PPM1B p.Ser132=
c.396A>T · rs375264230 · VCV750311
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00136%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.64 | GERP -5.4 |
| Overall | ||
| CADD | 3.809 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00136%
European (non-Finnish) · 16/1,180,036 alleles
Filtering AF
0.000803%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00065%
Overall
0.000991%
16/1,614,048 alleles · very rare
exomes 9/1,461,880 · genomes 7/152,168 · joint denominator
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
- PPM1B
- Protein
- p.Ser132=
- Coding
- c.396A>T
- MANE Select
- NM_002706
- dbSNP
- rs375264230
- Type
- single nucleotide variant
- Location
- chr2:44201595 (GRCh38)
- Gene constraint
- LOEUF 0.639 · pLI 0.21 (gnomAD)
- Structure
- AlphaFold pLDDT 85.52 · 1 PDB
- Residue 132
- the ppm-type phosphatase domain
Similar variants
- PPM1B p.Gln161Glu Uncertain significance ★★ ⚠ same type
- PPM1B c.1134+10A>G Benign ★★ same type
- PPM1B p.Ala201Thr Uncertain significance ★ ⚠ same type
- PPM1B p.Ala298Val Uncertain significance ★ ⚠ same type
- PPM1B p.Ala305Val Uncertain significance ★ ⚠ same type
- PPM1B p.Ala344Thr Uncertain significance ★ ⚠ same type
- PPM1B p.Ala395Thr Uncertain significance ★ ⚠ same type
- PPM1B p.Ala433Pro 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/ppm1b-p-ser132 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown