DLST p.Arg10=
c.30G>C · VCV4682045
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00173%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.057 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.7 | GERP -0.5, phastCons 1 |
| Overall | ||
| CADD | 12.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00173%
Admixed American · 1/57,682 alleles
Filtering AF
2.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000254%
4/1,573,280 alleles · very rare
exomes 2/1,421,064 · genomes 2/152,216 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00173% | 57,682 |
| Remaining individualsnot grpmax-eligible | 0.00164% | 61,158 |
| European (non-Finnish) | 0.000171% | 583,887 |
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.Arg10=
- Coding
- c.30G>C
- MANE Select
- NM_001933
- Type
- single nucleotide variant
- Location
- chr14:74881983 (GRCh38)
- Gene constraint
- LOEUF 0.489 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 77.40 · 2 PDB
Similar variants
- DLST p.Arg10Trp 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-arg10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown