DLST p.Val134=
c.402C>T · VCV3631741
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.22 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.72 | GERP -3.5 |
| Overall | ||
| CADD | 7.942 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,892 alleles
Filtering AF
0.000763%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000605%
Overall
0.00112%
18/1,613,938 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,892 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
| European (non-Finnish) | 0.00127% | 78,666 |
| South Asian | 0.0011% | 91,074 |
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
- DLST
- Protein
- p.Val134=
- Coding
- c.402C>T
- MANE Select
- NM_001933
- Type
- single nucleotide variant
- Location
- chr14:74891127 (GRCh38)
- Gene constraint
- LOEUF 0.489 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 77.40 · 2 PDB
- Residue 134
- the lipoyl-binding domain
Similar variants
- DLST p.Ala264Val Uncertain significance ★★ ⚠ same type
- DLST p.Arg437Cys Uncertain significance ★★ same type
- DLST p.Arg4Gln Uncertain significance ★★ ⚠ same type
- DLST p.Arg6Ser Uncertain significance ★★ ⚠ same type
- DLST p.Asn44Ser Uncertain significance ★★ ⚠ same type
- DLST p.Asn51Asp Uncertain significance ★★ ⚠ same type
- DLST p.Asp304Gly Uncertain significance ★★ ⚠ same type
- DLST p.Gly216Val 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/dlst-p-val134 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown