PPM1F p.Ala161=
c.483C>T · rs140881529 · VCV2764991
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.338%, 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 4.4 | GERP -0.053, phastCons 1 |
| Overall | ||
| CADD | 10.45 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.338%
African / African-American · 250/73,936 alleles
Filtering AF
0.304%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.29%
Overall
0.0258%
403/1,563,602 alleles · rare
exomes 202/1,411,240 · genomes 201/152,362 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.338% | 296 |
| Admixed American | 0.145% | 689 |
| Middle Eastern | 0.0509% | 1,964 |
| Remaining individualsnot grpmax-eligible | 0.0495% | 2,019 |
| European (non-Finnish) | 0.00355% | 28,151 |
| South Asian | 0.00353% | 28,350 |
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.Ala161=
- Coding
- c.483C>T
- MANE Select
- NM_014634
- dbSNP
- rs140881529
- Type
- single nucleotide variant
- Location
- chr22:21934099 (GRCh38)
- Gene constraint
- LOEUF 0.864 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.70
- Residue 161
- 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-ala161 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown