NCR3

natural cytotoxicity triggering receptor 3, the group of V-set domain containing|CD molecules

Basic information

Region (hg38): 6:31588895-31593006

Previous symbols: [ "LY117" ]

Links

ENSG00000204475 ∙ NCBI:259197 ∙ OMIM:611550 ∙ HGNC:19077 ∙ Uniprot:O14931 ∙ 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 NCR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCR3 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				3		3
missense			8	8		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	8	11	0

Variants in NCR3

This is a list of pathogenic ClinVar variants found in the NCR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31589068-C-T		NCR3-related disorder	Likely benign (Jul 15, 2019)
6-31589120-G-T		not specified	Uncertain significance (Jan 29, 2024)
6-31589128-G-A		not specified	Uncertain significance (Mar 28, 2023)
6-31589567-A-G		not specified	Uncertain significance (Jun 09, 2022)
6-31589580-C-T		not specified	Uncertain significance (Feb 15, 2023)
6-31589594-C-T		not specified	Uncertain significance (Nov 09, 2022)
6-31589616-C-T		not specified	Likely benign (Aug 02, 2021)
6-31589800-G-A		not specified	Likely benign (Nov 06, 2023)
6-31589818-C-T		not specified	Likely benign (Feb 17, 2022)
6-31589851-C-T		not specified	Uncertain significance (Oct 05, 2022)
6-31589943-C-T		not specified	Likely benign (Feb 11, 2022)
6-31589973-A-T		not specified	Uncertain significance (Feb 12, 2024)
6-31589974-C-A		not specified	Likely benign (Jul 05, 2023)
6-31589977-C-T		not specified	Likely benign (Jun 03, 2022)
6-31590057-G-A		not specified	Uncertain significance (Apr 12, 2022)
6-31590087-C-G		not specified	Likely benign (Oct 13, 2023)
6-31590095-A-C			Likely benign (Aug 13, 2018)
6-31590114-A-C			Likely benign (May 31, 2018)
6-31590128-TG-T		NCR3-related disorder	Likely benign (Apr 01, 2022)
6-31590134-C-T		NCR3-related disorder	Likely benign (Apr 01, 2022)
6-31592709-G-A		NCR3-related disorder	Likely benign (Nov 04, 2019)
6-31592893-C-T		Malaria, severe, susceptibility to	Pathogenic (Dec 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCR3	protein_coding	protein_coding	ENST00000340027	4	4091

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000368	0.633	125722	0	25	125747	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.822	95	120	0.789	0.00000697	1256
Missense in Polyphen		29	34.755	0.83441		403
Synonymous	0.488	46	50.4	0.913	0.00000298	459
Loss of Function	0.680	6	8.09	0.742	5.15e-7	74

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.000278	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000908	0.0000879
Middle Eastern	0.000278	0.000272
South Asian	0.000198	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell membrane receptor of natural killer/NK cells that is activated by binding of extracellular ligands including BAG6 and NCR3LG1. Stimulates NK cells cytotoxicity toward neighboring cells producing these ligands. It controls, for instance, NK cells cytotoxicity against tumor cells. Engagement of NCR3 by BAG6 also promotes myeloid dendritic cells (DC) maturation, both through killing DCs that did not acquire a mature phenotype, and inducing the release by NK cells of TNFA and IFNG which promote DC maturation. {ECO:0000269|PubMed:10562324, ECO:0000269|PubMed:15784725, ECO:0000269|PubMed:18055229, ECO:0000269|PubMed:18852879}.
• Pathway: Natural killer cell mediated cytotoxicity - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Intolerance Scores

• loftool: 0.820
• rvis_EVS: 0.77
• rvis_percentile_EVS: 87.01

Haploinsufficiency Scores

• pHI: 0.0459
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.319

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ncr3-ps

Gene ontology

• Biological process: immune response-activating cell surface receptor signaling pathway;inflammatory response;immune response;cell recognition;natural killer cell activation;positive regulation of natural killer cell mediated cytotoxicity;regulation of immune response
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: protein binding;identical protein binding