IDH1 p.Pro384Arg
c.1151C>G · VCV3285235
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely benign
0.1488 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/2 damaging
AlphaMissense, SaProt · REVEL indeterminate
Computational evidence
| Protein change | ||
| AlphaMissense | 0.1488 | likely benign |
|---|---|---|
| REVEL | 0.293 | indeterminate |
| SaProt | LLR -10.32 | damaging |
| ⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 9.8 | GERP 1.5, phastCons 1 |
| Regional constraint | o/e 0.82 | unconstrained · MANE · 14 kb · p 3e-05 · regional, not allelic |
| Overall | ||
| CADD | 24.2 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
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
- IDH1
- Protein
- p.Pro384Arg
- Coding
- c.1151C>G
- MANE Select
- NM_005896
- Type
- single nucleotide variant
- Location
- chr2:208239074 (GRCh38)
- Gene constraint
- LOEUF 0.829 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.00 · 64 PDB
- Residue 384
- an α-helix
Similar variants
- IDH1 p.Pro384= Likely benign ★ same residue
- IDH1 p.Arg132Cys Pathogenic/Likely pathogenic ★★ same type
- IDH1 p.Arg132His Pathogenic/Likely pathogenic ★★ same type
- IDH1 p.Arg317His Uncertain significance ★★ ⚠ same type
- IDH1 p.Asp38Asn Uncertain significance ★★ ⚠ same type
- IDH1 p.Met318Thr Uncertain significance ★★ ⚠ same type
- IDH1 c.122+105G>A Benign ★★ same type
- IDH1 c.123-4C>T Benign ★★ 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/idh1-p-pro384arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown