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    CLEC12B C-type lectin domain family 12 member B [ Homo sapiens (human) ]

    Gene ID: 387837, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CLEC12Bprovided by HGNC
    Official Full Name
    C-type lectin domain family 12 member Bprovided by HGNC
    Primary source
    HGNC:HGNC:31966
    See related
    Ensembl:ENSG00000256660 MIM:617573; AllianceGenome:HGNC:31966
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    UNQ5782
    Summary
    Enables protein phosphatase binding activity and signaling receptor inhibitor activity. Involved in several processes, including melanocyte proliferation; natural killer cell inhibitory signaling pathway; and regulation of signal transduction. Located in external side of plasma membrane. Part of protein-containing complex. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in testis (RPKM 8.0), skin (RPKM 1.6) and 1 other tissue See more
    Orthologs
    mouse all
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    Genomic context

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    See CLEC12B in Genome Data Viewer
    Location:
    12p13.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (10006209..10018800)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (9892551..9905204)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (10163226..10171399)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene CLEC12A antisense RNA 1 Neighboring gene uncharacterized LOC124902874 Neighboring gene C-type lectin domain family 12 member A Neighboring gene C-type lectin domain family 1 member B Neighboring gene uncharacterized LOC102724020 Neighboring gene C-type lectin domain family 1 member B pseudogene Neighboring gene C-type lectin domain containing 9A Neighboring gene C-type lectin domain family 1 member A Neighboring gene RN7SK pseudogene 161

    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. CLEC12B Is a Melanocytic Gene Regulating the Color of the Skin. Sormani L, et al. J Invest Dermatol, 2022 Jul. PMID 34896119
    2. CLEC12B suppresses lung cancer progression by inducing SHP-1 expression and inactivating the PI3K/AKT signaling pathway. Chi D, et al. Exp Cell Res, 2021 Dec 15. PMID 34780782
    3. Pinpointing a potential role for CLEC12B in cancer predisposition through familial exome sequencing. Derpoorter C, et al. Pediatr Blood Cancer, 2019 Feb. PMID 30350915
    4. Selective expression of a C-type lectin receptor, Clec12b, on skin mast cells. Iijima A, et al. Biochem Biophys Res Commun, 2021 Jul 5. PMID 34020140
    5. Differential proteomic analysis of caveolin-1 KO cells reveals Sh2b3 and Clec12b as novel interaction partners of caveolin-1 and Capns1 as a potential mediator of caveolin-1-induced apoptosis. Kulkarni YM, et al. Analyst, 2013 Nov 21. PMID 24091439, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CLEC12B Is a Melanocytic Gene Regulating the Color of the Skin.
      Title: CLEC12B Is a Melanocytic Gene Regulating the Color of the Skin.
    2. CLEC12B Decreases Melanoma Proliferation by Repressing Signal Transducer and Activator of Transcription 3.
      Title: CLEC12B Decreases Melanoma Proliferation by Repressing Signal Transducer and Activator of Transcription 3.
    3. CLEC12B suppresses lung cancer progression by inducing SHP-1 expression and inactivating the PI3K/AKT signaling pathway.
      Title: CLEC12B suppresses lung cancer progression by inducing SHP-1 expression and inactivating the PI3K/AKT signaling pathway.
    4. Selective expression of a C-type lectin receptor, Clec12b, on skin mast cells.
      Title: Selective expression of a C-type lectin receptor, Clec12b, on skin mast cells.
    5. we identified a potential deleterious, missense mutation in CLEC12B in two children affected by ganglioneuroma and neuroblastoma
      Title: Pinpointing a potential role for CLEC12B in cancer predisposition through familial exome sequencing.
    6. CLEC12B is an inhibitory receptor on myeloid cells
      Title: Identification of CLEC12B, an inhibitory receptor on myeloid cells.
    Submit: New GeneRIF Correction

    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
    Genome-wide association study of sensory disturbances in the inferior alveolar nerve after bilateral sagittal split ramus osteotomy.
    EBI GWAS Catalog
    Genome-wide meta-analysis of systolic blood pressure in children with sickle cell disease.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    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 protein phosphatase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein phosphatase binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein phosphatase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables signaling receptor inhibitor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in melanocyte proliferation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in natural killer cell inhibitory signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in natural killer cell inhibitory signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of natural killer cell mediated cytotoxicity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of receptor signaling pathway via STAT IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of signaling receptor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in external side of plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    part_of protein-containing complex IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    C-type lectin domain family 12 member B
    Names
    macrophage antigen h
    testis secretory sperm-binding protein Li 205a

    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_001129998.3 → NP_001123470.1  C-type lectin domain family 12 member B isoform 1

      See identical proteins and their annotated locations for NP_001123470.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC024224
      Consensus CDS
      CCDS44830.1
      UniProtKB/Swiss-Prot
      Q2HXU8, Q6UWF2, Q6ZRG0
      UniProtKB/TrEMBL
      A0A140VK10, B2RNC6
      Related
      ENSP00000344563.5, ENST00000338896.11
      Conserved Domains (1) summary
      cd03593
      Location:143 → 265
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    2. NM_001319241.1 → NP_001306170.1  C-type lectin domain family 12 member B isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the central region and initiates translation at a downstream start codon compared to variant 1. The resulting protein (isoform 3) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AI655492, AK131027, BG484230, BM563861
      Conserved Domains (1) summary
      cd03593
      Location:40 → 162
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    3. NM_001319242.1 → NP_001306171.1  C-type lectin domain family 12 member B isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the central region, initiates translation at a downstream start codon, and differs in the 3' coding region and 3' UTR compared to variant 1. The resulting protein (isoform 4) has a shorter N-terminus and a shorter, distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC024224, BC036036, BG484230
      Conserved Domains (1) summary
      cd03593
      Location:40 → 124
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    4. NM_001387138.1 → NP_001374067.1  C-type lectin domain family 12 member B isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC024224
      UniProtKB/TrEMBL
      B2RNC6
      Conserved Domains (1) summary
      cd03593
      Location:143 → 236
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    5. NM_205852.3 → NP_995324.2  C-type lectin domain family 12 member B isoform 2

      See identical proteins and their annotated locations for NP_995324.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR compared to variant 1. The resulting protein (isoform 2) has a shorter, distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK128243, AY358810, BC036036, BG484230, DQ368812
      Consensus CDS
      CCDS8610.1
      UniProtKB/TrEMBL
      B2RNC6
      Related
      ENSP00000379759.1, ENST00000396502.5
      Conserved Domains (1) summary
      cd03593
      Location:143 → 227
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    RNA

    1. NR_135049.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in the 3' region compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI655492, AY358810, BG484230, DQ368812

    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
      10006209..10018800
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428832.1 → XP_047284788.1  C-type lectin domain family 12 member B isoform X2

    2. XM_011520658.3 → XP_011518960.1  C-type lectin domain family 12 member B isoform X1

      UniProtKB/TrEMBL
      B2RNC6
      Conserved Domains (1) summary
      cd03593
      Location:134 → 256
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    3. XM_047428834.1 → XP_047284790.1  C-type lectin domain family 12 member B isoform X4

    4. XM_047428833.1 → XP_047284789.1  C-type lectin domain family 12 member B isoform X3

    5. XM_047428835.1 → XP_047284791.1  C-type lectin domain family 12 member B isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      9892551..9905204
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372032.1 → XP_054228007.1  C-type lectin domain family 12 member B isoform X4

    2. XM_054372031.1 → XP_054228006.1  C-type lectin domain family 12 member B isoform X3

    3. XM_054372029.1 → XP_054228004.1  C-type lectin domain family 12 member B isoform X7

      UniProtKB/TrEMBL
      B2RNC6

    4. XM_054372026.1 → XP_054228001.1  C-type lectin domain family 12 member B isoform X6

      UniProtKB/TrEMBL
      B2RNC6

    5. XM_054372030.1 → XP_054228005.1  C-type lectin domain family 12 member B isoform X2

    6. XM_054372027.1 → XP_054228002.1  C-type lectin domain family 12 member B isoform X6

      UniProtKB/TrEMBL
      B2RNC6

    7. XM_054372028.1 → XP_054228003.1  C-type lectin domain family 12 member B isoform X1

      UniProtKB/TrEMBL
      B2RNC6

    8. XM_054372033.1 → XP_054228008.1  C-type lectin domain family 12 member B isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q2HXU8.1 GenPept UniProtKB/Swiss-Prot:Q2HXU8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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