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

Gene ID: 387837, updated on 2-Nov-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, Nov 2024]
Expression
Biased expression in testis (RPKM 8.0), skin (RPKM 1.6) and 1 other tissue See more
Orthologs
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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 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)

Genotypes

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

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

  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

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

  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

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