Is IDH2 p.Asp264= (c.792C>T) pathogenic?

IDH2 p.Asp264= (c.792C>T) is classified Likely benign in IDH2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-24). Very rare (popmax 0.00133%, afr).

How common is IDH2 p.Asp264= (c.792C>T) in the general population?

IDH2 p.Asp264= (c.792C>T) is very rare (popmax 0.00133%, afr) (gnomAD).

IDH2 p.Asp264=

c.792C>T · VCV4926612

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

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 5.9	GERP -0.28, phastCons 1
Overall
CADD	9.922	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/75,048 alleles

Overall 6.2e-05% 1/1,614,204 alleles · very rare exomes 1/1,461,866 · genomes 0/152,338 · 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: IDH2
Protein: p.Asp264=
Coding: c.792C>T
MANE Select: NM_002168
Type: single nucleotide variant
Location: chr15:90087462 (GRCh38)
Gene constraint: LOEUF 0.502 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 92.07 · 13 PDB
Residue 264: an α-helix

Full IDH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

IDH2 p.Arg140Gln Pathogenic/Likely pathogenic ★★ same type
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-asp264 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown