NCR2

natural cytotoxicity triggering receptor 2, the group of V-set domain containing|CD molecules

Basic information

Region (hg38): 6:41335607-41350889

Previous symbols: [ "LY95" ]

Links

ENSG00000096264 ∙ NCBI:9436 ∙ OMIM:604531 ∙ HGNC:6732 ∙ Uniprot:O95944 ∙ 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 NCR2 gene.

• Inborn genetic diseases (17 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCR2 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			15	2	2	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	3

Variants in NCR2

This is a list of pathogenic ClinVar variants found in the NCR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-41335881-C-G		not specified	Uncertain significance (Oct 02, 2023)
6-41336093-A-G			Benign (Jun 13, 2018)
6-41336138-C-G		not specified	Uncertain significance (May 30, 2023)
6-41336177-T-C		not specified	Likely benign (Jun 24, 2022)
6-41336182-G-A		not specified	Uncertain significance (Jan 04, 2022)
6-41336255-C-T		not specified	Uncertain significance (Sep 16, 2021)
6-41336278-A-G		not specified	Likely benign (Aug 04, 2023)
6-41336401-G-A			Benign (Jun 12, 2018)
6-41336411-A-C		not specified	Uncertain significance (Dec 01, 2022)
6-41341826-C-T		not specified	Uncertain significance (Apr 13, 2022)
6-41341835-G-T		not specified	Uncertain significance (Jan 25, 2023)
6-41341868-C-T		not specified	Uncertain significance (Jan 27, 2022)
6-41341884-C-A		not specified	Uncertain significance (Mar 11, 2022)
6-41341902-C-A		not specified	Uncertain significance (Jan 09, 2024)
6-41342064-C-T		not specified	Uncertain significance (Oct 06, 2021)
6-41342116-A-G		not specified	Uncertain significance (Apr 13, 2023)
6-41350690-G-C		not specified	Uncertain significance (May 25, 2022)
6-41350708-G-C		not specified	Uncertain significance (Jun 02, 2023)
6-41350758-C-T		not specified	Uncertain significance (Dec 02, 2022)
6-41350763-C-G		not specified	Uncertain significance (Jan 10, 2022)
6-41350790-G-A		not specified	Uncertain significance (Jan 04, 2022)
6-41350840-T-C			Benign (Jun 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCR2	protein_coding	protein_coding	ENST00000373089	5	15233

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.47e-7	0.296	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.191	149	156	0.957	0.00000843	1736
Missense in Polyphen		22	24.733	0.8895		288
Synonymous	-1.26	79	66.0	1.20	0.00000400	589
Loss of Function	0.425	11	12.6	0.871	6.92e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000578	0.000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000163	0.000163
South Asian	0.000524	0.000523
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytotoxicity-activating receptor that may contribute to the increased efficiency of activated natural killer (NK) cells to mediate tumor cell lysis. {ECO:0000269|PubMed:10049942}.
• Pathway: Natural killer cell mediated cytotoxicity - Homo sapiens (human);DAP12 interactions;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.161

Intolerance Scores

• loftool: 0.742
• rvis_EVS: 1.24
• rvis_percentile_EVS: 93.39

Haploinsufficiency Scores

• pHI: 0.0226
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0000648

Gene Damage Prediction

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

Gene ontology

• Biological process: cellular defense response;signal transduction;innate immune response;regulation of immune response
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: transmembrane signaling receptor activity;protein binding