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

Gene ID: 51348, updated on 5-Mar-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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Location:
12p13.31
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (9800052..9845005)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (9686250..9731208)
105.20220307 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
  • 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. 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
  2. Cutting edge: NKp80 uses an atypical hemi-ITAM to trigger NK cytotoxicity. Dennehy KM, et al. J Immunol, 2011 Jan 15. PMID 21149606
  3. 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
  4. Identification of NKp80, a novel triggering molecule expressed by human NK cells. Vitale M, et al. Eur J Immunol, 2001 Jan. PMID 11265639
  5. Human dNK cell function is differentially regulated by extrinsic cellular engagement and intrinsic activating receptors in first and second trimester pregnancy. Zhang J, et al. Cell Mol Immunol, 2017 Feb. PMID 26277900, Free PMC Article

See all (21) 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 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 membrane TAS
Traceable Author Statement
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
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_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
    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

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