CLEC12A Gene (Protein Coding)

C-Type Lectin Domain Family 12 Member A

GC12P009951
GIFtS:
38
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 func... See more...

Aliases for CLEC12A Gene

Aliases for CLEC12A Gene

  • C-Type Lectin Domain Family 12 Member A 2 3 4 5
  • Myeloid Inhibitory C-Type Lectin-Like Receptor 2 3 4
  • Dendritic Cell-Associated Lectin 2 2 3 4
  • DCAL-2 2 3 4
  • CLL-1 2 3 4
  • MICL 2 3 4
  • CD371 2 3
  • CLL1 3 4
  • C-Type Lectin Domain Family 12, Member A 2
  • C-Type Lectin-Like Molecule-1 3
  • C-Type Lectin-Like Molecule 1 4
  • C-Type Lectin Protein CLL-1 3
  • CD371 Antigen 4
  • CLEC12A 5
  • DCAL2 4

External Ids for CLEC12A Gene

Previous GeneCards Identifiers for CLEC12A Gene

  • GC12P010016
  • GC12P010124
  • GC12P010103

Summaries for CLEC12A Gene

Entrez Gene Summary for CLEC12A Gene

  • 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]

GeneCards Summary for CLEC12A Gene

CLEC12A (C-Type Lectin Domain Family 12 Member A) is a Protein Coding gene. Diseases associated with CLEC12A include Coffin-Siris Syndrome 2 and 3Mc Syndrome. Among its related pathways are Innate Immune System and C-type lectin receptor signaling pathway. Gene Ontology (GO) annotations related to this gene include carbohydrate binding. An important paralog of this gene is CLEC1A.

UniProtKB/Swiss-Prot Summary for CLEC12A Gene

  • Cell surface receptor that modulates signaling cascades and mediates tyrosine phosphorylation of target MAP kinases.

Gene Wiki entry for CLEC12A Gene

Additional gene information for CLEC12A Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLEC12A Gene

Genomics for CLEC12A Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CLEC12A Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH12J009971 Promoter/Enhancer 1.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 349.2 +21.6 21633 3.4 SPI1 POLR2A REST CLEC12A OLR1 CLEC12B CLEC7A CLEC1B GABARAPL1 CLEC2B piR-38265-002 HSALNG0089186
GH12J009950 Promoter/Enhancer 0.8 EPDnew ENCODE dbSUPER 292 +0.2 152 0.8 RUNX3 CLEC12A CLEC12A-AS1 piR-41399-088 piR-30091-038 piR-32677-095 piR-36240-027 piR-36393-095 piR-43099-102 piR-43408-049 piR-43583-097
GH12J009964 Promoter/Enhancer 0.7 FANTOM5 Ensembl dbSUPER 107.6 +15.7 15733 4.4 piR-38265-002 piR-32804-010 piR-47960-009 CLEC12A LINC02470 CLEC7A CLEC2B OLR1 HSALNG0089186 CLEC12B
GH12J009960 Enhancer 0.5 FANTOM5 dbSUPER 86.3 +9.4 9422 0.4 SPI1 piR-41245-062 CLEC12A OLR1 CLEC7A GABARAPL1 CLEC2B CD69 piR-53431-110 CLEC12B
GH12J009646 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 15.4 -299.5 -299535 10 BCLAF1 SP1 ZNF207 NCOR1 MYC IKZF1 ZNF592 POLR2A CEBPA ZIC2 CLEC2D piR-31199-064 LOC374443 KLRA1P KLRB1 CLECL1 CLEC7A CLEC12A DDX12P ENSG00000214776
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLEC12A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLEC12A

Top Transcription factor binding sites by QIAGEN in the CLEC12A gene promoter:
  • CUTL1
  • FOXO4
  • NF-kappaB
  • NF-kappaB1
  • POU2F1
  • POU2F1a
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for CLEC12A Gene

Latest Assembly
chr12:9,951,268-9,995,694
(GRCh38/hg38)
Size:
44,427 bases
Orientation:
Plus strand

Previous Assembly
chr12:10,103,867-10,138,194
(GRCh37/hg19 by Entrez Gene)
Size:
34,328 bases
Orientation:
Plus strand

chr12:10,103,915-10,148,293
(GRCh37/hg19 by Ensembl)
Size:
44,379 bases
Orientation:
Plus strand

Genomic View for CLEC12A Gene

Genes around CLEC12A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLEC12A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLEC12A Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CLEC12A Gene

Proteins for CLEC12A Gene

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  • Protein details for CLEC12A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5QGZ9-CL12A_HUMAN
    Recommended name:
    C-type lectin domain family 12 member A
    Protein Accession:
    Q5QGZ9
    Secondary Accessions:
    • B2RA16
    • Q6P4H1
    • Q6RH77
    • Q6RH78
    • Q8TDQ6

    Protein attributes for CLEC12A Gene

    Size:
    265 amino acids
    Molecular mass:
    30762 Da
    Quaternary structure:
    • Interacts with PTPN6 and PTPN11.
    Miscellaneous:
    • [Isoform 3]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Alternative splice isoforms for CLEC12A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLEC12A Gene

Protein Expression for CLEC12A Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CLEC12A Gene

  • Highly N-glycosylated. Glycosylation varies between cell types.
  • Glycosylation at Asn80, Asn88, Asn98, Asn105, Asn165, and Asn210
  • Modification sites at PhosphoSitePlus

Other Protein References for CLEC12A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLEC12A Gene

Domains & Families for CLEC12A Gene

Gene Families for CLEC12A Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for CLEC12A Gene

InterPro:

Suggested Antigen Peptide Sequences for CLEC12A Gene

GenScript: Design optimal peptide antigens:
  • Myeloid inhibitory C-type lectin-like receptor (CL12A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5QGZ9

UniProtKB/Swiss-Prot:

CL12A_HUMAN :
  • Contains 1 copy of a cytoplasmic motif that is referred to as the immunoreceptor tyrosine-based inhibitor motif (ITIM). This motif is involved in modulation of cellular responses. The phosphorylated ITIM motif can bind the SH2 domain of several SH2-containing phosphatases.
Domain:
  • Contains 1 copy of a cytoplasmic motif that is referred to as the immunoreceptor tyrosine-based inhibitor motif (ITIM). This motif is involved in modulation of cellular responses. The phosphorylated ITIM motif can bind the SH2 domain of several SH2-containing phosphatases.
genes like me logo Genes that share domains with CLEC12A: view

Function for CLEC12A Gene

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  6. Cell Lines for research

Molecular function for CLEC12A Gene

UniProtKB/Swiss-Prot Function:
Cell surface receptor that modulates signaling cascades and mediates tyrosine phosphorylation of target MAP kinases.
UniProtKB/Swiss-Prot Induction:
Down-regulated in activated leukocytes recruited to a site of inflammation.

Phenotypes From GWAS Catalog for CLEC12A Gene

Gene Ontology (GO) - Molecular Function for CLEC12A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 32296183
GO:0030246 carbohydrate binding IEA --
GO:0030545 receptor regulator activity IEA --
genes like me logo Genes that share ontologies with CLEC12A: view
genes like me logo Genes that share phenotypes with CLEC12A: view

Animal Models for CLEC12A Gene

MGI Knock Outs for CLEC12A:

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLEC12A

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CLEC12A Gene

Localization for CLEC12A Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLEC12A Gene

Cell membrane. Single-pass type II membrane protein. Note=Ligand binding leads to internalization.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLEC12A gene
Compartment Confidence
plasma membrane 5
extracellular 3
cytosol 2
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CLEC12A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0035579 specific granule membrane TAS --
GO:0070821 tertiary granule membrane TAS --
genes like me logo Genes that share ontologies with CLEC12A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLEC12A Gene

Pathways & Interactions for CLEC12A Gene

genes like me logo Genes that share pathways with CLEC12A: view

Pathways by source for CLEC12A Gene

3 Reactome pathways for CLEC12A Gene

Gene Ontology (GO) - Biological Process for CLEC12A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043312 neutrophil degranulation TAS --
genes like me logo Genes that share ontologies with CLEC12A: view

No data available for SIGNOR curated interactions for CLEC12A Gene

Drugs & Compounds for CLEC12A Gene

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  1. Drug products for research

(11) Drugs for CLEC12A Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(12) Additional Compounds for CLEC12A Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CLEC12A: view

Transcripts for CLEC12A Gene

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mRNA/cDNA for CLEC12A Gene

5 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLEC12A

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for CLEC12A Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8
SP1: - -
SP2: -
SP3: -
SP4:

Relevant External Links for CLEC12A Gene

GeneLoc Exon Structure for
CLEC12A

Expression for CLEC12A Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLEC12A Gene

mRNA expression in normal human tissues for CLEC12A Gene
mRNA expression by GTEx for CLEC12A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLEC12A Gene

This gene is overexpressed in Whole Blood (x36.9) and Spleen (x4.1).

Protein differential expression in normal tissues from HIPED for CLEC12A Gene

This gene is overexpressed in Monocytes (32.6), Peripheral blood mononuclear cells (29.9), and Spleen (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLEC12A Gene



Protein tissue co-expression partners for CLEC12A Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLEC12A

SOURCE GeneReport for Unigene cluster for CLEC12A Gene:

Hs.190519

mRNA Expression by UniProt/SwissProt for CLEC12A Gene:

Q5QGZ9-CL12A_HUMAN
Tissue specificity: Detected in normal myeloid cells and in acute myeloid leukemia cells. Detected in neutrophils, eosinophils, monocytes and dendritic cells. Detected in spleen macrophage-rich red pulp and in lymph node (at protein level). Detected in peripheral blood leukocytes, dendritic cells, bone marrow, monocytes, mononuclear leukocytes and macrophages.

Evidence on tissue expression from TISSUES for CLEC12A Gene

  • Bone marrow(4.6)
  • Blood(4.5)
  • Lung(4.3)
  • Spleen(2.5)
  • Lymph node(2.2)
genes like me logo Genes that share expression patterns with CLEC12A: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CLEC12A Gene

Orthologs for CLEC12A Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLEC12A Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia CLEC12A 29 30
  • 98.79 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia CLEC12A 29 30
  • 73.72 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia CLEC12A 29 30
  • 71.24 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Clec12a 29 16 30
  • 67.18 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Clec12a 29
  • 64.86 (n)
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 30
  • 45 (a)
 ManyToMany
-- 30
  • 35 (a)
 ManyToMany
-- 30
  • 35 (a)
 ManyToMany
-- 30
  • 34 (a)
 ManyToMany
-- 30
  • 31 (a)
 ManyToMany
-- 30
  • 28 (a)
 ManyToMany
Lizard
(Anolis carolinensis)
 Reptilia -- 30
  • 32 (a)
 OneToMany
Species where no ortholog for CLEC12A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for CLEC12A Gene

ENSEMBL:
Gene Tree for CLEC12A (if available)
TreeFam:
Gene Tree for CLEC12A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLEC12A: view image
Alliance of Genome Resources:
Additional Orthologs for CLEC12A

Paralogs for CLEC12A Gene

Paralogs for CLEC12A Gene

(5) SIMAP similar genes for CLEC12A Gene using alignment to 3 proteins:

  • CL12A_HUMAN
  • A8MVL9_HUMAN
  • L8EAV5_HUMAN
genes like me logo Genes that share paralogs with CLEC12A: view

Variants for CLEC12A Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLEC12A Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
rs479499 -- p.Lys244Gln

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CLEC12A Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CLEC12A Gene

Variant ID Type Subtype PubMed ID
dgv1374n100 CNV gain 25217958
nsv1038226 CNV gain 25217958
nsv1044587 CNV loss 25217958
nsv1051530 CNV gain 25217958
nsv523050 CNV loss 19592680
nsv525593 CNV loss 19592680

Variation tolerance for CLEC12A Gene

Residual Variation Intolerance Score: 80.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.92; 19.00% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLEC12A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLEC12A
Leiden Open Variation Database (LOVD)
CLEC12A

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLEC12A Gene

Disorders for CLEC12A Gene

MalaCards: The human disease database

(8) MalaCards diseases for CLEC12A Gene - From: COP and GCD

Disorder Aliases PubMed IDs
coffin-siris syndrome 2
  • css2
3mc syndrome
  • craniofacial-ulnar-renal syndrome
human immunodeficiency virus type 1
  • human immunodeficiency virus type 1, susceptibility to
myelodysplastic syndrome
  • mds
immune deficiency disease
  • primary immunodeficiency disease
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CLEC12A

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CLEC12A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLEC12A Gene

Publications for CLEC12A Gene

  1. Human MICL (CLEC12A) is differentially glycosylated and is down-regulated following cellular activation. (PMID: 16838277) Marshall AS … Brown GD (European journal of immunology 2006) 3 4 22
  2. C-type lectin-like molecule-1: a novel myeloid cell surface marker associated with acute myeloid leukemia. (PMID: 15548716) Bakker AB … Kruisbeek AM (Cancer research 2004) 3 4 22
  3. Identification and characterization of a novel human myeloid inhibitory C-type lectin-like receptor (MICL) that is predominantly expressed on granulocytes and monocytes. (PMID: 14739280) Marshall AS … Brown GD (The Journal of biological chemistry 2004) 3 4 22
  4. Characterisation of murine MICL (CLEC12A) and evidence for an endogenous ligand. (PMID: 18350551) Pyz E … Brown GD (European journal of immunology 2008) 3 22
  5. The novel AML stem cell associated antigen CLL-1 aids in discrimination between normal and leukemic stem cells. (PMID: 17609428) van Rhenen A … Jan Schuurhuis G (Blood 2007) 3 22

ExternalLinks

View latest publications for CLEC12A gene in Mastermind

Products for CLEC12A Gene

Sources for CLEC12A Gene