PPM1F p.Glu170=
c.510G>A · VCV4749534
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00712%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.071 | GERP -1.4, phastCons 0.9 |
| Overall | ||
| CADD | 8.633 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00712%
East Asian · 3/42,110 alleles
Filtering AF
0.00189%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00102%
Overall
0.000212%
3/1,412,622 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- PPM1F
- Protein
- p.Glu170=
- Coding
- c.510G>A
- MANE Select
- NM_014634
- Type
- single nucleotide variant
- Location
- chr22:21934072 (GRCh38)
- Gene constraint
- LOEUF 0.864 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.70
- Residue 170
- the ppm-type phosphatase domain
Similar variants
- PPM1F p.Arg149Gln Uncertain significance ★★ ⚠ same type
- PPM1F p.Glu103Lys Uncertain significance ★★ ⚠ same type
- PPM1F p.Glu82Lys Uncertain significance ★★ ⚠ same type
- PPM1F p.Gly320Arg Uncertain significance ★★ ⚠ same type
- PPM1F p.Gly386Glu Uncertain significance ★★ ⚠ same type
- PPM1F p.His378Tyr Uncertain significance ★★ ⚠ same type
- PPM1F p.Met63Val Uncertain significance ★★ ⚠ same type
- PPM1F p.Pro430Leu Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ppm1f-p-glu170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown