KLRF1

protein-coding

killer cell lectin like receptor F1, the group of Killer cell lectin like receptors|C-type lectin domain containing

Gene 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]

MANE transcript

NM_016523.3

Inheritance

—

ClinVar variants

U:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.9

Max pathogenic AF

—

Genomic locus

chr12:9,827,481-9,845,007

External References & Databases

Ensembl (ENSG00000150045)

Transcript & Mutation Effects

hg38 • Region Span ~17.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KLRF1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016523.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			6 clinvar			6
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	6	0	0	6

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016523.3	RefSeq	NP_057607.1	6	MANE Select
ENST00000617889.5	Ensembl	ENSP00000483713.1	6	MANE Select
NM_001291822.2	RefSeq	NP_001278751.1	5	Standard
NM_001291823.2	RefSeq	NP_001278752.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Immune System
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Adaptive Immune System

Biological Process

cell surface receptor signaling pathway
regulation of immune response

Molecular Function

transmembrane signaling receptor activity
carbohydrate binding
MHC class I receptor activity

Cellular Component

plasma membrane
integral component of plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000279544
Coding exons: 6
Length: 17530
Individuals with no LoFs: 124646
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 124661
p: 0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.462	97	111	0.876	0.00000496	1529
Missense (PolyPhen)		23	17.79	1.2928		241
Synonymous	-0.503	45	40.9	1.10	0.00000211	395
Loss of Function	0.322	11	12.2	0.900	5.14e-7	159

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00013	rare
Latino/Admixed American	0.00019	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000037	0.000035	rare
South Asian	0.000037	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the natural killer (NK)-mediated cytolysis of PHA-induced lymphoblasts.;

Recessive Scores

pRec: 0.0678

Intolerance Scores

RVIS EVS: 0.39
RVIS percentile EVS: 76.05

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00908

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium