NCR1

natural cytotoxicity triggering receptor 1, the group of CD molecules|Immunoglobulin like domain containing

Basic information

Region (hg38): 19:54906148-54916140

Previous symbols: [ "LY94" ]

Links

ENSG00000189430 ∙ NCBI:9437 ∙ OMIM:604530 ∙ HGNC:6731 ∙ Uniprot:O76036 ∙ 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 NCR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCR1 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			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	3	0

Variants in NCR1

This is a list of pathogenic ClinVar variants found in the NCR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54906197-A-G		not specified	Uncertain significance (Aug 02, 2022)
19-54906540-T-G		not specified	Uncertain significance (Dec 11, 2023)
19-54906579-A-G		not specified	Uncertain significance (Feb 15, 2023)
19-54906633-C-A		not specified	Uncertain significance (May 29, 2024)
19-54906633-C-G		not specified	Uncertain significance (Feb 28, 2024)
19-54906634-A-G		not specified	Uncertain significance (Nov 08, 2021)
19-54906678-G-C		not specified	Uncertain significance (Jan 09, 2024)
19-54906715-T-G		not specified	Uncertain significance (Jul 12, 2022)
19-54906723-C-T		not specified	Uncertain significance (Dec 21, 2022)
19-54906783-A-G		not specified	Likely benign (Feb 22, 2023)
19-54906791-G-A			Likely benign (Jun 01, 2020)
19-54909315-C-G		not specified	Uncertain significance (Apr 09, 2024)
19-54909331-A-C		not specified	Uncertain significance (Feb 28, 2024)
19-54909371-C-T		not specified	Uncertain significance (Jun 30, 2022)
19-54909383-A-G		not specified	Uncertain significance (Feb 13, 2024)
19-54909422-G-A		not specified	Uncertain significance (Apr 22, 2024)
19-54909455-G-A		not specified	Uncertain significance (Jan 24, 2023)
19-54910027-A-G		not specified	Likely benign (Oct 29, 2021)
19-54912720-A-G		not specified	Uncertain significance (May 24, 2024)
19-54912729-G-A		not specified	Uncertain significance (Dec 19, 2022)
19-54912758-G-T		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCR1	protein_coding	protein_coding	ENST00000291890	7	10001

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.33e-11	0.0734	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.247	187	178	1.05	0.0000102	1967
Missense in Polyphen		34	42.102	0.80757		509
Synonymous	-1.17	82	69.6	1.18	0.00000428	609
Loss of Function	0.156	16	16.7	0.959	0.00000107	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000272	0.000272
South Asian	0.000131	0.000131
Other	0.00	0.00

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:9730896}.
• 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)

Recessive Scores

• pRec: 0.273

Intolerance Scores

• loftool: 0.952
• rvis_EVS: 0
• rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

• pHI: 0.0537
• hipred: N
• hipred_score: 0.158
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.320

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ncr1
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; homeostasis/metabolism phenotype; immune system phenotype

Gene ontology

• Biological process: cellular defense response;signal transduction;natural killer cell activation;regulation of natural killer cell mediated cytotoxicity;regulation of immune response
• Cellular component: plasma membrane;integral component of plasma membrane;SWI/SNF complex
• Molecular function: protein binding