IMPACT
Basic information
Region (hg38): 18:24426634-24453531
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 IMPACT 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in IMPACT
This is a list of pathogenic ClinVar variants found in the IMPACT region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 18-24427934-G-T | not specified | Uncertain significance (Aug 02, 2021) | ||
| 18-24430347-C-T | not specified | Uncertain significance (Sep 17, 2021) | ||
| 18-24437964-C-G | not specified | Uncertain significance (Oct 20, 2021) | ||
| 18-24440544-A-C | not specified | Uncertain significance (Aug 15, 2023) | ||
| 18-24443111-A-T | not specified | Uncertain significance (Nov 07, 2022) | ||
| 18-24449824-G-C | not specified | Uncertain significance (Jan 03, 2024) | ||
| 18-24449888-C-T | not specified | Uncertain significance (Jul 20, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IMPACT | protein_coding | protein_coding | ENST00000284202 | 11 | 26920 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 4.83e-8 | 0.625 | 125674 | 0 | 72 | 125746 | 0.000286 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.169 | 165 | 171 | 0.964 | 0.00000890 | 2123 |
| Missense in Polyphen | 57 | 58.268 | 0.97824 | 693 | ||
| Synonymous | -0.641 | 63 | 56.9 | 1.11 | 0.00000316 | 545 |
| Loss of Function | 1.15 | 14 | 19.5 | 0.718 | 9.09e-7 | 256 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000591 | 0.000590 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00160 | 0.00147 |
| Finnish | 0.0000469 | 0.0000462 |
| European (Non-Finnish) | 0.000152 | 0.000149 |
| Middle Eastern | 0.00160 | 0.00147 |
| South Asian | 0.000421 | 0.000392 |
| Other | 0.000328 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Translational regulator that ensures constant high levels of translation upon a variety of stress conditions, such as amino acid starvation, UV-C irradiation, proteasome inhibitor treatment and glucose deprivation. Plays a role as a negative regulator of the EIF2AK4/GCN2 kinase activity; impairs GCN1- mediated EIF2AK4/GCN2 activation, and hence EIF2AK4/GCN2-mediated eIF-2-alpha phosphorylation and subsequent down-regulation of protein synthesis. May be required to regulate translation in specific neuronal cells under amino acid starvation conditions by preventing GCN2 activation and therefore ATF4 synthesis. Through its inhibitory action on EIF2AK4/GCN2, plays a role in differentiation of neuronal cells by stimulating neurite outgrowth. {ECO:0000250|UniProtKB:O55091}.;
Recessive Scores
- pRec
- 0.119
Intolerance Scores
- loftool
- 0.758
- rvis_EVS
- 0.26
- rvis_percentile_EVS
- 70.26
Haploinsufficiency Scores
- pHI
- 0.243
- hipred
- N
- hipred_score
- 0.306
- ghis
- 0.529
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.283
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Impact
- Phenotype
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;negative regulation of protein phosphorylation;biological_process;negative regulation of protein complex assembly;negative regulation of protein autophosphorylation;cellular response to amino acid starvation;cellular response to glucose starvation;positive regulation of neuron differentiation;negative regulation of cell death;regulation of eIF2 alpha phosphorylation by amino acid starvation;cellular response to hydrogen peroxide;positive regulation of translational initiation in response to starvation;cellular response to acidic pH;cellular response to UV-C;cellular response to benomyl;negative regulation of transcription from RNA polymerase II promoter in response to stress;neuron projection extension;cellular response to leucine starvation
- Cellular component
- cellular_component;cytoplasm;polysome
- Molecular function
- molecular_function;actin binding;ribosome binding