PPM1F p.Ala301=
c.903G>T · rs559570000 · VCV1974020
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00129%, nfe)
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 -0.38 | GERP -4.1, phastCons 0.086 |
| Overall | ||
| CADD | 3.097 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00129%
European (non-Finnish) · 15/1,163,066 alleles
Filtering AF
0.000774%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000614%
Overall
0.000944%
15/1,589,100 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.Ala301=
- Coding
- c.903G>T
- MANE Select
- NM_014634
- dbSNP
- rs559570000
- Type
- single nucleotide variant
- Location
- chr22:21925651 (GRCh38)
- Gene constraint
- LOEUF 0.864 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.70
- Residue 301
- 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-ala301 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown