Name: C-type lectin domain containing 10Aprovided by HGNC
Primary source: HGNC:HGNC:16916
See related: Ensembl:ENSG00000132514 MIM:605999; AllianceGenome:HGNC:16916
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: HML; MGL; HML2; CD301; CLECSF13; CLECSF14
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 function as a cell surface antigen. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
Expression: Broad expression in appendix (RPKM 13.9), small intestine (RPKM 10.3) and 21 other tissues See more
Orthologs: all
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Genomic context

Location:: 17p13.1

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (7074537..7080251, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (6975209..6980923, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (6977856..6983570, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

High expression of CLEC10A in head and neck squamous cell carcinoma indicates favorable prognosis and high-level immune infiltration status.
Title: High expression of CLEC10A in head and neck squamous cell carcinoma indicates favorable prognosis and high-level immune infiltration status.
N-Glycoproteins Have a Major Role in MGL Binding to Colorectal Cancer Cell Lines: Associations with Overall Proteome Diversity.
Title: N-Glycoproteins Have a Major Role in MGL Binding to Colorectal Cancer Cell Lines: Associations with Overall Proteome Diversity.
The C-type lectin receptor MGL senses N-acetylgalactosamine on the unique Staphylococcus aureus ST395 wall teichoic acid.
Title: The C-type lectin receptor MGL senses N-acetylgalactosamine on the unique Staphylococcus aureus ST395 wall teichoic acid.
The MGL can be used to discriminate tumor from the corresponding healthy tissues.
Title: Characterization of Macrophage Galactose-type Lectin (MGL) ligands in colorectal cancer cell lines.
our data provide new insight into the identification and structure of novel MGL ligands that presumably act as modulatory molecules in cancer immune responses.
Title: Glycoproteomic Analysis of MGL-Binding Proteins on Acute T-Cell Leukemia Cells.
CLEC10A represents not only a candidate to better define CD1c(+) dendritic cells-due to its high endocytic potential-CLEC10A also exhibits an interesting candidate receptor for future antigen-targeting approaches.
Title: CLEC10A Is a Specific Marker for Human CD1c(+) Dendritic Cells and Enhances Their Toll-Like Receptor 7/8-Induced Cytokine Secretion.
this paper shows that key gene of intermediate proinflammatory monocytes, such as CLEC10A, is expressed three- to fourfold more in juvenile idiopathic arthritis-enthesitis-related arthritis
Title: Intermediate monocytes are increased in enthesitis-related arthritis, a category of juvenile idiopathic arthritis.
BRAF(V600E) mutation induces MGL ligand expression, thereby providing a direct link between oncogenic transformation and aberrant expression of immunosuppressive glycans in colorectal neoplasms.
Title: MGL ligand expression is correlated to BRAF mutation and associated with poor survival of stage III colon cancer patients.
These results indicate a role of MGL as an immunomodulator within the tumour microenvironment interfering with Treg functions, suggesting its possible use in the design of anticancer vaccines.
Title: The Macrophage Galactose-Type C-Type Lectin (MGL) Modulates Regulatory T Cell Functions.
expression of GalNAc moieties mirrors the T cell activation status, and thus only highly stimulated T cells are prone to the suppressive action of MGL.
Title: Human T cell activation results in extracellular signal-regulated kinase (ERK)-calcineurin-dependent exposure of Tn antigen on the cell surface and binding of the macrophage galactose-type lectin (MGL).

Submit: New GeneRIF Correction See all GeneRIFs (14)

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 transmembrane glycoprotein gp41	env	A synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 downregulates the expression of C-type lectin domain family 10, member A (CLEC10A) in peptide-treated PBMCs	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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables D-mannose binding	IBA Inferred from Biological aspect of Ancestor more info
enables carbohydrate binding	TAS Traceable Author Statement more info	PubMed
enables fucose binding	IBA Inferred from Biological aspect of Ancestor 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 endocytosis	IEA Inferred from Electronic Annotation more info
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in innate immune response	IEA Inferred from Electronic Annotation 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 plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: C-type lectin domain family 10 member A

Names: C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13 (macrophage-derived); C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 14 (macrophage-derived); macrophage lectin 2 (calcium dependent)

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.

Genomic

NG_029878.1 RefSeqGene

Range

5031..10745

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001330070.2 → NP_001316999.1 C-type lectin domain family 10 member A isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1.

Source sequence(s)

AC120057, BM974488

Consensus CDS

CCDS82049.1

UniProtKB/TrEMBL

J3KR22

Related

ENSP00000414938.2, ENST00000416562.7

Conserved Domains (2) summary

cd03590
Location:154 → 278

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)

pfam03954
Location:18 → 143

Lectin_N; Hepatic lectin, N-terminal domain
NM_006344.4 → NP_006335.2 C-type lectin domain family 10 member A isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) 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)

BC027858, BC039011, BM974488, D50532, DA620172

Consensus CDS

CCDS45597.1

UniProtKB/Swiss-Prot

Q8IUN9

Related

ENSP00000460252.1, ENST00000571664.1

Conserved Domains (2) summary

cd03590
Location:157 → 281

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)

pfam03954
Location:18 → 143

Lectin_N; Hepatic lectin, N-terminal domain
NM_182906.4 → NP_878910.1 C-type lectin domain family 10 member A isoform 1

See identical proteins and their annotated locations for NP_878910.1

Status: REVIEWED

Description

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

Source sequence(s)

BC027858, BC039011, BM974488, DA620172

Consensus CDS

CCDS11087.1

UniProtKB/Swiss-Prot

A8K8J8, Q14538, Q6PIW3, Q8IUN9

Related

ENSP00000254868.4, ENST00000254868.8

Conserved Domains (2) summary

cd03590
Location:181 → 305

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)

pfam03954
Location:18 → 170

Lectin_N; Hepatic lectin, N-terminal domain

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_000017.11 Reference GRCh38.p14 Primary Assembly

Range

7074537..7080251 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011523615.2 → XP_011521917.1 C-type lectin domain family 10 member A isoform X2

Conserved Domains (2) summary

cd03590
Location:184 → 304

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)

pfam03954
Location:18 → 170

Lectin_N; Hepatic lectin, N-terminal domain
XM_011523613.2 → XP_011521915.1 C-type lectin domain family 10 member A isoform X1

See identical proteins and their annotated locations for XP_011521915.1

Conserved Domains (2) summary

cd03590
Location:184 → 308

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)

pfam03954
Location:18 → 170

Lectin_N; Hepatic lectin, N-terminal domain

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

6975209..6980923 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054314701.1 → XP_054170676.1 C-type lectin domain family 10 member A isoform X2
XM_054314700.1 → XP_054170675.1 C-type lectin domain family 10 member A isoform X1