KLRC1

killer cell lectin like receptor C1, the group of CD molecules|Killer cell lectin like receptors|C-type lectin domain containing

Basic information

Region (hg38): 12:10442264-10454685

Previous symbols: [ "NKG2" ]

Links

ENSG00000134545 ∙ NCBI:3821 ∙ OMIM:161555 ∙ HGNC:6374 ∙ Uniprot:P26715 ∙ 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 KLRC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLRC1 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in KLRC1

This is a list of pathogenic ClinVar variants found in the KLRC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10446568-A-T		not specified	Uncertain significance (May 26, 2023)
12-10446571-G-A		not specified	Uncertain significance (Dec 27, 2023)
12-10447538-T-C		not specified	Uncertain significance (Jan 11, 2023)
12-10447587-G-A		not specified	Uncertain significance (Nov 28, 2023)
12-10449241-T-C		not specified	Uncertain significance (Jul 20, 2022)
12-10449930-A-T		not specified	Uncertain significance (Jan 22, 2024)
12-10450490-T-C		not specified	Uncertain significance (Oct 07, 2024)
12-10450507-A-G		not specified	Uncertain significance (Jul 14, 2023)
12-10450996-C-T		not specified	Uncertain significance (Mar 25, 2024)
12-10451035-G-A		not specified	Uncertain significance (Dec 20, 2023)
12-10451060-C-T		not specified	Uncertain significance (Jul 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLRC1	protein_coding	protein_coding	ENST00000544822	6	12422

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000414	0.642	125693	1	24	125718	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0721	122	120	1.02	0.00000581	1520
Missense in Polyphen		29	27.178	1.067		394
Synonymous	0.675	36	41.5	0.867	0.00000200	428
Loss of Function	0.844	8	11.0	0.726	5.62e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00126	0.00117
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000449	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000335	0.0000327
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);Graft-versus-host disease - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);ras-independent pathway in nk cell-mediated cytotoxicity;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.191

Intolerance Scores

• loftool: 0.978
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.0646
• hipred: N
• hipred_score: 0.304
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klrc1
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; respiratory system phenotype; liver/biliary system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: cell surface receptor signaling pathway;regulation of 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