KLRC2

killer cell lectin like receptor C2, the group of Killer cell lectin like receptors|C-type lectin domain containing|CD molecules

Basic information

Region (hg38): 12:10426854-10442300

Links

ENSG00000205809 ∙ NCBI:3822 ∙ OMIM:602891 ∙ HGNC:6375 ∙ Uniprot:P26717 ∙ 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 KLRC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLRC2 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					1	1
missense			10	2	3	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	2	4

Variants in KLRC2

This is a list of pathogenic ClinVar variants found in the KLRC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10431151-G-C		not specified	Uncertain significance (Oct 12, 2022)
12-10431157-C-T		not specified	Uncertain significance (Mar 11, 2022)
12-10431173-G-A		not specified	Uncertain significance (Jun 16, 2024)
12-10431205-T-A		not specified	Uncertain significance (Dec 19, 2023)
12-10433823-T-G		not specified	Uncertain significance (Nov 30, 2022)
12-10433880-C-T		not specified	Likely benign (Oct 24, 2023)
12-10433894-C-T		not specified	Likely benign (Oct 26, 2021)
12-10433907-T-C		not specified	Uncertain significance (Jun 22, 2021)
12-10433939-C-T		not specified	Uncertain significance (Jan 03, 2024)
12-10433940-G-A		not specified	Uncertain significance (Jul 17, 2023)
12-10434512-A-G			Benign (Jun 08, 2017)
12-10435375-C-A		not specified	Uncertain significance (Jan 24, 2024)
12-10435815-T-C		not specified	Uncertain significance (Aug 12, 2021)
12-10435819-A-G			Benign (May 17, 2018)
12-10435821-C-T		not specified	Uncertain significance (Nov 08, 2022)
12-10435931-C-G			Benign (Dec 31, 2019)
12-10435982-T-C			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLRC2	protein_coding	protein_coding	ENST00000381902	6	15447

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.87e-10	0.0319	125722	5	11	125738	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.269	125	117	1.07	0.00000581	1483
Missense in Polyphen		19	17.535	1.0835		264
Synonymous	-0.214	41	39.3	1.04	0.00000200	397
Loss of Function	-0.635	13	10.8	1.21	4.54e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000322	0.000322
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000544	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.000132	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role as a receptor for the recognition of MHC class I HLA-E molecules by NK cells and some cytotoxic T-cells.
• Pathway: Antigen processing and presentation - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);DAP12 signaling;DAP12 interactions;ras-independent pathway in nk cell-mediated cytotoxicity;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.875
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.316
• hipred: N
• hipred_score: 0.139
• ghis: 0.445

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.318

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klrc2

Gene ontology

• Biological process: natural killer cell mediated immunity;cellular defense response;signal transduction;innate immune response
• Cellular component: plasma membrane;integral component of plasma membrane;receptor complex
• Molecular function: transmembrane signaling receptor activity;protein binding;MHC class I protein complex binding;carbohydrate binding;protein antigen binding