KLRF1

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

Basic information

Region (hg38): 12:9827480-9845007

Links

ENSG00000150045 ∙ NCBI:51348 ∙ OMIM:605029 ∙ HGNC:13342 ∙ Uniprot:Q9NZS2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KLRF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLRF1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in KLRF1

This is a list of pathogenic ClinVar variants found in the KLRF1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-9827588-A-G		not specified	Uncertain significance (Jul 26, 2021)
12-9832354-G-A		not specified	Uncertain significance (Apr 07, 2022)
12-9832391-C-T		not specified	Uncertain significance (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLRF1	protein_coding	protein_coding	ENST00000279544	6	17530

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.80e-7	0.252	124646	0	15	124661	0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.462	97	111	0.876	0.00000496	1529
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000326	0.000320
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000559	0.0000556
Finnish	0.0000466	0.0000464
European (Non-Finnish)	0.0000367	0.0000353
Middle Eastern	0.0000559	0.0000556
South Asian	0.0000374	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the natural killer (NK)-mediated cytolysis of PHA-induced lymphoblasts.
• Pathway: Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.0678

Intolerance Scores

• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.112
• ghis: 0.386

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00908

Gene Damage Prediction

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

Gene ontology

• Biological process: cell surface receptor signaling pathway;regulation of immune response
• Cellular component: plasma membrane;integral component of plasma membrane;membrane
• Molecular function: transmembrane signaling receptor activity;carbohydrate binding;MHC class I receptor activity