GeneBe

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.

  • not_specified (43 variants)
  • not_provided (1 variants)

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. These statistics are base on transcript: NM_000004829.7. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
40
clinvar
3
clinvar
 43
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 40 4 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NCR1protein_codingprotein_codingENST00000291890 710001
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
7.33e-110.07341257150331257480.000131
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2471871781.050.00001021967
Missense in Polyphen3442.1020.80757509
Synonymous-1.178269.61.180.00000428609
Loss of Function0.1561616.70.9590.00000107155

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001810.000181
Ashkenazi Jewish0.000.00
East Asian0.0002720.000272
Finnish0.000.00
European (Non-Finnish)0.0001760.000176
Middle Eastern0.0002720.000272
South Asian0.0001310.000131
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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