PPM1F p.Ala390=
c.1170C>T · VCV4739499
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0347%, 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 -3.7 | GERP -4.1 |
| Overall | ||
| CADD | 0.206 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0347%
African / African-American · 26/74,902 alleles
Filtering AF
0.0243%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0208%
Overall
0.00304%
49/1,613,310 alleles · ultra-rare
exomes 28/1,461,182 · genomes 21/152,128 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0347% | 2,881 |
| Middle Eastern | 0.0164% | 6,080 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,413 |
| East Asian | 0.00891% | 11,223 |
| Admixed American | 0.00834% | 11,996 |
| South Asian | 0.00329% | 30,356 |
| European (non-Finnish) | 0.000339% | 294,988 |
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.Ala390=
- Coding
- c.1170C>T
- MANE Select
- NM_014634
- Type
- single nucleotide variant
- Location
- chr22:21923287 (GRCh38)
- Gene constraint
- LOEUF 0.864 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.70
- Residue 390
- the ppm-type phosphatase domain
Similar variants
- PPM1F p.Ala390Thr Uncertain significance ★ ⚠ same residue
- 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
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-ala390 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown