Is DBT p.Cys38Tyr (c.113G>A) pathogenic?

DBT p.Cys38Tyr (c.113G>A) is classified Uncertain significance in DBT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-20). AlphaMissense: likely benign (0.0731); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DBT p.Cys38Tyr (c.113G>A)?

DBT p.Cys38Tyr (c.113G>A) is associated with Inborn genetic diseases (ClinVar).

How common is DBT p.Cys38Tyr (c.113G>A) in the general population?

DBT p.Cys38Tyr (c.113G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DBT p.Cys38Tyr (c.113G>A)?

AlphaMissense predicts likely benign (score 0.0731) — an in-silico prediction, not a clinical call.

DBT p.Cys38Tyr

c.113G>A · VCV4237761

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0731 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,609,150)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0731	likely benign
REVEL	0.099	moderately benign-leaning
SaProt	LLR -6.74	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.39	GERP 0.55, phastCons 0.96
Regional constraint	o/e 0.88	unconstrained · MANE · 54 kb · p 0.0036 · regional, not allelic
Overall
CADD	15.34	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,609,150). 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: DBT
Protein: p.Cys38Tyr
Coding: c.113G>A
MANE Select: NM_001918
Type: single nucleotide variant
Location: chr1:100240823 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DBT p.Cys38fs Pathogenic/Likely pathogenic ★★ same residue
DBT c.1281+5A>G Uncertain significance ★★ same condition
DBT p.Arg61Cys Uncertain significance ★★ ⚠ same condition
DBT p.Cys279Phe Uncertain significance ★★ ⚠ same condition
DBT p.Thr171Ile Uncertain significance ★★ ⚠ same condition
DBT p.Thr407Ala Uncertain significance ★★ ⚠ same condition
DBT p.Asn326= Likely benign ★★ same condition
DBT p.Ala458Val Uncertain significance ★ ⚠ 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-cys38tyr (accessed [today's date]).

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