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    KLRF1 killer cell lectin like receptor F1 [ Homo sapiens (human) ]

    Gene ID: 51348, updated on 2-Nov-2024

    Summary

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    Official Symbol
    KLRF1provided by HGNC
    Official Full Name
    killer cell lectin like receptor F1provided by HGNC
    Primary source
    HGNC:HGNC:13342
    See related
    Ensembl:ENSG00000150045 MIM:605029; AllianceGenome:HGNC:13342
    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
    NKp80; CLEC5C
    Summary
    KLRF1, an activating homodimeric C-type lectin-like receptor (CTLR), is expressed on nearly all natural killer (NK) cells and stimulates their cytoxicity and cytokine release (Kuttruff et al., 2009 [PubMed 18922855]).[supplied by OMIM, Oct 2009]
    Expression
    Biased expression in spleen (RPKM 7.2), bone marrow (RPKM 3.9) and 10 other tissues See more
    Orthologs
    all
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    Genomic context

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    See KLRF1 in Genome Data Viewer
    Location:
    12p13.31
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (9800052..9845005)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (9686250..9731208)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (9952648..9997604)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes 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 Neighboring gene CRISPRi-validated cis-regulatory element chr12.520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5954 Neighboring gene Sharpr-MPRA regulatory region 11505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5956 Neighboring gene CRISPRi-validated cis-regulatory element chr12.528 Neighboring gene CD69 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5957 Neighboring gene GCNA pseudogene 1 Neighboring gene C-type lectin domain family 2 member B Neighboring gene C-type lectin domain family 2 member A Neighboring gene killer cell lectin like receptor F2

    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. Identification of NKp80, a novel triggering molecule expressed by human NK cells. Vitale M, et al. Eur J Immunol, 2001 Jan. PMID 11265639
    2. Molecular characterization of two novel alternative spliced variants of the KLRF1 gene and subcellular distribution of KLRF1 isoforms. Roda-Navarro P, et al. Biochim Biophys Acta, 2001 Aug 30. PMID 11513955
    3. NKp80 Defines a Critical Step during Human Natural Killer Cell Development. Freud AG, et al. Cell Rep, 2016 Jul 12. PMID 27373165, Free PMC Article
    4. Cutting edge: NKp80 uses an atypical hemi-ITAM to trigger NK cytotoxicity. Dennehy KM, et al. J Immunol, 2011 Jan 15. PMID 21149606
    5. Mutual activation of natural killer cells and monocytes mediated by NKp80-AICL interaction. Welte S, et al. Nat Immunol, 2006 Dec. PMID 17057721

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NKp80 is a marker of natural killer (NK) cell maturity in secondary lymphoid tissues and supports NK cell development through a stage 4a intermediate with ILC3-associated features.
      Title: NKp80 Defines a Critical Step during Human Natural Killer Cell Development.
    2. In the second trimester, functional markers of Decidual natural killer activation, i.e., angiogenic factor production (e.g., vascular endothelial growth factor, interleukin-8, interferon-gamma), remained stable despite an increase in NKp80 or NKG2D surface expression.
      Title: Human dNK cell function is differentially regulated by extrinsic cellular engagement and intrinsic activating receptors in first and second trimester pregnancy.
    3. IL-15+IL-12 has an immunomodulatory effect on NK cell subsets from HIV-infected individuals viz down-regulation of iNKRs, elevation of activatory receptors NKp46 and NKG2D, and induction of coreceptor NKp80.
      Title: Effect of recombinant cytokines on the expression of natural killer cell receptors from patients with TB or/and HIV infection.
    4. our data report a previously unrecognized regulatory circuit enabling autonomous control of human NK cell responses via the NKp80-AICL axis.
      Title: Genetically coupled receptor-ligand pair NKp80-AICL enables autonomous control of human NK cell responses.
    5. Two non-consensus amino acids of NKp80, in particular arginine 6, critically impair both hemi-immunoreceptor tyrosine-based activation motif phosphorylation and Syk recruitment.
      Title: Attenuated natural killer (NK) cell activation through C-type lectin-like receptor NKp80 is due to an anomalous hemi-immunoreceptor tyrosine-based activation motif (HemITAM) with impaired Syk kinase recruitment capacity.
    6. Activating receptor NKp80 induces cytotoxicity by using an atypical hemi-ITAM amino acid seqeuence and the Syk-kinase pathway.
      Title: Cutting edge: NKp80 uses an atypical hemi-ITAM to trigger NK cytotoxicity.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: New genetic associations detected in a host response study to hepatitis B vaccine.
    8. NKp80 is expressed on a highly responsive subset of effector memory CD8 T cells with an inflammatory NK-like phenotype and promotes T-cell responses toward AICL-expressing cells.
      Title: NKp80 defines and stimulates a reactive subset of CD8 T 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

    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

    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

    Clone Names

    • MGC119907, MGC119908, MGC119909

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables MHC class I receptor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transmembrane signaling receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in NK T cell activation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cell surface receptor signaling pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in plasma membrane IC
    Inferred by Curator
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    killer cell lectin-like receptor subfamily F member 1
    Names
    C-type lectin domain family 5 member C
    activating coreceptor NKp80
    killer cell lectin-like receptor subfamily F, member 1
    lectin-like receptor F1

    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_001291822.2 → NP_001278751.1  killer cell lectin-like receptor subfamily F member 1 isoform KLRF1-s

      See identical proteins and their annotated locations for NP_001278751.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (KLRF1-s) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (KLRF1-s) that is shorter than isoform 1.
      Source sequence(s)
      AF175207, AJ305370
      Consensus CDS
      CCDS76526.1
      UniProtKB/Swiss-Prot
      Q9NZS2
      UniProtKB/TrEMBL
      A0A0C4DFN7
      Related
      ENSP00000279545.4, ENST00000279545.7
      Conserved Domains (2) summary
      cd03593
      Location:64 → 180
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
      PHA03097
      Location:28 → 179
      PHA03097; C-type lectin-like protein; Provisional

    2. NM_001291823.2 → NP_001278752.1  killer cell lectin-like receptor subfamily F member 1 isoform KLRF1-s3

      See identical proteins and their annotated locations for NP_001278752.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (KLRF1-s3) lacks three alternate coding exons that result in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (KLRF1-s3) has a distinct C-terminus and is significantly shorter than isoform 1.
      Source sequence(s)
      AF267245, AJ305370
      Consensus CDS
      CCDS76527.1
      UniProtKB/Swiss-Prot
      Q9NZS2
      Related
      ENSP00000346919.3, ENST00000354855.7

    3. NM_001366534.1 → NP_001353463.1  killer cell lectin-like receptor subfamily F member 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC007068, BC096734
      Consensus CDS
      CCDS91652.1
      UniProtKB/TrEMBL
      Q4KN05, Q4KN30
      Related
      ENSP00000443054.1, ENST00000537723.5

    4. NM_016523.3 → NP_057607.1  killer cell lectin-like receptor subfamily F member 1 isoform 1

      See identical proteins and their annotated locations for NP_057607.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AF175206, AJ305370
      Consensus CDS
      CCDS41750.1
      UniProtKB/Swiss-Prot
      A0A0C4DGY9, Q4KMT5, Q96PR2, Q96PR3, Q9NZS1, Q9NZS2
      Related
      ENSP00000483713.1, ENST00000617889.5
      Conserved Domains (1) summary
      cd03593
      Location:114 → 230
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    RNA

    1. NR_120305.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (KLRF1-s2) lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF267244, AJ305370
      Related
      ENST00000612321.4

    2. NR_159359.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC007068, KF573680

    3. NR_159360.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC007068, BC098257
      Related
      ENST00000617793.4

    4. NR_159361.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC007068, BC098166

    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
      9800052..9845005
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017019415.2 → XP_016874904.1  killer cell lectin-like receptor subfamily F member 1 isoform X1

    2. XM_047428956.1 → XP_047284912.1  killer cell lectin-like receptor subfamily F member 1 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      9686250..9731208
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372198.1 → XP_054228173.1  killer cell lectin-like receptor subfamily F member 1 isoform X1

    2. XM_054372199.1 → XP_054228174.1  killer cell lectin-like receptor subfamily F member 1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NZS2.3 GenPept UniProtKB/Swiss-Prot:Q9NZS2

    Gene LinkOut

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

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