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    CLEC12A C-type lectin domain family 12 member A [ Homo sapiens (human) ]

    Gene ID: 160364, updated on 14-Nov-2024

    Summary

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    Official Symbol
    CLEC12Aprovided by HGNC
    Official Full Name
    C-type lectin domain family 12 member Aprovided by HGNC
    Primary source
    HGNC:HGNC:31713
    See related
    Ensembl:ENSG00000172322 MIM:612088; AllianceGenome:HGNC:31713
    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
    CLL1; MICL; CD371; CLL-1; DCAL-2
    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 signaling, glycoprotein turnover, and roles in inflammation and immune response. The protein encoded by this gene is a negative regulator of granulocyte and monocyte function. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. This gene is closely linked to other CTL/CTLD superfamily members in the natural killer gene complex region on chromosome 12p13. [provided by RefSeq, May 2011]
    Expression
    Biased expression in bone marrow (RPKM 14.2), appendix (RPKM 4.4) and 7 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CLEC12A in Genome Data Viewer
    Location:
    12p13.31-p13.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (9951268..10006150)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (9837492..9892550)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (10103867..10138194)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene C-type lectin domain family 2 member A Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:10051719-10052273 Neighboring gene killer cell lectin like receptor F2 Neighboring gene MPRA-validated peak1567 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:10062769-10063968 Neighboring gene long intergenic non-protein coding RNA 2470 Neighboring gene CLEC12A antisense RNA 1 Neighboring gene uncharacterized LOC124902874 Neighboring gene C-type lectin domain family 1 member B Neighboring gene uncharacterized LOC102724020 Neighboring gene C-type lectin domain family 12 member B Neighboring gene C-type lectin domain family 1 member B pseudogene Neighboring gene C-type lectin domain containing 9A

    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. Crystal structure of the complex of CLEC12A and an antibody that interferes with binding of diverse ligands. Mori S, et al. Int Immunol, 2024 Apr 27. PMID 38386511
    2. C-type lectin-like molecule-1: a novel myeloid cell surface marker associated with acute myeloid leukemia. Bakker AB, et al. Cancer Res, 2004 Nov 15. PMID 15548716
    3. Dendritic-cell-associated C-type lectin 2 (DCAL-2) alters dendritic-cell maturation and cytokine production. Chen CH, et al. Blood, 2006 Feb 15. PMID 16239426, Free PMC Article
    4. Human MICL (CLEC12A) is differentially glycosylated and is down-regulated following cellular activation. Marshall AS, et al. Eur J Immunol, 2006 Aug. PMID 16838277
    5. A genetic association study of the CLEC12A gene in rheumatoid arthritis. Michou L, et al. Joint Bone Spine, 2012 Oct. PMID 22341585

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Recognition and control of neutrophil extracellular trap formation by MICL.
      Title: Recognition and control of neutrophil extracellular trap formation by MICL.
    2. Crystal structure of the complex of CLEC12A and an antibody that interferes with binding of diverse ligands.
      Title: Crystal structure of the complex of CLEC12A and an antibody that interferes with binding of diverse ligands.
    3. Mechanistic insights into the C-type lectin receptor CLEC12A-mediated immune recognition of monosodium urate crystal.
      Title: Mechanistic insights into the C-type lectin receptor CLEC12A-mediated immune recognition of monosodium urate crystal.
    4. Behcet syndrome: The disturbed balance between anti- (CLEC12A, CLC) and proinflammatory (IFI27) gene expressions.
      Title: Behçet syndrome: The disturbed balance between anti- (CLEC12A, CLC) and proinflammatory (IFI27) gene expressions.
    5. Identification of two early blood biomarkers ACHE and CLEC12A for improved risk stratification of critically ill COVID-19 patients.
      Title: Identification of two early blood biomarkers ACHE and CLEC12A for improved risk stratification of critically ill COVID-19 patients.
    6. Mycobacterial mycolic acids trigger inhibitory receptor Clec12A to suppress host immune responses.
      Title: Mycobacterial mycolic acids trigger inhibitory receptor Clec12A to suppress host immune responses.
    7. CLEC12A plays an important role in immunomodulatory function and prognostic significance of patients with acute myeloid leukemia.
      Title: CLEC12A plays an important role in immunomodulatory function and prognostic significance of patients with acute myeloid leukemia.
    8. Exploring blast composition in myelodysplastic syndromes and myelodysplastic/myeloproliferative neoplasms: CD45RA and CD371 improve diagnostic value of flow cytometry through assessment of myeloblast heterogeneity and stem cell aberrancy.
      Title: Exploring blast composition in myelodysplastic syndromes and myelodysplastic/myeloproliferative neoplasms: CD45RA and CD371 improve diagnostic value of flow cytometry through assessment of myeloblast heterogeneity and stem cell aberrancy.
    9. The Fusion of CLEC12A and MIR223HG Arises from a trans-Splicing Event in Normal and Transformed Human Cells.
      Title: The Fusion of CLEC12A and MIR223HG Arises from a trans-Splicing Event in Normal and Transformed Human Cells.
    10. Bimodal expression of potential drug target CLL-1 (CLEC12A) on CD34+ blasts of AML patients.
      Title: Bimodal expression of potential drug target CLL-1 (CLEC12A) on CD34+ blasts of AML patients.
    Submit: New GeneRIF Correction See all GeneRIFs (39)

    Phenotypes

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    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC70602

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables pattern recognition receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables pattern recognition receptor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables signaling receptor regulator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transmembrane signaling receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transmembrane signaling receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transmembrane signaling receptor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of dendritic cell differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of immune response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of inflammatory response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of natural killer cell activation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of neutrophil activation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of type I interferon production ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in 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
    		  
    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 12 member A
    Names
    C-type lectin protein CLL-1
    C-type lectin-like molecule-1
    dendritic cell-associated lectin 2
    myeloid inhibitory C-type lectin-like receptor

    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_029426.2 RefSeqGene

      Range
      25143..39329
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001207010.2 → NP_001193939.1  C-type lectin domain family 12 member A isoform 3

      See identical proteins and their annotated locations for NP_001193939.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. This variant encodes isoform 3, which has a longer N-terminus, compared to isoform 1.
      Source sequence(s)
      AC091814, AY547296
      Consensus CDS
      CCDS55803.1
      UniProtKB/Swiss-Prot
      Q5QGZ9
      Related
      ENSP00000347916.4, ENST00000355690.8
      Conserved Domains (1) summary
      cd03593
      Location:143 → 260
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    2. NM_001300730.2 → NP_001287659.1  C-type lectin domain family 12 member A isoform 4

      See identical proteins and their annotated locations for NP_001287659.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has multiple differences compared to variant 3. These differences result in distinct 5' and 3' UTRs, and cause translation initiation at a downstream start codon, compared to variant 3. The encoded isoform (4) has a shorter N-terminus, and a distinct C-terminus, compared to isoform 3.
      Source sequence(s)
      AC091814, BC063424, CD642076
      Consensus CDS
      CCDS73442.1
      UniProtKB/Swiss-Prot
      Q5QGZ9
      Related
      ENSP00000405244.2, ENST00000434319.6
      Conserved Domains (1) summary
      cd03593
      Location:133 → 212
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    3. NM_138337.6 → NP_612210.4  C-type lectin domain family 12 member A isoform 1

      See identical proteins and their annotated locations for NP_612210.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1, also referred to as alpha).
      Source sequence(s)
      AY547296, BC126289, CD642076
      Consensus CDS
      CCDS8608.1
      UniProtKB/Swiss-Prot
      B2RA16, Q5QGZ9, Q6P4H1, Q6RH77, Q6RH78, Q8TDQ6
      Related
      ENSP00000302804.4, ENST00000304361.9
      Conserved Domains (1) summary
      cd03593
      Location:133 → 250
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    4. NM_201623.4 → NP_963917.2  C-type lectin domain family 12 member A isoform 2

      See identical proteins and their annotated locations for NP_963917.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2, also referred to as beta), compared to isoform 1.
      Source sequence(s)
      AY498551, AY547296, CD642076
      Consensus CDS
      CCDS8609.1
      UniProtKB/Swiss-Prot
      Q5QGZ9
      Related
      ENSP00000345448.4, ENST00000350667.4
      Conserved Domains (1) summary
      cd03593
      Location:100 → 217
      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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      9951268..10006150
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428399.1 → XP_047284355.1  C-type lectin domain family 12 member A isoform X8

    2. XM_047428400.1 → XP_047284356.1  C-type lectin domain family 12 member A isoform X9

    3. XM_047428397.1 → XP_047284353.1  C-type lectin domain family 12 member A isoform X4

    4. XM_047428401.1 → XP_047284357.1  C-type lectin domain family 12 member A isoform X10

    5. XM_011520570.1 → XP_011518872.1  C-type lectin domain family 12 member A isoform X2

      See identical proteins and their annotated locations for XP_011518872.1

      UniProtKB/Swiss-Prot
      B2RA16, Q5QGZ9, Q6P4H1, Q6RH77, Q6RH78, Q8TDQ6
      Conserved Domains (1) summary
      cd03593
      Location:133 → 250
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    6. XM_006719033.4 → XP_006719096.1  C-type lectin domain family 12 member A isoform X1

      Conserved Domains (1) summary
      cd03593
      Location:150 → 267
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    7. XM_011520571.3 → XP_011518873.3  C-type lectin domain family 12 member A isoform X3

    8. XM_006719035.4 → XP_006719098.2  C-type lectin domain family 12 member A isoform X5

    9. XM_011520573.3 → XP_011518875.2  C-type lectin domain family 12 member A isoform X6

    10. XM_006719036.4 → XP_006719099.2  C-type lectin domain family 12 member A isoform X7

    11. XM_047428402.1 → XP_047284358.1  C-type lectin domain family 12 member A isoform X11

    12. XM_005253324.3 → XP_005253381.1  C-type lectin domain family 12 member A isoform X2

      See identical proteins and their annotated locations for XP_005253381.1

      UniProtKB/Swiss-Prot
      B2RA16, Q5QGZ9, Q6P4H1, Q6RH77, Q6RH78, Q8TDQ6
      Conserved Domains (1) summary
      cd03593
      Location:133 → 250
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      9837492..9892550
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371228.1 → XP_054227203.1  C-type lectin domain family 12 member A isoform X8

    2. XM_054371229.1 → XP_054227204.1  C-type lectin domain family 12 member A isoform X9

    3. XM_054371224.1 → XP_054227199.1  C-type lectin domain family 12 member A isoform X4

    4. XM_054371230.1 → XP_054227205.1  C-type lectin domain family 12 member A isoform X10

    5. XM_054371221.1 → XP_054227196.1  C-type lectin domain family 12 member A isoform X2

    6. XM_054371220.1 → XP_054227195.1  C-type lectin domain family 12 member A isoform X1

    7. XM_054371223.1 → XP_054227198.1  C-type lectin domain family 12 member A isoform X3

    8. XM_054371225.1 → XP_054227200.1  C-type lectin domain family 12 member A isoform X5

    9. XM_054371226.1 → XP_054227201.1  C-type lectin domain family 12 member A isoform X6

    10. XM_054371227.1 → XP_054227202.1  C-type lectin domain family 12 member A isoform X7

    11. XM_054371222.1 → XP_054227197.1  C-type lectin domain family 12 member A isoform X2

    12. XM_054371231.1 → XP_054227206.1  C-type lectin domain family 12 member A isoform X11

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_201625.1: Suppressed sequence

      Description
      NM_201625.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5QGZ9.3 GenPept UniProtKB/Swiss-Prot:Q5QGZ9

    Gene LinkOut

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