PPM1B
Basic information
Region (hg38): 2:44167969-44244384
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (46 variants)
- not_provided (8 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPM1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002706.6. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | |||||
| missense | 44 | 48 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 44 | 8 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPM1B | protein_coding | protein_coding | ENST00000282412 | 5 | 76416 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00908 | 0.989 | 125731 | 0 | 17 | 125748 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.600 | 236 | 263 | 0.896 | 0.0000136 | 3149 |
| Missense in Polyphen | 45 | 95.308 | 0.47215 | 1118 | ||
| Synonymous | 0.701 | 83 | 91.5 | 0.907 | 0.00000465 | 915 |
| Loss of Function | 2.68 | 7 | 19.9 | 0.352 | 0.00000116 | 248 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000156 | 0.000156 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000128 | 0.000114 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Enzyme with a broad specificity. Dephosphorylates CDK2 and CDK6 in vitro. Dephosphorylates PRKAA1 and PRKAA2. Inhibits TBK1-mediated antiviral signaling by dephosphorylating it at 'Ser- 172'. Plays an important role in the termination of TNF-alpha- mediated NF-kappa-B activation through dephosphorylating and inactivating IKBKB/IKKB. {ECO:0000269|PubMed:18930133, ECO:0000269|PubMed:22750291}.;
- Pathway
- MAPK signaling pathway - Homo sapiens (human);MAPK Signaling Pathway;Cytokine Signaling in Immune system;Immune System;ISG15 antiviral mechanism;Antiviral mechanism by IFN-stimulated genes;Interferon Signaling
(Consensus)
Recessive Scores
- pRec
- 0.212
Intolerance Scores
- loftool
- 0.424
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.51
Haploinsufficiency Scores
- pHI
- 1.00
- hipred
- Y
- hipred_score
- 0.792
- ghis
- 0.638
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.965
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppm1b
- Phenotype
- embryo 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); cellular phenotype;
Gene ontology
- Biological process
- protein dephosphorylation;N-terminal protein myristoylation;negative regulation of interferon-beta production;peptidyl-threonine dephosphorylation;negative regulation of I-kappaB kinase/NF-kappaB signaling;negative regulation of defense response to virus;negative regulation of NIK/NF-kappaB signaling
- Cellular component
- nucleus;nucleolus;cytosol;membrane
- Molecular function
- magnesium ion binding;protein serine/threonine phosphatase activity;magnesium-dependent protein serine/threonine phosphatase activity;protein binding;manganese ion binding