IDH2 p.Pro87=
c.261A>C · rs2505796833 · VCV3034645
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
IDH2-related disorder
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 -2.7 | GERP -3.1 |
| Overall | ||
| CADD | 7.509 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- IDH2
- Protein
- p.Pro87=
- Coding
- c.261A>C
- MANE Select
- NM_002168
- dbSNP
- rs2505796833
- Type
- single nucleotide variant
- Location
- chr15:90090591 (GRCh38)
- Gene constraint
- LOEUF 0.502 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 92.07 · 13 PDB
- Residue 87
- an α-helix
Disease context
IDH2-related disorder
Similar variants
- IDH2 p.Arg140Gln Pathogenic/Likely pathogenic ★★ same condition
- IDH2 c.1271+3G>A Uncertain significance ★★ same type
- IDH2 c.534+2T>C Uncertain significance ★★ same type
- IDH2 p.Ala214Thr Uncertain significance ★★ ⚠ same type
- IDH2 p.Arg362Trp Uncertain significance ★★ ⚠ same type
- IDH2 p.Arg393Lys Uncertain significance ★★ ⚠ same type
- IDH2 p.Arg60His Uncertain significance ★★ ⚠ same type
- IDH2 p.Arg89Cys 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/idh2-p-pro87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown