PPM1L
protein phosphatase, Mg2+/Mn2+ dependent 1L, the group of Protein phosphatases, Mg2+/Mn2+ dependent
Basic information
Region (hg38): 3:160755602-161078902
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 PPM1L 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 | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 0 | 0 |
Variants in PPM1L
This is a list of pathogenic ClinVar variants found in the PPM1L region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-160756384-C-G | not specified | Uncertain significance (Oct 12, 2021) | ||
| 3-160756466-G-A | not specified | Uncertain significance (Feb 07, 2023) | ||
| 3-160756474-G-A | not specified | Uncertain significance (Aug 15, 2024) | ||
| 3-160756526-G-C | not specified | Uncertain significance (Feb 06, 2024) | ||
| 3-160756566-G-C | not specified | Uncertain significance (May 27, 2022) | ||
| 3-160756578-C-G | not specified | Uncertain significance (Jan 04, 2024) | ||
| 3-160756655-C-T | not specified | Uncertain significance (Dec 11, 2023) | ||
| 3-160756693-G-A | not specified | Uncertain significance (May 09, 2024) | ||
| 3-160756700-G-C | not specified | Uncertain significance (Nov 08, 2022) | ||
| 3-160961757-T-C | not specified | Uncertain significance (Feb 01, 2023) | ||
| 3-160961761-G-A | not specified | Uncertain significance (Aug 21, 2024) | ||
| 3-160961799-G-A | not specified | Uncertain significance (Nov 09, 2023) | ||
| 3-160961829-T-C | not specified | Uncertain significance (Jul 26, 2022) | ||
| 3-160961863-T-C | not specified | Uncertain significance (Aug 01, 2024) | ||
| 3-161065415-T-C | not specified | Uncertain significance (Nov 08, 2022) | ||
| 3-161065532-A-G | not specified | Uncertain significance (Mar 07, 2024) | ||
| 3-161068852-A-G | not specified | Uncertain significance (Sep 07, 2022) | ||
| 3-161068870-T-A | not specified | Uncertain significance (Jun 18, 2024) | ||
| 3-161068885-C-T | not specified | Uncertain significance (Nov 21, 2023) | ||
| 3-161068886-C-T | not specified | Uncertain significance (Dec 11, 2023) | ||
| 3-161068940-T-A | not specified | Uncertain significance (Dec 01, 2024) | ||
| 3-161069012-C-T | not specified | Uncertain significance (Apr 29, 2024) | ||
| 3-161069088-A-C | not specified | Uncertain significance (Jan 10, 2023) | ||
| 3-161069104-A-G | not specified | Uncertain significance (Feb 21, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPM1L | protein_coding | protein_coding | ENST00000498165 | 4 | 323306 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.473 | 0.526 | 125737 | 0 | 11 | 125748 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.06 | 123 | 206 | 0.596 | 0.0000103 | 2377 |
| Missense in Polyphen | 36 | 73.821 | 0.48767 | 811 | ||
| Synonymous | -0.187 | 86 | 83.8 | 1.03 | 0.00000450 | 688 |
| Loss of Function | 2.80 | 3 | 14.5 | 0.207 | 8.31e-7 | 159 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000140 | 0.000139 |
| European (Non-Finnish) | 0.0000543 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as a suppressor of the SAPK signaling pathways by associating with and dephosphorylating MAP3K7/TAK1 and MAP3K5, and by attenuating the association between MAP3K7/TAK1 and MAP2K4 or MAP2K6. {ECO:0000269|PubMed:17456047}.;
- Pathway
- Amino Acid metabolism;Metabolism of lipids;Metabolism;Sphingolipid de novo biosynthesis;Sphingolipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.167
Intolerance Scores
- loftool
- 0.250
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.22
Haploinsufficiency Scores
- pHI
- 0.999
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.501
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.450
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppm1l
- 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region 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); 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); homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Gene ontology
- Biological process
- MAPK cascade;protein dephosphorylation;transmembrane receptor protein serine/threonine kinase signaling pathway;sphingolipid biosynthetic process
- Cellular component
- endoplasmic reticulum membrane;integral component of membrane;extracellular exosome
- Molecular function
- protein serine/threonine phosphatase activity;magnesium-dependent protein serine/threonine phosphatase activity;metal ion binding