KLRF2

killer cell lectin like receptor F2, the group of Killer cell lectin like receptors|C-type lectin domain containing

Basic information

Region (hg38): 12:9881488-9895833

Links

ENSG00000256797 ∙ NCBI:100431172 ∙ OMIM:618814 ∙ HGNC:37646 ∙ Uniprot:D3W0D1 ∙ 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 KLRF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLRF2 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			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	0

Variants in KLRF2

This is a list of pathogenic ClinVar variants found in the KLRF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-9881621-C-T		not specified	Likely benign (Mar 01, 2023)
12-9884978-G-C		not specified	Uncertain significance (Aug 29, 2023)
12-9884982-G-A		not specified	Uncertain significance (May 26, 2022)
12-9885020-C-A		not specified	Uncertain significance (Aug 12, 2021)
12-9888745-A-C		not specified	Uncertain significance (Feb 26, 2024)
12-9888754-A-C		not specified	Uncertain significance (Nov 15, 2021)
12-9893024-C-G		not specified	Uncertain significance (Sep 17, 2021)
12-9893038-C-T		not specified	Uncertain significance (Sep 17, 2021)
12-9893061-G-A		not specified	Uncertain significance (Sep 30, 2021)
12-9893070-T-C		not specified	Uncertain significance (Dec 21, 2022)
12-9893112-C-T		not specified	Uncertain significance (Dec 15, 2022)
12-9893116-A-T		not specified	Uncertain significance (Mar 07, 2023)
12-9893150-T-G		not specified	Uncertain significance (Jan 04, 2022)
12-9893436-T-C		not specified	Uncertain significance (Jun 04, 2024)
12-9893443-C-G		not specified	Likely benign (Dec 19, 2023)
12-9893444-A-T		not specified	Uncertain significance (Dec 20, 2023)
12-9893457-G-C		not specified	Uncertain significance (Dec 21, 2023)
12-9893464-T-G		not specified	Uncertain significance (Sep 28, 2022)
12-9893523-A-C		not specified	Uncertain significance (Dec 26, 2023)
12-9895735-A-T		not specified	Uncertain significance (Nov 07, 2022)
12-9895808-C-T		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLRF2	protein_coding	protein_coding	ENST00000535540	6	14345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.71e-11	0.0109	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.187	79	83.8	0.943	0.00000432	1370
Missense in Polyphen		17	15.024	1.1315		236
Synonymous	1.35	22	31.7	0.694	0.00000187	343
Loss of Function	-1.35	13	8.71	1.49	4.05e-7	132

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: C-type lectin-like receptor involved in natural killer cell mediated cytotoxicity and cytokine secretion in keratinocytes via its interaction with CLEC2A. {ECO:0000269|PubMed:20194751}.

Haploinsufficiency Scores

• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: natural killer cell degranulation;cytokine secretion
• Cellular component: integral component of plasma membrane
• Molecular function: protein binding;carbohydrate binding;protein homodimerization activity