DLST p.Ala171=
c.513G>A · VCV4534105
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0283%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.6 | GERP -3.8 |
| Overall | ||
| CADD | 0.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0283%
Admixed American · 17/59,978 alleles
Filtering AF
0.018%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0147%
Overall
0.00285%
46/1,614,068 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0283% | 3,528 |
| South Asian | 0.0143% | 7,005 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,835 |
| African / African-American | 0.00133% | 75,012 |
| European (non-Finnish) | 0.00102% | 98,334 |
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.Ala171=
- Coding
- c.513G>A
- MANE Select
- NM_001933
- Type
- single nucleotide variant
- Location
- chr14:74892904 (GRCh38)
- Gene constraint
- LOEUF 0.489 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 77.40 · 2 PDB
- Residue 171
- the 'disordered' region
Similar variants
- DLST p.Ala171Val Uncertain significance ★ ⚠ same residue
- 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
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-ala171 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown