DDIT4
DNA damage inducible transcript 4
Basic information
Region (hg38): 10:72273919-72276036
Links
Phenotypes
GenCC
Source:
No genCC data.
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 DDIT4 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 | 16 | 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 | 16 | 0 | 0 |
Variants in DDIT4
This is a list of pathogenic ClinVar variants found in the DDIT4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 10-72274223-A-G | not specified | Uncertain significance (Feb 28, 2024) | ||
| 10-72274226-C-T | not specified | Uncertain significance (Jan 22, 2024) | ||
| 10-72274227-T-C | not specified | Uncertain significance (Jun 14, 2023) | ||
| 10-72274292-C-T | not specified | Uncertain significance (Jun 16, 2023) | ||
| 10-72274298-C-T | not specified | Uncertain significance (Apr 19, 2023) | ||
| 10-72274359-G-T | not specified | Uncertain significance (Apr 19, 2024) | ||
| 10-72274371-C-T | not specified | Uncertain significance (Mar 30, 2024) | ||
| 10-72274707-T-C | not specified | Uncertain significance (Oct 24, 2024) | ||
| 10-72274733-G-C | not specified | Uncertain significance (May 18, 2022) | ||
| 10-72274765-G-C | not specified | Uncertain significance (Mar 19, 2024) | ||
| 10-72274773-A-G | not specified | Uncertain significance (Jul 26, 2021) | ||
| 10-72274812-G-A | not specified | Uncertain significance (May 08, 2024) | ||
| 10-72274827-G-T | not specified | Uncertain significance (Jul 09, 2021) | ||
| 10-72274846-G-T | not specified | Uncertain significance (Oct 21, 2024) | ||
| 10-72274886-C-T | not specified | Uncertain significance (Aug 02, 2021) | ||
| 10-72274902-A-G | not specified | Uncertain significance (Jan 04, 2024) | ||
| 10-72274935-T-C | not specified | Uncertain significance (Nov 13, 2024) | ||
| 10-72274949-G-A | not specified | Uncertain significance (Jul 14, 2022) | ||
| 10-72274955-A-G | not specified | Uncertain significance (Dec 08, 2023) | ||
| 10-72274966-C-G | not specified | Uncertain significance (Jul 20, 2021) | ||
| 10-72275070-G-T | not specified | Uncertain significance (Aug 15, 2023) | ||
| 10-72275183-T-C | not specified | Uncertain significance (Jan 23, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DDIT4 | protein_coding | protein_coding | ENST00000307365 | 2 | 2117 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000683 | 0.762 | 125730 | 0 | 18 | 125748 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.105 | 130 | 133 | 0.974 | 0.00000660 | 1460 |
| Missense in Polyphen | 38 | 41.244 | 0.92135 | 442 | ||
| Synonymous | -0.0391 | 67 | 66.6 | 1.01 | 0.00000334 | 522 |
| Loss of Function | 0.989 | 6 | 9.24 | 0.649 | 5.31e-7 | 75 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000183 | 0.000181 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000715 | 0.0000703 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000163 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Regulates cell growth, proliferation and survival via inhibition of the activity of the mammalian target of rapamycin complex 1 (mTORC1). Inhibition of mTORC1 is mediated by a pathway that involves DDIT4/REDD1, AKT1, the TSC1-TSC2 complex and the GTPase RHEB. Plays an important role in responses to cellular energy levels and cellular stress, including responses to hypoxia and DNA damage. Regulates p53/TP53-mediated apoptosis in response to DNA damage via its effect on mTORC1 activity. Its role in the response to hypoxia depends on the cell type; it mediates mTORC1 inhibition in fibroblasts and thymocytes, but not in hepatocytes (By similarity). Required for mTORC1-mediated defense against viral protein synthesis and virus replication (By similarity). Inhibits neuronal differentiation and neurite outgrowth mediated by NGF via its effect on mTORC1 activity. Required for normal neuron migration during embryonic brain development. Plays a role in neuronal cell death. {ECO:0000250, ECO:0000269|PubMed:15545625, ECO:0000269|PubMed:15632201, ECO:0000269|PubMed:15988001, ECO:0000269|PubMed:17005863, ECO:0000269|PubMed:17379067, ECO:0000269|PubMed:19557001, ECO:0000269|PubMed:20166753, ECO:0000269|PubMed:21460850}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);mTOR signaling pathway - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Target Of Rapamycin (TOR) Signaling;TP53 Regulates Metabolic Genes;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;TP53 Regulates Metabolic Genes;Transcriptional Regulation by TP53;Direct p53 effectors;mTOR signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.192
Intolerance Scores
- loftool
- 0.535
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.46
Haploinsufficiency Scores
- pHI
- 0.454
- hipred
- Y
- hipred_score
- 0.692
- ghis
- 0.490
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.982
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ddit4
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye 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); cellular phenotype;
Zebrafish Information Network
- Gene name
- ddit4
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- bent
Gene ontology
- Biological process
- response to hypoxia;neuron migration;brain development;cell population proliferation;negative regulation of peptidyl-threonine phosphorylation;neuron differentiation;negative regulation of TOR signaling;protein-containing complex disassembly;negative regulation of peptidyl-serine phosphorylation;intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;negative regulation of glycolytic process;neurotrophin TRK receptor signaling pathway;defense response to virus;cellular response to dexamethasone stimulus;reactive oxygen species metabolic process;positive regulation of neuron death;negative regulation of intracellular signal transduction
- Cellular component
- cytoplasm;mitochondrion;cytosol
- Molecular function
- 14-3-3 protein binding