GADD45A
growth arrest and DNA damage inducible alpha
Basic information
Region (hg38): 1:67685201-67688334
Previous symbols: [ "DDIT1" ]
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 GADD45A 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 | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 0 | 1 |
Variants in GADD45A
This is a list of pathogenic ClinVar variants found in the GADD45A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-67686077-C-G | not specified | Uncertain significance (Sep 28, 2022) | ||
| 1-67686488-G-A | Benign (Apr 16, 2018) | |||
| 1-67686516-G-A | not specified | Uncertain significance (Jul 25, 2023) | ||
| 1-67687727-C-T | not specified | Uncertain significance (May 17, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GADD45A | protein_coding | protein_coding | ENST00000370986 | 4 | 3278 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0441 | 0.859 | 125554 | 0 | 4 | 125558 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.41 | 60 | 99.5 | 0.603 | 0.00000478 | 1076 |
| Missense in Polyphen | 15 | 47.084 | 0.31858 | 494 | ||
| Synonymous | -1.31 | 54 | 43.0 | 1.25 | 0.00000200 | 328 |
| Loss of Function | 1.36 | 3 | 6.84 | 0.439 | 2.91e-7 | 81 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000309 | 0.0000309 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000900 | 0.00000881 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000990 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: In T-cells, functions as a regulator of p38 MAPKs by inhibiting p88 phosphorylation and activity (By similarity). Might affect PCNA interaction with some CDK (cell division protein kinase) complexes; stimulates DNA excision repair in vitro and inhibits entry of cells into S phase. {ECO:0000250}.;
- Pathway
- Non-small cell lung cancer - Homo sapiens (human);Chronic myeloid leukemia - Homo sapiens (human);Gastric cancer - Homo sapiens (human);Melanoma - Homo sapiens (human);Cell cycle - Homo sapiens (human);p53 signaling pathway - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Breast cancer - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);Basal cell carcinoma - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Glioma - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Apoptosis - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Thyroid cancer - Homo sapiens (human);Pancreatic cancer - Homo sapiens (human);Endometrial cancer - Homo sapiens (human);Colorectal cancer - Homo sapiens (human);Cell Cycle;miRNA Regulation of DNA Damage Response;TP53 Network;Integrated Breast Cancer Pathway;Adipogenesis;Spinal Cord Injury;ATM Signaling Pathway;Vitamin D Receptor Pathway;Imatinib and Chronic Myeloid Leukemia;TP53 Regulates Transcription of Cell Cycle Genes;MAPK Signaling Pathway;Oxidative Damage;Endometrial cancer;Chromosomal and microsatellite instability in colorectal cancer;G1 to S cell cycle control;DNA Damage Response;Gene expression (Transcription);hypoxia and p53 in the cardiovascular system;Generic Transcription Pathway;RNA Polymerase II Transcription;ATF-2 transcription factor network;Aurora A signaling;cell cycle: g2/m checkpoint;p53 signaling pathway;TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest;atm signaling pathway;TP53 Regulates Transcription of Cell Cycle Genes;Validated transcriptional targets of TAp63 isoforms;Transcriptional Regulation by TP53;Direct p53 effectors;Validated targets of C-MYC transcriptional repression;p38 MAPK signaling pathway;FoxO family signaling
(Consensus)
Recessive Scores
- pRec
- 0.838
Intolerance Scores
- loftool
- 0.341
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.636
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.540
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.981
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Gadd45a
- Phenotype
- embryo phenotype; 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); reproductive system phenotype; 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); 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); renal/urinary system phenotype; immune system phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Gene ontology
- Biological process
- regulation of cyclin-dependent protein serine/threonine kinase activity;activation of MAPKKK activity;DNA repair;negative regulation of protein kinase activity;apoptotic process;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;cell cycle arrest;centrosome cycle;signal transduction in response to DNA damage;positive regulation of apoptotic process;positive regulation of JNK cascade;regulation of cell cycle;cellular response to mechanical stimulus;cellular response to ionizing radiation;mitotic cell cycle arrest;positive regulation of p38MAPK cascade;positive regulation of reactive oxygen species metabolic process
- Cellular component
- nucleus;nucleoplasm;cytoplasm;nuclear speck
- Molecular function
- RNA polymerase II core promoter sequence-specific DNA binding;protein binding;kinase binding;protein homodimerization activity;protein heterodimerization activity;protein N-terminus binding