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

Gene ID: 29121, updated on 17-Jun-2019

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
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

Genomic context

See CLEC2D in Genome Data Viewer
Location:
12p13.31
Exon count:
6
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (9669708..9699555)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (9822304..9852151)

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 glutamic-oxaloacetic transaminase 2 pseudogene 3 Neighboring gene nucleophosmin 1 pseudogene 7 Neighboring gene long intergenic non-protein coding RNA 2390 Neighboring gene C-type lectin like 1

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
NHGRI GWA 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 BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystem (from REACTOME)
    Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystemA number of receptors and cell adhesion molecules play a key role in modifying the response of cells of lymphoid origin (such as B-, T- and NK cells) to self and tumor antigens, as well as to pathoge...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
carbohydrate binding IEA
Inferred from Electronic Annotation
more info
 
transmembrane signaling receptor activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
cell surface receptor signaling pathway TAS
Traceable Author Statement
more info
PubMed 
regulation of immune response TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
membrane TAS
Traceable Author Statement
more info
PubMed 
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)

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/Swiss-Prot
    Q9UHP7
    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/Swiss-Prot
    Q9UHP7
    UniProtKB/TrEMBL
    W8JXM2
    Related
    ENSP00000261339.6, ENST00000261339.10
    Conserved Domains (1) summary
    cl25419
    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/Swiss-Prot
    Q9UHP7
    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/Swiss-Prot
    Q9UHP7
    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
    Q9UHP7
    Related
    ENSP00000290855.6, ENST00000290855.11
    Conserved Domains (1) summary
    cl25419
    Location:65187
    PHA02642; C-type lectin-like protein; Provisional

RNA

  1. NR_036693.2 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: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    9669708..9699555
    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.
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