PPM1N

Chr 19

protein phosphatase, Mg2+/Mn2+ dependent 1N (putative)

NCBI Gene: 147699ENSG00000213889UniProt: Q8N819

This protein serine/threonine phosphatase regulates canonical Wnt signaling and NF-kappaB signal transduction pathways in the cytosol and nucleus. Mutations cause autosomal recessive intellectual disability with microcephaly, seizures, and developmental delays. The gene shows low constraint against loss-of-function variants (pLI <0.001), consistent with the recessive inheritance pattern observed clinically.

ResearchSummary from RefSeq
MultiplemechanismLOEUF 1.43
Clinical Summary— PPM1N
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
8 unique Pathogenic / Likely Pathogenic· 79 VUS of 99 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.43LOEUF
pLI 0.000
Z-score 0.55
OE 0.82 (0.49–1.43)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
1.20Z-score
OE missense 0.76 (0.67–0.87)
153 obs / 200.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.82 (0.49–1.43)
0≤0.351.4
Missense OE0.76 (0.67–0.87)
0≤0.61.4
Synonymous OE0.85
0≤1.21.6
LoF obs/exp: 9 / 10.9Missense obs/exp: 153 / 200.7Syn Z: 1.10
DN
0.6841th %ile
GOF
0.72top 25%
LOF
0.2777th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median
DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

99 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic6
Likely Pathogenic2
VUS79
Likely Benign4
6
Pathogenic
2
Likely Pathogenic
79
VUS
4
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
6
0
6
Likely Pathogenic
0
0
2
0
2
VUS
1
73
5
0
79
Likely Benign
0
3
0
1
4
Benign
0
0
0
0
0
Total17613191

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

PPM1N · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 2 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients