GADD45B
Basic information
Region (hg38): 19:2476122-2478805
Previous symbols: [ "MYD118" ]
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 GADD45B 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 | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 0 |
Variants in GADD45B
This is a list of pathogenic ClinVar variants found in the GADD45B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-2476386-G-A | not specified | Uncertain significance (Oct 02, 2023) | ||
| 19-2476392-G-A | not specified | Uncertain significance (Feb 10, 2022) | ||
| 19-2477576-C-T | not specified | Uncertain significance (Jan 03, 2024) | ||
| 19-2477579-A-G | not specified | Uncertain significance (Dec 21, 2023) | ||
| 19-2477581-A-G | not specified | Uncertain significance (Jun 10, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GADD45B | protein_coding | protein_coding | ENST00000215631 | 4 | 2138 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.211 | 0.753 | 125318 | 0 | 7 | 125325 | 0.0000279 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.21 | 63 | 96.3 | 0.654 | 0.00000452 | 1042 |
| Missense in Polyphen | 18 | 37.966 | 0.47411 | 412 | ||
| Synonymous | -0.381 | 43 | 39.9 | 1.08 | 0.00000192 | 305 |
| Loss of Function | 1.74 | 2 | 6.96 | 0.287 | 3.01e-7 | 76 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000628 | 0.0000621 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000443 | 0.0000441 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the regulation of growth and apoptosis. Mediates activation of stress-responsive MTK1/MEKK4 MAPKKK.;
- 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);NF-kappa B signaling pathway - 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);miRNA Regulation of DNA Damage Response;Adipogenesis;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Endometrial cancer;Chromosomal and microsatellite instability in colorectal cancer;DNA Damage Response;p38 MAPK signaling pathway;IL12-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.383
Intolerance Scores
- loftool
- 0.336
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.432
- hipred
- Y
- hipred_score
- 0.807
- ghis
- 0.569
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.973
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Gadd45b
- Phenotype
- cellular phenotype; renal/urinary system phenotype; immune system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- activation of MAPKKK activity;activation of MAPKK activity;negative regulation of protein kinase activity;apoptotic process;multicellular organism development;cell differentiation;positive regulation of apoptotic process;positive regulation of JNK cascade;regulation of cell cycle;positive regulation of p38MAPK cascade
- Cellular component
- nucleus;cytoplasm
- Molecular function
- protein binding