PPM1N
protein-codingprotein phosphatase, Mg2+/Mn2+ dependent 1N (putative), the group of Protein phosphatases, Mg2+/Mn2+ dependent
Gene summary
Predicted to enable protein serine/threonine phosphatase activity. Predicted to be involved in positive regulation of canonical Wnt signaling pathway and regulation of canonical NF-kappaB signal transduction. Predicted to be active in cytosol and nucleus. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~14.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PPM1N variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001080401.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 1 | 3 | |||
| missense | 73 | 3 | 76 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 76 | 4 | 0 | 80 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001073870.1 | 5 | MANE Select | |
| Ensembl | ENSP00000397050.2 | 5 | MANE Select | |
| Ensembl | ENSP00000379961.2 | 4 | Standard | |
| Ensembl | ENSP00000379961.2 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- protein dephosphorylation
Molecular Function
- magnesium ion binding
- protein serine/threonine phosphatase activity
- magnesium-dependent protein serine/threonine phosphatase activity
- manganese ion binding
Cellular Component
- nucleus
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000451287
- Coding exons
- 5
- Length
- 13734
- Individuals with no LoFs
- 124585
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 59
- Defined
- 124644
- p
- 0.000237
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.20 | 153 | 201 | 0.762 | 0.00000946 | 2623 |
| Missense (PolyPhen) | 48 | 63.717 | 0.75333 | 833 | ||
| Synonymous | 1.10 | 76 | 89.2 | 0.852 | 0.00000439 | 953 |
| Loss of Function | 0.545 | 9 | 10.9 | 0.822 | 4.73e-7 | 147 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00021 | 0.00019 | rare |
| Latino/Admixed American | 0.00040 | 0.00038 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.0019 | 0.0019 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000056 | 0.000053 | rare |
| South Asian | 0.000034 | 0.000033 | rare |
| Other | 0.00017 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |