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

Gene ID: 160364, updated on 22-Apr-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
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Genomic context

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Location:
12p13.31-p13.2
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (9951268..10006150)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (9837492..9892550)
105.20220307 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
  • 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. CLEC12A plays an important role in immunomodulatory function and prognostic significance of patients with acute myeloid leukemia. Li Q, et al. Leuk Lymphoma, 2022 Sep. PMID 35481814
  2. Regulation of the Expression, Oligomerisation and Signaling of the Inhibitory Receptor CLEC12A by Cysteine Residues in the Stalk Region. Vitry J, et al. Int J Mol Sci, 2021 Sep 22. PMID 34638548, Free PMC Article
  3. The Inhibitory Receptor CLEC12A Regulates PI3K-Akt Signaling to Inhibit Neutrophil Activation and Cytokine Release. Paré G, et al. Front Immunol, 2021. PMID 34234773, Free PMC Article
  4. Bimodal expression of potential drug target CLL-1 (CLEC12A) on CD34+ blasts of AML patients. Ngai LL, et al. Eur J Haematol, 2021 Sep. PMID 34053123, Free PMC Article
  5. C-Type Lectin-Like Molecule-1 as a Biomarker for Diagnosis and Prognosis in Acute Myeloid Leukemia: A Preliminary Study. Wang J, et al. Biomed Res Int, 2021. PMID 33778076, Free PMC Article

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. Regulation of the Expression, Oligomerisation and Signaling of the Inhibitory Receptor CLEC12A by Cysteine Residues in the Stalk Region.
    Title: Regulation of the Expression, Oligomerisation and Signaling of the Inhibitory Receptor CLEC12A by Cysteine Residues in the Stalk Region.
  10. The Inhibitory Receptor CLEC12A Regulates PI3K-Akt Signaling to Inhibit Neutrophil Activation and Cytokine Release.
    Title: The Inhibitory Receptor CLEC12A Regulates PI3K-Akt Signaling to Inhibit Neutrophil Activation and Cytokine Release.
Submit: New GeneRIF Correction See all GeneRIFs (37)

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)

Genotypes

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 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
  
Process Evidence Code Pubs
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
  
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_2023_10

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

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