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

Gene ID: 10462, updated on 2-Nov-2024

Summary

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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

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See CLEC10A in Genome Data Viewer
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_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11596 Neighboring gene solute carrier family 16 member 13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8082 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8083 Neighboring gene uncharacterized LOC124903909 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8085 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11597 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11598 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11599 Neighboring gene solute carrier family 16 member 11 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11601 Neighboring gene asialoglycoprotein receptor 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7015987-7016487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7018293-7019079 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7034277-7034814 Neighboring gene uncharacterized LOC105371512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11602

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. High expression of CLEC10A in head and neck squamous cell carcinoma indicates favorable prognosis and high-level immune infiltration status. Zou M, et al. Cell Immunol, 2022 Feb. PMID 35093731
  2. Molecular cloning and expression of cDNA encoding human macrophage C-type lectin. Its unique carbohydrate binding specificity for Tn antigen. Suzuki N, et al. J Immunol, 1996 Jan 1. PMID 8598452
  3. Variation of Neisseria gonorrhoeae lipooligosaccharide directs dendritic cell-induced T helper responses. van Vliet SJ, et al. PLoS Pathog, 2009 Oct. PMID 19834553, Free PMC Article
  4. Targeting of macrophage galactose-type C-type lectin (MGL) induces DC signaling and activation. Napoletano C, et al. Eur J Immunol, 2012 Apr. PMID 22531918
  5. Protein domain histochemistry (PDH): binding of the carbohydrate recognition domain (CRD) of recombinant human glycoreceptor CLEC10A (CD301) to formalin-fixed, paraffin-embedded breast cancer tissues. Nollau P, et al. J Histochem Cytochem, 2013 Mar. PMID 23275449, Free PMC Article

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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)

Genotypes

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

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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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

Homology

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

  1. NG_029878.1 RefSeqGene

    Range
    5031..10745
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  3. 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

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    7074537..7080251 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    6975209..6980923 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IUN9.1 GenPept UniProtKB/Swiss-Prot:Q8IUN9

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