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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
    mouse all
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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 variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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

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