PPM1G
Basic information
Region (hg38): 2:27381195-27409591
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 PPM1G 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 PPM1G
This is a list of pathogenic ClinVar variants found in the PPM1G region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
2-27381615-T-G | not specified | Uncertain significance (Aug 13, 2021) | ||
2-27381616-T-C | not specified | Uncertain significance (Aug 13, 2021) | ||
2-27381703-G-C | not specified | Uncertain significance (Oct 02, 2023) | ||
2-27383552-T-G | not specified | Uncertain significance (Aug 16, 2022) | ||
2-27383582-T-C | not specified | Uncertain significance (Sep 25, 2023) | ||
2-27384740-T-C | not specified | Uncertain significance (Oct 26, 2021) | ||
2-27384749-C-T | not specified | Uncertain significance (Feb 23, 2023) | ||
2-27384845-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
2-27384903-T-A | not specified | Uncertain significance (Apr 18, 2023) | ||
2-27384917-T-G | not specified | Uncertain significance (Jan 02, 2024) | ||
2-27384999-C-T | not specified | Uncertain significance (Jul 10, 2024) | ||
2-27385749-T-C | not specified | Uncertain significance (Feb 27, 2023) | ||
2-27385768-T-C | not specified | Uncertain significance (Dec 17, 2023) | ||
2-27385855-T-C | not specified | Uncertain significance (Jun 24, 2022) | ||
2-27386252-T-C | not specified | Uncertain significance (Nov 03, 2023) | ||
2-27409396-G-T | not specified | Uncertain significance (Aug 14, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PPM1G | protein_coding | protein_coding | ENST00000344034 | 10 | 28494 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.960 | 0.0396 | 125739 | 0 | 9 | 125748 | 0.0000358 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.34 | 136 | 298 | 0.456 | 0.0000154 | 3605 |
Missense in Polyphen | 4 | 57.875 | 0.069115 | 632 | ||
Synonymous | 1.79 | 90 | 114 | 0.787 | 0.00000622 | 1037 |
Loss of Function | 4.17 | 4 | 27.7 | 0.144 | 0.00000168 | 312 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000457 | 0.000272 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000264 | 0.0000264 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Pathway
- mRNA Processing
(Consensus)
Recessive Scores
- pRec
- 0.128
Intolerance Scores
- loftool
- 0.100
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 34.32
Haploinsufficiency Scores
- pHI
- 0.999
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.641
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.781
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppm1g
- 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); 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);
Zebrafish Information Network
- Gene name
- ppm1g
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- protein dephosphorylation;cell cycle arrest;peptidyl-threonine dephosphorylation
- Cellular component
- nucleus;nucleoplasm;cytoplasm;membrane
- Molecular function
- protein serine/threonine phosphatase activity;magnesium-dependent protein serine/threonine phosphatase activity;protein binding;metal ion binding