PPP2R5D p.Pro201=
c.603C>A · rs771264774 · VCV1982287
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.046 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.35 | GERP -1.7, phastCons 0.1 |
| Overall | ||
| CADD | 7.591 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,022 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000186%
3/1,614,154 alleles · very rare
exomes 3/1,461,884 · genomes 0/152,270 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 30,011 |
| South Asian | 0.0011% | 91,082 |
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.Pro201=
- Coding
- c.603C>A
- MANE Select
- NM_006245
- dbSNP
- rs771264774
- Type
- single nucleotide variant
- Location
- chr6:43007276 (GRCh38)
- Gene constraint
- LOEUF 0.234 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 80.69 · 2 PDB
- Residue 201
- a UniProt-annotated variant site (in hjs1; likely pathogenic; decreases binding to subunit ppp2ca; decreases binding to subunit ppp2r1a); an α-helix
Similar variants
- PPP2R5D p.Pro201Arg Pathogenic ★★ same residue
- PPP2R5D p.Pro201Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown