Is DBT p.Ile98Met (c.294C>G) pathogenic?

DBT p.Ile98Met (c.294C>G) is classified Pathogenic in DBT (ClinVar, No assertion criteria, 1 submitter; last evaluated 1998-01-01). AlphaMissense: likely pathogenic (0.6504); Absent from gnomAD v4.1; Associated with maple syrup urine disease type 2.

What condition is associated with DBT p.Ile98Met (c.294C>G)?

DBT p.Ile98Met (c.294C>G) is associated with maple syrup urine disease type 2 (ClinVar).

How common is DBT p.Ile98Met (c.294C>G) in the general population?

DBT p.Ile98Met (c.294C>G) is absent from gnomAD v4.1 (gnomAD).

How is Maple syrup urine disease inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about DBT p.Ile98Met (c.294C>G)?

AlphaMissense predicts likely pathogenic (score 0.6504) — an in-silico prediction, not a clinical call.

DBT p.Ile98Met

c.294C>G · rs121965001 · VCV11948

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6504 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

maple syrup urine disease type 2

Computational evidence

Protein change
AlphaMissense	0.6504	likely pathogenic ✓ concordant with ClinVar
REVEL	0.362	indeterminate
SaProt	LLR -10.98	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.3	GERP 2.5, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 54 kb · p 0.0036 · regional, not allelic
Overall
CADD	25.1	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: DBT
Protein: p.Ile98Met
Coding: c.294C>G
MANE Select: NM_001918
dbSNP: rs121965001
Type: single nucleotide variant
Location: chr1:100230872 (GRCh38)
Gene constraint: LOEUF 1.255 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 78.71 · 5 PDB
Residue 98: the lipoyl-binding domain; a UniProt-annotated variant site (in msud2)

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

Disease context

maple syrup urine disease type 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Maple syrup urine disease (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Worldwide)

Similar variants

DBT p.Ile98Val Uncertain significance ★★ ⚠ same residue
DBT c.1018-550A>G Pathogenic/Likely pathogenic ★★ same condition
DBT c.1281+1G>A Pathogenic/Likely pathogenic ★★ same condition
DBT c.51+1G>T Pathogenic/Likely pathogenic ★★ same condition
DBT c.773-2A>G Pathogenic ★★ same condition
DBT p.Arg169Ter Pathogenic/Likely pathogenic ★★ same condition
DBT p.Arg301Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
DBT p.Arg376Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition

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/dbt-p-ile98met (accessed [today's date]).

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