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    CLEC2D C-type lectin domain family 2 member D [ Homo sapiens (human) ]

    Gene ID: 29121, updated on 20-May-2024

    Summary

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    Official Symbol
    CLEC2Dprovided by HGNC
    Official Full Name
    C-type lectin domain family 2 member Dprovided by HGNC
    Primary source
    HGNC:HGNC:14351
    See related
    Ensembl:ENSG00000069493 MIM:605659; AllianceGenome:HGNC:14351
    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
    CLAX; LLT1; OCIL
    Summary
    This gene encodes a member of the natural killer cell receptor C-type lectin family. The encoded protein inhibits osteoclast formation and contains a transmembrane domain near the N-terminus as well as the C-type lectin-like extracellular domain. Several alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Oct 2010]
    Expression
    Broad expression in lymph node (RPKM 24.3), appendix (RPKM 12.2) and 24 other tissues See more
    Orthologs
    all
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    Genomic context

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    See CLEC2D in Genome Data Viewer
    Location:
    12p13.31
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (9669713..9699553)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (9555955..9585762)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (9822309..9852149)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene C-type lectin domain family 2 member D pseudogene Neighboring gene uncharacterized LOC105369728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5943 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5946 Neighboring gene GOT2 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5948 Neighboring gene nucleophosmin 1 pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4231 Neighboring gene long intergenic non-protein coding RNA 2390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5950 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5951 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4232 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4233 Neighboring gene C-type lectin like 1, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4234

    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. Lectin-like transcript 1 (LLT1) expression is associated with nodal metastasis in patients with head and neck cutaneous squamous cell carcinoma. Santos-Juanes J, et al. Arch Dermatol Res, 2019 Jul. PMID 30955082
    2. Expression of Lectin-Like Transcript 1, the Ligand for CD161, in Rheumatoid Arthritis. Chalan P, et al. PLoS One, 2015. PMID 26147876, Free PMC Article
    3. Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states. Skálová T, et al. Acta Crystallogr D Biol Crystallogr, 2015 Mar. PMID 25760607, Free PMC Article
    4. The Asn19Lys substitution in the osteoclast inhibitory lectin (OCIL) gene is associated with a reduction of bone mineral density in postmenopausal women. Pineda B, et al. Calcif Tissue Int, 2008 May. PMID 18465072
    5. The LLT1 receptor induces IFN-gamma production by human natural killer cells. Mathew PA, et al. Mol Immunol, 2004 Mar. PMID 15104121

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Lectin-like Transcript-1 (LLT1) Expression in Oral Squamous Cell Carcinomas: Prognostic Significance and Relationship with the Tumor Immune Microenvironment.
      Title: Lectin-like Transcript-1 (LLT1) Expression in Oral Squamous Cell Carcinomas: Prognostic Significance and Relationship with the Tumor Immune Microenvironment.
    2. Immune checkpoint CD161/LLT1-associated immunological landscape and diagnostic value in oral squamous cell carcinoma.
      Title: Immune checkpoint CD161/LLT1-associated immunological landscape and diagnostic value in oral squamous cell carcinoma.
    3. SARS-CoV-2 infection impairs NK cell functions via activation of the LLT1-CD161 axis.
      Title: SARS-CoV-2 infection impairs NK cell functions via activation of the LLT1-CD161 axis.
    4. LLT1-CD161 Interaction in Cancer: Promises and Challenges.
      Title: LLT1-CD161 Interaction in Cancer: Promises and Challenges.
    5. Role of LLT1 and PCNA as Natural Killer Cell Immune Evasion Strategies of HCT 116 Cells.
      Title: Role of LLT1 and PCNA as Natural Killer Cell Immune Evasion Strategies of HCT 116 Cells.
    6. Docetaxel suppresses immunotherapy efficacy of natural killer cells toward castration-resistant prostate cancer cells via altering androgen receptor-lectin-like transcript 1 signals.
      Title: Docetaxel suppresses immunotherapy efficacy of natural killer cells toward castration-resistant prostate cancer cells via altering androgen receptor-lectin-like transcript 1 signals.
    7. The authors identify Clec2d as a sensor for cell death through histone recognition and show that such interaction in macrophages shuttles histone-DNA complexes into endosomes to stimulate toll-like receptors. The consequent inflammation amplifies collateral tissue damage in a liver injury model.
      Title: Immune Sensing of Cell Death through Recognition of Histone Sequences by C-Type Lectin-Receptor-2d Causes Inflammation and Tissue Injury.
    8. LLT1 strong expression was a significant risk factor for nodal metastasis in patients with head and neck cutaneous squamous cell carcinoma (cSCC) and for cSCC specific mortality. Strong LLT1 expression is an independent predictor of nodal metastasis and poor disease-specific survival and it might be helpful for risk stratification of patients with cSCC.
      Title: Lectin-like transcript 1 (LLT1) expression is associated with nodal metastasis in patients with head and neck cutaneous squamous cell carcinoma.
    9. REVIEW: Biological and Clinical Significance of Human NKRP1A/LLT1 Receptor/Ligand Interactions
      Title: Biological and Clinical Significance of Human NKRP1A/LLT1 Receptor/Ligand Interactions.
    10. These results show that susceptibility of normal articular chondrocytes to lysis by NK cells is modulated by NKR-P1A/LLT1 interactions. Thus, NKR-P1A/LLT1 interaction might provide some novel target for therapeutic interventions in the course of pathological cartilage injury.
      Title: A Role of NKR-P1A (CD161) and Lectin-like Transcript 1 in Natural Cytotoxicity against Human Articular Chondrocytes.
    Submit: New GeneRIF Correction See all GeneRIFs (26)

    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 14,000 cases of seven common diseases and 3,000 shared controls.
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vif vif HIV-1 Vif downregulates the expression of C-type lectin domain family 2, member D (CLEC2D) in Vif-expression T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transmembrane signaling receptor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell surface receptor signaling pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    C-type lectin domain family 2 member D
    Names
    C-type lectin related f
    C-type lectin superfamily 2, member D
    LLT-1
    lectin-like NK cell receptor
    lectin-like transcript 1
    osteoclast inhibitory lectin

    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_001004419.5 → NP_001004419.1  C-type lectin domain family 2 member D isoform 2

      See identical proteins and their annotated locations for NP_001004419.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) includes an additional exon, compared to variant 1, that causes a frameshift. The resulting isoform (2) is longer and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC007068, AF285089, DA814760
      Consensus CDS
      CCDS31741.1
      UniProtKB/TrEMBL
      W8JD10
      Related
      ENSP00000261340.7, ENST00000261340.11
      Conserved Domains (1) summary
      cd03593
      Location:75 → 171
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    2. NM_001197317.3 → NP_001184246.1  C-type lectin domain family 2 member D isoform 3

      See identical proteins and their annotated locations for NP_001184246.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the 5' region, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AC007068, DB111977, FN813350
      Consensus CDS
      CCDS55801.1
      UniProtKB/TrEMBL
      W8JE22, W8JXM2
      Related
      ENSP00000261339.6, ENST00000261339.10
      Conserved Domains (1) summary
      PHA02642
      Location:28 → 150
      PHA02642; C-type lectin-like protein; Provisional

    3. NM_001197318.3 → NP_001184247.1  C-type lectin domain family 2 member D isoform 4

      See identical proteins and their annotated locations for NP_001184247.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an exon in the 3' region, compared to variant 1, that causes a frame-shift. The resulting isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC007068, DB124897, FN813349
      Consensus CDS
      CCDS55800.1
      UniProtKB/TrEMBL
      W8JNK3
      Related
      ENSP00000443065.1, ENST00000543300.5
      Conserved Domains (1) summary
      cl02432
      Location:75 → 119
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain

    4. NM_001197319.3 → NP_001184248.1  C-type lectin domain family 2 member D isoform 5

      See identical proteins and their annotated locations for NP_001184248.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an in-frame exon in the 5' region and an exon in the 3' region, compared to variant 1, that causes a frame-shift. The resulting isoform (5) lacks an internal segment and has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC007068, DB111977, FN813351
      Consensus CDS
      CCDS55802.1
      UniProtKB/TrEMBL
      W8T7N2
      Related
      ENSP00000444818.1, ENST00000545918.5
      Conserved Domains (1) summary
      cl02432
      Location:38 → 82
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain

    5. NM_013269.6 → NP_037401.1  C-type lectin domain family 2 member D isoform 1

      See identical proteins and their annotated locations for NP_037401.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the most frequently occurring transcript. It encodes isoform 1.
      Source sequence(s)
      AC007068, AK313554, DB111977
      Consensus CDS
      CCDS8602.1
      UniProtKB/Swiss-Prot
      D6CI39, D6CI40, D6CI41, Q6YID5, Q8WUP7, Q9HD37, Q9HD38, Q9UHP7
      UniProtKB/TrEMBL
      W8JE22
      Related
      ENSP00000290855.6, ENST00000290855.11
      Conserved Domains (1) summary
      cl25419
      Location:65 → 187
      PHA02642; C-type lectin-like protein; Provisional

    RNA

    1. NR_036693.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) has an additional segment and lacks an exon in the 3' region, compared to variant 1. The transcript is a nonsense-mediated mRNA decay candidate and probably does not make a functional protein.
      Source sequence(s)
      AC007068, AK310554, DB111977

    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
      9669713..9699553
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      9555955..9585762
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001004420.1: Suppressed sequence

      Description
      NM_001004420.1: 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
    Q9UHP7.1 GenPept UniProtKB/Swiss-Prot:Q9UHP7

    Gene LinkOut

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

    Chemical Information
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