DDIT3
DNA damage inducible transcript 3, the group of MicroRNA protein coding host genes
Basic information
Region (hg38): 12:57516588-57521737
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 DDIT3 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 | 14 | ||||
| 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 | 1 | 2 |
Variants in DDIT3
This is a list of pathogenic ClinVar variants found in the DDIT3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-57516849-C-T | not specified | Uncertain significance (Dec 01, 2022) | ||
| 12-57516883-C-T | Likely benign (Aug 14, 2018) | |||
| 12-57516928-C-T | not specified | Uncertain significance (Jan 08, 2024) | ||
| 12-57516931-T-C | not specified | Uncertain significance (Sep 22, 2022) | ||
| 12-57516943-C-G | not specified | Uncertain significance (Jun 29, 2023) | ||
| 12-57516946-G-C | not specified | Uncertain significance (Feb 15, 2023) | ||
| 12-57516963-C-T | not specified | Uncertain significance (Nov 17, 2023) | ||
| 12-57516972-C-G | not specified | Uncertain significance (Jan 04, 2024) | ||
| 12-57517056-C-G | not specified | Uncertain significance (Jan 10, 2022) | ||
| 12-57517315-G-A | not specified | Uncertain significance (Dec 20, 2023) | ||
| 12-57517406-T-A | not specified | Uncertain significance (Jan 17, 2024) | ||
| 12-57517429-A-G | Benign (Aug 06, 2018) | |||
| 12-57517444-G-C | not specified | Uncertain significance (Nov 08, 2022) | ||
| 12-57517463-G-C | Benign (Dec 31, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DDIT3 | protein_coding | protein_coding | ENST00000551116 | 2 | 3930 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.591 | 0.400 | 125740 | 0 | 8 | 125748 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0964 | 104 | 107 | 0.974 | 0.00000591 | 1238 |
| Missense in Polyphen | 33 | 31.704 | 1.0409 | 377 | ||
| Synonymous | -0.565 | 43 | 38.5 | 1.12 | 0.00000180 | 390 |
| Loss of Function | 2.10 | 1 | 7.00 | 0.143 | 2.99e-7 | 86 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Pathway
- Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Apoptosis - Homo sapiens (human);Celecoxib Pathway, Pharmacodynamics;EGF-Core;ATF4 activates genes;White fat cell differentiation;Adipogenesis;ATF6 (ATF6-alpha) activates chaperone genes;Preimplantation Embryo;Photodynamic therapy-induced unfolded protein response;MAPK Signaling Pathway;p38 MAPK Signaling Pathway;White fat cell differentiation;Transcriptional cascade regulating adipogenesis;RAGE;p38 mapk signaling pathway;ATF-2 transcription factor network;Signaling mediated by p38-alpha and p38-beta;Validated targets of C-MYC transcriptional repression
(Consensus)
Recessive Scores
- pRec
- 0.377
Intolerance Scores
- loftool
- 0.575
- rvis_EVS
- 0.24
- rvis_percentile_EVS
- 68.98
Haploinsufficiency Scores
- pHI
- 0.367
- hipred
- Y
- hipred_score
- 0.553
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ddit3
- 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); immune system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm; hematopoietic system 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); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- ddit3
- Affected structure
- lipid biosynthetic process
- Phenotype tag
- abnormal
- Phenotype quality
- process quality
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;blood vessel maturation;regulation of transcription, DNA-templated;cellular response to DNA damage stimulus;ER overload response;response to unfolded protein;cell cycle arrest;Wnt signaling pathway;positive regulation of interleukin-8 production;negative regulation of CREB transcription factor activity;response to endoplasmic reticulum stress;PERK-mediated unfolded protein response;ATF6-mediated unfolded protein response;response to starvation;mRNA transcription by RNA polymerase II;proteasome-mediated ubiquitin-dependent protein catabolic process;negative regulation of DNA-binding transcription factor activity;positive regulation of neuron apoptotic process;regulation of DNA-templated transcription in response to stress;regulation of transcription involved in anterior/posterior axis specification;cell redox homeostasis;negative regulation of fat cell differentiation;negative regulation of myoblast differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of DNA-binding transcription factor activity;release of sequestered calcium ion into cytosol;protein complex oligomerization;negative regulation of protein kinase B signaling;intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress;establishment of protein localization to mitochondrion;negative regulation of canonical Wnt signaling pathway;negative regulation of cold-induced thermogenesis;positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway;negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding;positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress;intrinsic apoptotic signaling pathway in response to nitrosative stress;negative regulation of determination of dorsal identity
- Cellular component
- nucleus;nucleoplasm;cytoplasm;late endosome;cytosol;protein-DNA complex;transcription factor AP-1 complex;CHOP-C/EBP complex;CHOP-ATF4 complex;CHOP-ATF3 complex
- Molecular function
- transcription regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription corepressor activity;protein binding;transcription factor binding;cAMP response element binding protein binding;protein homodimerization activity;leucine zipper domain binding;transcription regulatory region DNA binding;protein heterodimerization activity