NCK2
Basic information
Region (hg38): 2:105744912-105894274
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 NCK2 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 | 0 | |||||
missense | 11 | 11 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 11 | 0 | 0 |
Variants in NCK2
This is a list of pathogenic ClinVar variants found in the NCK2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
2-105855127-G-A | not specified | Uncertain significance (Jan 30, 2024) | ||
2-105881385-C-T | not specified | Uncertain significance (Oct 06, 2022) | ||
2-105881390-G-A | not specified | Uncertain significance (Sep 30, 2021) | ||
2-105881413-C-A | not specified | Uncertain significance (Jan 22, 2024) | ||
2-105881433-A-T | not specified | Uncertain significance (Oct 13, 2023) | ||
2-105881561-A-T | not specified | Uncertain significance (Sep 26, 2023) | ||
2-105881657-G-T | not specified | Uncertain significance (Oct 03, 2022) | ||
2-105881787-A-C | not specified | Uncertain significance (Nov 17, 2023) | ||
2-105881847-A-G | not specified | Uncertain significance (Aug 28, 2023) | ||
2-105881868-G-A | not specified | Uncertain significance (Sep 27, 2021) | ||
2-105881933-G-A | not specified | Uncertain significance (Feb 06, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
NCK2 | protein_coding | protein_coding | ENST00000233154 | 3 | 149377 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.458 | 0.541 | 125720 | 0 | 5 | 125725 | 0.0000199 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.45 | 161 | 275 | 0.584 | 0.0000202 | 2481 |
Missense in Polyphen | 72 | 145.41 | 0.49515 | 1353 | ||
Synonymous | 0.471 | 131 | 138 | 0.949 | 0.0000121 | 745 |
Loss of Function | 2.77 | 3 | 14.3 | 0.209 | 6.14e-7 | 157 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000289 | 0.0000289 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000267 | 0.0000264 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Adapter protein which associates with tyrosine- phosphorylated growth factor receptors or their cellular substrates. Maintains low levels of EIF2S1 phosphorylation by promoting its dephosphorylation by PP1. Plays a role in ELK1- dependent transcriptional activation in response to activated Ras signaling. {ECO:0000269|PubMed:10026169, ECO:0000269|PubMed:16835242}.;
- Pathway
- T cell receptor signaling pathway - Homo sapiens (human);ErbB signaling pathway - Homo sapiens (human);Axon guidance - Homo sapiens (human);Pathogenic Escherichia coli infection - Homo sapiens (human);Pathogenic Escherichia coli infection;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;EGF-EGFR Signaling Pathway;Developmental Biology;Signal Transduction;VEGFA-VEGFR2 Pathway;Signaling by PDGF;EPH-Ephrin signaling;Ephrin signaling;Activation of RAC1;BDNF;EGFR1;Downstream signal transduction;Ephrin B reverse signaling;Signaling by ROBO receptors;Signaling by VEGF;Axon guidance;Regulation of cortical dendrite branching;Integrin-linked kinase signaling;Signaling by Receptor Tyrosine Kinases;Nephrin family interactions;Cell-Cell communication;Insulin Pathway;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Signaling events mediated by focal adhesion kinase;Reelin signaling pathway;IGF1 pathway;PDGFR-beta signaling pathway;Signaling events mediated by VEGFR1 and VEGFR2;Nephrin/Neph1 signaling in the kidney podocyte
(Consensus)
Recessive Scores
- pRec
- 0.259
Intolerance Scores
- loftool
- 0.223
- rvis_EVS
- -0.71
- rvis_percentile_EVS
- 14.4
Haploinsufficiency Scores
- pHI
- 0.248
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.571
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.881
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nck2
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; embryo phenotype; renal/urinary system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- immunological synapse formation;actin filament organization;signal transduction;signal complex assembly;epidermal growth factor receptor signaling pathway;regulation of epidermal growth factor-activated receptor activity;negative regulation of cell population proliferation;cell migration;lamellipodium assembly;positive regulation of actin filament polymerization;negative regulation of peptidyl-serine phosphorylation;positive regulation of translation in response to endoplasmic reticulum stress;positive regulation of T cell proliferation;T cell activation;positive regulation of transcription by RNA polymerase II;vascular endothelial growth factor receptor signaling pathway;ephrin receptor signaling pathway;dendritic spine development;positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway;negative regulation of PERK-mediated unfolded protein response;negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation;negative regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress
- Cellular component
- cytoplasm;endoplasmic reticulum;cytosol;vesicle membrane;postsynaptic density
- Molecular function
- phosphotyrosine residue binding;SH3/SH2 adaptor activity;protein binding;cytoskeletal adaptor activity;receptor signaling complex scaffold activity;protein-containing complex binding;scaffold protein binding