PPP2R5D p.Pro64=
c.192G>A · rs765929202 · VCV1196012
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00935%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.44 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.6 | GERP -3.7 |
| Overall | ||
| CADD | 3.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00935%
African / African-American · 7/74,866 alleles
Filtering AF
0.00438%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00309%
Overall
0.00316%
51/1,613,638 alleles · very rare
exomes 45/1,461,666 · genomes 6/151,972 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00935% | 10,695 |
| East Asian | 0.00446% | 22,435 |
| European (non-Finnish) | 0.00331% | 30,254 |
| South Asian | 0.00329% | 30,353 |
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
- PPP2R5D
- Protein
- p.Pro64=
- Coding
- c.192G>A
- MANE Select
- NM_006245
- dbSNP
- rs765929202
- Type
- single nucleotide variant
- Location
- chr6:43006549 (GRCh38)
- Gene constraint
- LOEUF 0.234 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 80.69 · 2 PDB
- Residue 64
- an α-helix; the 'disordered' region
Similar variants
- PPP2R5D p.Arg253Pro Pathogenic/Likely pathogenic ★★ same type
- PPP2R5D p.Asp251Ala Pathogenic/Likely pathogenic ★★ same type
- PPP2R5D p.Asp251His Pathogenic/Likely pathogenic ★★ same type
- PPP2R5D p.Glu197Lys Pathogenic/Likely pathogenic ★★ same type
- PPP2R5D p.Glu200Lys Pathogenic/Likely pathogenic ★★ same type
- PPP2R5D p.Glu420Lys Pathogenic ★★ same type
- PPP2R5D p.His209Tyr Pathogenic/Likely pathogenic ★★ same type
- PPP2R5D p.Pro201Arg Pathogenic ★★ 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/ppp2r5d-p-pro64 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown