Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.69%, afr)
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 -13 | GERP -4.1 |
| Overall | ||
| CADD | 0.156 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.69%
African / African-American · 3,519/74,994 alleles
Filtering AF
4.56%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.51%
Overall
0.246%
3,974/1,613,376 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.69% | 21 |
| Remaining individualsnot grpmax-eligible | 0.278% | 359 |
| Admixed American | 0.263% | 380 |
| Middle Eastern | 0.115% | 866 |
| East Asian | 0.114% | 880 |
| South Asian | 0.0187% | 5,357 |
| European (non-Finnish) | 0.00407% | 24,581 |
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.Ser385=
- Coding
- c.1155C>T
- MANE Select
- NM_014634
- dbSNP
- rs240061
- Type
- single nucleotide variant
- Location
- chr22:21923302 (GRCh38)
- Gene constraint
- LOEUF 0.864 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.70
- Residue 385
- 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-ser385 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown