Is IDO2 p.Val95Ala (c.284T>C) pathogenic?

IDO2 p.Val95Ala (c.284T>C) is classified Uncertain significance in IDO2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-26). AlphaMissense: likely benign (0.3143); Absent from gnomAD v4.1.

How common is IDO2 p.Val95Ala (c.284T>C) in the general population?

IDO2 p.Val95Ala (c.284T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about IDO2 p.Val95Ala (c.284T>C)?

AlphaMissense predicts likely benign (score 0.3143) — an in-silico prediction, not a clinical call.

IDO2 p.Val95Ala

c.284T>C · rs1808304261 · VCV2291244

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3143 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,599,996)

Computational evidence

Protein change
AlphaMissense	0.3143	likely benign
REVEL	0.349	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.7, phastCons 1
Regional constraint	o/e 1.11	unconstrained · MANE · 66 kb · p 0.018 · regional, not allelic
Overall
CADD	25.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM V108A vs ClinVar V95A) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,599,996). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: IDO2
Protein: p.Val95Ala
Coding: c.284T>C
MANE Select: NM_194294
dbSNP: rs1808304261
Type: single nucleotide variant
Location: chr8:39979155 (GRCh38)
Gene constraint: LOEUF 1.256 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.25 · 11 PDB

Full IDO2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

IDO2 p.Arg235Trp Benign ★★ same type
IDO2 p.Ile127Val Benign ★★ same type
IDO2 p.Tyr346Ter Benign ★★ same type
IDO2 p.Ala172Ser Uncertain significance ★ ⚠ same type
IDO2 p.Ala276Ser Uncertain significance ★ ⚠ same type
IDO2 p.Ala276Val Uncertain significance ★ ⚠ same type
IDO2 p.Ala339Thr Uncertain significance ★ ⚠ same type
IDO2 p.Ala341Gly 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/ido2-p-val95ala (accessed [today's date]).

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