Is DBT p.Ala458Ser (c.1372G>T) pathogenic?

DBT p.Ala458Ser (c.1372G>T) is classified Uncertain significance in DBT (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-25). AlphaMissense: ambiguous (0.3569); Very rare (popmax 0.00128%, nfe); Associated with maple syrup urine disease.

What condition is associated with DBT p.Ala458Ser (c.1372G>T)?

DBT p.Ala458Ser (c.1372G>T) is associated with maple syrup urine disease (ClinVar).

How common is DBT p.Ala458Ser (c.1372G>T) in the general population?

DBT p.Ala458Ser (c.1372G>T) is very rare (popmax 0.00128%, nfe) (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.Ala458Ser (c.1372G>T)?

AlphaMissense predicts ambiguous (score 0.3569) — an in-silico prediction, not a clinical call.

DBT p.Ala458Ser

c.1372G>T · rs763881630 · VCV2418660

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3569 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00128%, nfe)

Conditions

maple syrup urine disease

Computational evidence

Protein change
AlphaMissense	0.3569	ambiguous
REVEL	0.54	indeterminate
SaProt	LLR -11.96	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.1, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 54 kb · p 0.0036 · regional, not allelic
Overall
CADD	23.7	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

Grpmax group 0.00128% European (non-Finnish) · 15/1,173,392 alleles

Filtering AF 0.000768% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000609%

Overall 0.000939% 15/1,597,294 alleles · very rare

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: DBT
Protein: p.Ala458Ser
Coding: c.1372G>T
MANE Select: NM_001918
dbSNP: rs763881630
Type: single nucleotide variant
Location: chr1:100196332 (GRCh38)
Gene constraint: LOEUF 1.255 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 78.71 · 5 PDB

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

Disease context

maple syrup urine disease — 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.Ala458Val 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.1281+1G>T Pathogenic/Likely pathogenic ★★ same condition
DBT c.51+1G>T Pathogenic/Likely pathogenic ★★ same condition
DBT c.52-1G>A Pathogenic/Likely pathogenic ★★ same condition
DBT p.Arg291Ter Pathogenic ★★ same condition
DBT p.Arg301Cys 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-ala458ser (accessed [today's date]).

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