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

    Gene ID: 29121, updated on 9-Dec-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CLEC2D in Genome Data Viewer
    Location:
    12p13.31
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (9669713..9699553)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (9555955..9585762)
    RS_2024_09 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
    EBI GWAS Catalog

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 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

    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)

    NEW Try the new Transcript table

    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_001004419.5NP_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:75171
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
    2. NM_001197317.3NP_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:28150
      PHA02642; C-type lectin-like protein; Provisional
    3. NM_001197318.3NP_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:75119
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
    4. NM_001197319.3NP_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:3882
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
    5. NM_013269.6NP_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:65187
      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_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
      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.