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    KLRD1 killer cell lectin like receptor D1 [ Homo sapiens (human) ]

    Gene ID: 3824, updated on 2-Nov-2024

    Summary

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    Official Symbol
    KLRD1provided by HGNC
    Official Full Name
    killer cell lectin like receptor D1provided by HGNC
    Primary source
    HGNC:HGNC:6378
    See related
    Ensembl:ENSG00000134539 MIM:602894; AllianceGenome:HGNC:6378
    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
    CD94
    Summary
    Natural killer (NK) cells are a distinct lineage of lymphocytes that mediate cytotoxic activity and secrete cytokines upon immune stimulation. Several genes of the C-type lectin superfamily, including members of the NKG2 family, are expressed by NK cells and may be involved in the regulation of NK cell function. KLRD1 (CD94) is an antigen preferentially expressed on NK cells and is classified as a type II membrane protein because it has an external C terminus. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2017]
    Expression
    Broad expression in spleen (RPKM 3.3), lung (RPKM 0.9) and 15 other tissues See more
    Orthologs
    all
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    Genomic context

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    See KLRD1 in Genome Data Viewer
    Location:
    12p13.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (10238961..10329608)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (10125682..10216423)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (10391560..10482207)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:10331989-10333188 Neighboring gene oxidized low density lipoprotein receptor 1 Neighboring gene transmembrane protein 52B Neighboring gene MPRA-validated peak1569 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4236 Neighboring gene GABARAPL1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:10364713-10365255 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4237 Neighboring gene GABA type A receptor associated protein like 1 Neighboring gene uncharacterized LOC124902875 Neighboring gene uncharacterized LOC105369656 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:10490627-10491205 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:10491206-10491785 Neighboring gene long intergenic non-protein coding RNA 2617 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:10513466-10514066 Neighboring gene long intergenic non-protein coding RNA 2598

    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. Structure of CD94 reveals a novel C-type lectin fold: implications for the NK cell-associated CD94/NKG2 receptors. Boyington JC, et al. Immunity, 1999 Jan. PMID 10023772
    2. The immunosuppressive agent FK506 enhances the cytolytic activity of inhibitory natural killer cell receptor (CD94/NKG2A)-expressing CD8 T cells. Tanaka J, et al. Transplantation, 2005 Dec 27. PMID 16378079
    3. Synergistic inhibition of natural killer cells by the nonsignaling molecule CD94. Cheent KS, et al. Proc Natl Acad Sci U S A, 2013 Oct 15. PMID 24082146, Free PMC Article
    4. Uncommon endocytic and trafficking pathway of the natural killer cell CD94/NKG2A inhibitory receptor. Masilamani M, et al. Traffic, 2008 Jun. PMID 18363778
    5. Differential expression of NK receptors CD94 and NKG2A by T cells in rheumatoid arthritis patients in remission compared to active disease. Walsh CE, et al. PLoS One, 2011. PMID 22102879, Free PMC Article

    See all (82) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Early expression of CD94 and loss of CD96 on CD8+ T cells after allogeneic stem cell tranplantation is predictive of subsequent relapse and survival.
      Title: Early expression of CD94 and loss of CD96 on CD8+ T cells after allogeneic stem cell tranplantation is predictive of subsequent relapse and survival.
    2. Reduced expansion of CD94/NKG2C(+) NK cells in chronic lymphocytic leukemia and CLL-like monoclonal B-cell lymphocytosis is not related to increased human cytomegalovirus seronegativity or NKG2C deletions.
      Title: Reduced expansion of CD94/NKG2C(+) NK cells in chronic lymphocytic leukemia and CLL-like monoclonal B-cell lymphocytosis is not related to increased human cytomegalovirus seronegativity or NKG2C deletions.
    3. KLRD1, FOSL2 and LILRB3 as potential biomarkers for plaques progression in acute myocardial infarction and stable coronary artery disease.
      Title: KLRD1, FOSL2 and LILRB3 as potential biomarkers for plaques progression in acute myocardial infarction and stable coronary artery disease.
    4. CD94 expression patterns in reactive and neoplastic T-cell and NK-cell proliferations.
      Title: CD94 expression patterns in reactive and neoplastic T-cell and NK-cell proliferations.
    5. The CD94/NKG2A inhibitory receptor educates uterine NK cells to optimize pregnancy outcomes in humans and mice.
      Title: The CD94/NKG2A inhibitory receptor educates uterine NK cells to optimize pregnancy outcomes in humans and mice.
    6. HLAs, TCRs, and KIRs, a Triumvirate of Human Cell-Mediated Immunity.
      Title: HLAs, TCRs, and KIRs, a Triumvirate of Human Cell-Mediated Immunity.
    7. NKG2A/CD94 Is a New Immune Receptor for HLA-G and Distinguishes Amino Acid Differences in the HLA-G Heavy Chain.
      Title: NKG2A/CD94 Is a New Immune Receptor for HLA-G and Distinguishes Amino Acid Differences in the HLA-G Heavy Chain.
    8. The inhibitory receptor CD94/NKG2A on CD8(+) tumor-infiltrating lymphocytes in colorectal cancer: a promising new druggable immune checkpoint in the context of HLAE/beta2m overexpression.
      Title: The inhibitory receptor CD94/NKG2A on CD8(+) tumor-infiltrating lymphocytes in colorectal cancer: a promising new druggable immune checkpoint in the context of HLAE/β2m overexpression.
    9. an early response by KLRD1-expressing Natural killer cells may control influenza infection.
      Title: KLRD1-expressing natural killer cells predict influenza susceptibility.
    10. Collectively, these results provide evidence for the first time that CD94/NKG2C is involved in chronic graft-versus-host disease prevention
      Title: The Activating NKG2C Receptor Is Significantly Reduced in NK Cells after Allogeneic Stem Cell Transplantation in Patients with Severe Graft-versus-Host Disease.
    Submit: New GeneRIF Correction See all GeneRIFs (52)

    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 analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
    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)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    HIV/tuberculosis coinfection upregulates KLRD1 expression in pleural fluid mononuclear cells (PFMC) isolated from antiretroviral-naive coinfected patients (relative to patients infected with only tuberculosis) 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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    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables HLA-E specific inhibitory MHC class Ib receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables MHC class I protein complex binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables MHC class Ib protein binding, via antigen binding groove IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein antigen binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transmembrane signaling receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell surface receptor signaling pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in natural killer cell mediated immunity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of T cell mediated cytotoxicity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of natural killer cell mediated cytotoxicity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of natural killer cell mediated cytotoxicity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of natural killer cell mediated cytotoxicity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of natural killer cell activation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in stimulatory C-type lectin receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in stimulatory C-type lectin receptor signaling pathway IDA
    Inferred from Direct Assay
    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 plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    part_of receptor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of receptor complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of receptor complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    natural killer cells antigen CD94
    Names
    CD94 antigen
    KP43
    NK cell receptor
    killer cell lectin-like receptor subfamily D, member 1

    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_001114396.3 → NP_001107868.2  natural killer cells antigen CD94 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3), as well as variants 1 and 5, encodes isoform 1.
      Source sequence(s)
      AC022075, AK291506
      Consensus CDS
      CCDS8621.1
      UniProtKB/Swiss-Prot
      O43321, O43773, Q13241, Q9UBE3, Q9UEQ0
      UniProtKB/TrEMBL
      Q53ZY6
      Related
      ENSP00000371333.4, ENST00000381908.7
      Conserved Domains (1) summary
      cd03593
      Location:61 → 176
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    2. NM_001351060.2 → NP_001337989.1  natural killer cells antigen CD94 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) encodes the longest isoform (3).
      Source sequence(s)
      AC022075, AC115676
      UniProtKB/TrEMBL
      Q53ZY6
      Conserved Domains (1) summary
      cd03593
      Location:61 → 174
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    3. NM_001351062.2 → NP_001337991.1  natural killer cells antigen CD94 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5), as well as variants 1 and 3, encodes isoform 1.
      Source sequence(s)
      AC022075
      Consensus CDS
      CCDS8621.1
      UniProtKB/Swiss-Prot
      O43321, O43773, Q13241, Q9UBE3, Q9UEQ0
      UniProtKB/TrEMBL
      Q53ZY6
      Conserved Domains (1) summary
      cd03593
      Location:61 → 176
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    4. NM_001351063.2 → NP_001337992.1  natural killer cells antigen CD94 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) encodes isoform 4.
      Source sequence(s)
      AC022075, AY327501
      Consensus CDS
      CCDS86281.1
      UniProtKB/TrEMBL
      F6WZH4, Q5YLG5
      Related
      ENSP00000443584.1, ENST00000543777.5
      Conserved Domains (1) summary
      cd03593
      Location:40 → 155
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    5. NM_001414224.1 → NP_001401153.1  natural killer cells antigen CD94 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC022075

    6. NM_001414225.1 → NP_001401154.1  natural killer cells antigen CD94 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC022075

    7. NM_002262.5 → NP_002253.2  natural killer cells antigen CD94 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) , as well as variants 3 and 5, encodes isoform 1.
      Source sequence(s)
      AC022075, U30610
      Consensus CDS
      CCDS8621.1
      UniProtKB/Swiss-Prot
      O43321, O43773, Q13241, Q9UBE3, Q9UEQ0
      UniProtKB/TrEMBL
      Q53ZY6
      Related
      ENSP00000338130.4, ENST00000336164.9
      Conserved Domains (1) summary
      cd03593
      Location:61 → 176
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    8. NM_007334.3 → NP_031360.1  natural killer cells antigen CD94 isoform 2

      See identical proteins and their annotated locations for NP_031360.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) encodes isoform 2.
      Source sequence(s)
      AB009597, AC022075
      Consensus CDS
      CCDS8622.1
      UniProtKB/TrEMBL
      F5H2B7
      Related
      ENSP00000310929.7, ENST00000350274.9
      Conserved Domains (1) summary
      cd03593
      Location:30 → 145
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    RNA

    1. NR_147038.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC022075

    2. NR_147039.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC022075, AF498040

    3. NR_147040.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC022075, AF498041

    4. NR_182262.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC022075

    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
      10238961..10329608
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428821.1 → XP_047284777.1  natural killer cells antigen CD94 isoform X1

    2. XM_011520651.4 → XP_011518953.1  natural killer cells antigen CD94 isoform X6

      UniProtKB/TrEMBL
      Q53ZY6
      Conserved Domains (1) summary
      cd03593
      Location:61 → 174
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    3. XM_024448974.2 → XP_024304742.1  natural killer cells antigen CD94 isoform X3

      UniProtKB/TrEMBL
      Q53ZY6
      Conserved Domains (1) summary
      cd03593
      Location:61 → 174
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    4. XM_047428822.1 → XP_047284778.1  natural killer cells antigen CD94 isoform X2

    5. XM_047428823.1 → XP_047284779.1  natural killer cells antigen CD94 isoform X4

    6. XM_047428824.1 → XP_047284780.1  natural killer cells antigen CD94 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      10125682..10216423
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372009.1 → XP_054227984.1  natural killer cells antigen CD94 isoform X1

    2. XM_054372014.1 → XP_054227989.1  natural killer cells antigen CD94 isoform X6

    3. XM_054372011.1 → XP_054227986.1  natural killer cells antigen CD94 isoform X3

    4. XM_054372008.1 → XP_054227983.1  natural killer cells antigen CD94 isoform X1

    5. XM_054372010.1 → XP_054227985.1  natural killer cells antigen CD94 isoform X2

    6. XM_054372012.1 → XP_054227987.1  natural killer cells antigen CD94 isoform X4

    7. XM_054372013.1 → XP_054227988.1  natural killer cells antigen CD94 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q13241.2 GenPept UniProtKB/Swiss-Prot:Q13241

    Gene LinkOut

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