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CLEC5A C-type lectin domain containing 5A [ Homo sapiens (human) ]

Gene ID: 23601, updated on 2-Nov-2024

Summary

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Official Symbol
CLEC5Aprovided by HGNC
Official Full Name
C-type lectin domain containing 5Aprovided by HGNC
Primary source
HGNC:HGNC:2054
See related
Ensembl:ENSG00000258227 MIM:604987; AllianceGenome:HGNC:2054
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
MDL1; MDL-1; CLECSF5
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 II transmembrane protein interacts with dnax-activation protein 12 and may play a role in cell activation. Alternative splice variants have been described but their full-length sequence has not been determined. [provided by RefSeq, Jul 2008]
Expression
Biased expression in bone marrow (RPKM 12.6), appendix (RPKM 4.1) and 6 other tissues See more
Orthologs
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Genomic context

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See CLEC5A in Genome Data Viewer
Location:
7q34
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (141927357..141946974, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (143243134..143262731, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (141627157..141646774, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak6800 silencer Neighboring gene olfactory receptor family 9 subfamily N member 1 pseudogene Neighboring gene uncharacterized LOC124901761 Neighboring gene olfactory receptor family 9 subfamily A member 4 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:141645256-141646455 Neighboring gene OCT4 hESC enhancer GRCh37_chr7:141654062-141654628 Neighboring gene taste 2 receptor member 38 Neighboring gene NANOG hESC enhancer GRCh37_chr7:141695377-141695878 Neighboring gene maltase-glucoamylase

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. [Overexpression of CLEC5A inhibits cell proliferation and metastasis and reverses epithelial-mesenchymal transition in hepatocellular carcinoma]. Lin J, et al. Nan Fang Yi Ke Da Xue Xue Bao, 2023 Jan 20. PMID 36856214, Free PMC Article
  2. Association of rs1285933 single nucleotide polymorphism in CLEC5A gene with dengue severity and its functional effects. Xavier-Carvalho C, et al. Hum Immunol, 2017 Oct. PMID 28764923
  3. A potential role of myeloid DAP12-associating lectin (MDL)-1 in the regulation of inflammation in rheumatoid arthritis patients. Chen DY, et al. PLoS One, 2014. PMID 24465901, Free PMC Article
  4. CLEC5A is critical for dengue virus-induced inflammasome activation in human macrophages. Wu MF, et al. Blood, 2013 Jan 3. PMID 23152543
  5. C-type lectin domain family 5, member A (CLEC5A, MDL-1) promotes brain glioblastoma tumorigenesis by regulating PI3K/Akt signalling. Fan HW, et al. Cell Prolif, 2019 May. PMID 30834619, Free PMC Article

See all (38) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The influence of CLEC5A on early macrophage-mediated inflammation in COPD progression.
    Title: The influence of CLEC5A on early macrophage-mediated inflammation in COPD progression.
  2. [Overexpression of CLEC5A inhibits cell proliferation and metastasis and reverses epithelial-mesenchymal transition in hepatocellular carcinoma].
    Title: [Overexpression of CLEC5A inhibits cell proliferation and metastasis and reverses epithelial-mesenchymal transition in hepatocellular carcinoma].
  3. CLEC5A expression can be triggered by spike glycoprotein and may be a potential target for COVID-19 therapy.
    Title: CLEC5A expression can be triggered by spike glycoprotein and may be a potential target for COVID-19 therapy.
  4. CLEC5A and TLR2 are critical in SARS-CoV-2-induced NET formation and lung inflammation.
    Title: CLEC5A and TLR2 are critical in SARS-CoV-2-induced NET formation and lung inflammation.
  5. Activation of the Innate Immune Checkpoint CLEC5A on Myeloid Cells in the Absence of Danger Signals Modulates Macrophages' Function but Does Not Trigger the Adaptive T Cell Immune Response.
    Title: Activation of the Innate Immune Checkpoint CLEC5A on Myeloid Cells in the Absence of Danger Signals Modulates Macrophages' Function but Does Not Trigger the Adaptive T Cell Immune Response.
  6. CLEC5A expressed on myeloid cells as a M2 biomarker relates to immunosuppression and decreased survival in patients with glioma.
    Title: CLEC5A expressed on myeloid cells as a M2 biomarker relates to immunosuppression and decreased survival in patients with glioma.
  7. Genetic association analysis of CLEC5A and CLEC7A gene single-nucleotide polymorphisms and Crohn's disease.
    Title: Genetic association analysis of CLEC5A and CLEC7A gene single-nucleotide polymorphisms and Crohn's disease.
  8. CLEC2 and CLEC5A: Pathogenic Host Factors in Acute Viral Infections.
    Title: CLEC2 and CLEC5A: Pathogenic Host Factors in Acute Viral Infections.
  9. CLEC5A promotes the proliferation of gastric cancer cells by activating the PI3K/AKT/mTOR pathway.
    Title: CLEC5A promotes the proliferation of gastric cancer cells by activating the PI3K/AKT/mTOR pathway.
  10. CEBPB can inhibit the proliferation of osteosarcoma cells via regulating the expression of CLEC5A.
    Title: Transcription factor CEBPB inhibits the proliferation of osteosarcoma by regulating downstream target gene CLEC5A.
Submit: New GeneRIF Correction See all GeneRIFs (25)

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

EBI GWAS Catalog

Description
Genetic variants associated with disordered eating.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

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

Clone Names

  • MGC138304

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables carbohydrate binding IEA
Inferred from Electronic Annotation
more info
  
enables virus receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables virus receptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular defense response TAS
Traceable Author Statement
more info
 PubMed 
involved_in innate immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in innate immune response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in myeloid cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of myeloid cell apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in osteoblast development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of cytokine production IEA
Inferred from Electronic Annotation
more info
  
involved_in signal transduction TAS
Traceable Author Statement
more info
 PubMed 
involved_in symbiont entry into host cell IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cell surface ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  
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 5 member A
Names
C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 5
C-type lectin superfamily member 5
myeloid DAP12-associating lectin-1

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)

  1. NM_001301167.2 → NP_001288096.1  C-type lectin domain family 5 member A isoform 2

    See identical proteins and their annotated locations for NP_001288096.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AC073647, AK295200, AK307095
    Consensus CDS
    CCDS75670.1
    UniProtKB/TrEMBL
    C9JPR7, Q14DL9
    Related
    ENSP00000446890.2, ENST00000551012.6
    Conserved Domains (1) summary
    cd03593
    Location:48 → 162
    CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

  2. NM_013252.3 → NP_037384.1  C-type lectin domain family 5 member A isoform 1

    See identical proteins and their annotated locations for NP_037384.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AI418484, AJ271684, BQ005467, BQ446122
    Consensus CDS
    CCDS5870.1
    UniProtKB/Swiss-Prot
    Q52M11, Q9NY25, Q9UKQ0
    UniProtKB/TrEMBL
    A4D1U7
    Related
    ENSP00000449999.1, ENST00000546910.6
    Conserved Domains (1) summary
    cd03593
    Location:71 → 185
    CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    141927357..141946974 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011515995.3 → XP_011514297.1  C-type lectin domain family 5 member A isoform X1

    See identical proteins and their annotated locations for XP_011514297.1

    Conserved Domains (1) summary
    cd03593
    Location:28 → 142
    CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

RNA

  1. XR_007059995.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    143243134..143262731 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054357726.1 → XP_054213701.1  C-type lectin domain family 5 member A isoform X1

RNA

  1. XR_008487549.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NY25.1 GenPept UniProtKB/Swiss-Prot:Q9NY25

Gene LinkOut

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