KLRC3

killer cell lectin like receptor C3, the group of Killer cell lectin like receptors|C-type lectin domain containing

Basic information

Region (hg38): 12:10412314-10420595

Links

ENSG00000205810 ∙ NCBI:3823 ∙ OMIM:602892 ∙ HGNC:6376 ∙ Uniprot:Q07444 ∙ 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 KLRC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLRC3 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			10	2	4	16
nonsense						0
start loss						0
frameshift					2	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	2	6

Variants in KLRC3

This is a list of pathogenic ClinVar variants found in the KLRC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10415650-T-TAA			Benign (Dec 31, 2019)
12-10415652-TTA-T			Benign (Dec 31, 2019)
12-10415672-T-C		not specified	Uncertain significance (Oct 14, 2023)
12-10415678-G-A		not specified	Likely benign (Aug 04, 2023)
12-10415727-G-T		not specified	Uncertain significance (Jun 13, 2023)
12-10415730-C-G		not specified	Uncertain significance (May 13, 2022)
12-10415751-G-A		not specified	Uncertain significance (Nov 10, 2022)
12-10415755-C-T		not specified	Uncertain significance (Jun 24, 2022)
12-10416670-T-A		not specified	Likely benign (Dec 17, 2023)
12-10418387-T-G		not specified	Uncertain significance (May 05, 2023)
12-10418396-C-T		not specified	Uncertain significance (Apr 20, 2024)
12-10418447-C-T		not specified	Uncertain significance (Feb 15, 2023)
12-10418495-C-A			Benign (Jul 11, 2017)
12-10418496-G-A		not specified	Uncertain significance (Dec 16, 2023)
12-10420486-C-T		not specified	Uncertain significance (Jul 11, 2023)
12-10420493-G-T		not specified	Uncertain significance (Jun 30, 2023)
12-10420495-C-G			Benign (Jul 24, 2017)
12-10420496-A-G			Benign (Jul 24, 2017)
12-10420546-C-T			Benign (Jul 24, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLRC3	protein_coding	protein_coding	ENST00000381903	6	8284

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000172	0.256	123694	82	1839	125615	0.00768

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0202	118	117	1.01	0.00000592	1682
Missense in Polyphen		16	16.326	0.98004		253
Synonymous	-1.21	46	36.7	1.25	0.00000173	454
Loss of Function	0.116	9	9.38	0.959	3.97e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.102	0.102
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00686	0.00686
European (Non-Finnish)	0.000727	0.000722
Middle Eastern	0.00	0.00
South Asian	0.000230	0.000229
Other	0.00377	0.00376

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);ras-independent pathway in nk cell-mediated cytotoxicity;Validated nuclear estrogen receptor alpha network (Consensus)

Intolerance Scores

• loftool: 0.965
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.78

Haploinsufficiency Scores

• pHI: 0.0476
• hipred: N
• hipred_score: 0.158

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.526

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klrc3

Gene ontology

• Biological process: cellular defense response
• Cellular component: integral component of membrane
• Molecular function: transmembrane signaling receptor activity;carbohydrate binding