NCR2
Basic information
Region (hg38): 6:41335608-41350889
Previous symbols: [ "LY95" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 17 | 21 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 17 | 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) | |||
6-41336117-T-C | not specified | Uncertain significance (Oct 11, 2024) | ||
6-41336138-C-G | not specified | Uncertain significance (May 30, 2023) | ||
6-41336168-C-T | not specified | Uncertain significance (Nov 22, 2024) | ||
6-41336177-T-C | not specified | Likely benign (Jun 24, 2022) | ||
6-41336182-G-A | not specified | Uncertain significance (Dec 07, 2024) | ||
6-41336255-C-T | not specified | Uncertain significance (Sep 16, 2021) | ||
6-41336278-A-G | not specified | Likely benign (Aug 04, 2023) | ||
6-41336387-C-T | not specified | Uncertain significance (Dec 03, 2024) | ||
6-41336401-G-A | Benign (Jun 12, 2018) | |||
6-41336411-A-C | not specified | Uncertain significance (Dec 01, 2022) | ||
6-41341812-C-T | not specified | Uncertain significance (Oct 08, 2024) | ||
6-41341826-C-T | not specified | Uncertain significance (Apr 13, 2022) | ||
6-41341835-G-T | not specified | Uncertain significance (Jan 25, 2023) | ||
6-41341844-C-G | not specified | Uncertain significance (Aug 19, 2024) | ||
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) | ||
6-41342088-C-T | not specified | Uncertain significance (Aug 27, 2024) | ||
6-41342116-A-G | not specified | Uncertain significance (Apr 13, 2023) | ||
6-41342142-G-A | not specified | Likely benign (Aug 07, 2024) | ||
6-41350690-G-C | not specified | Uncertain significance (May 25, 2022) | ||
6-41350708-G-C | not specified | Uncertain significance (Jun 02, 2023) |
GnomAD
Source:
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:
- 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
- ghis
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