DARS1 p.Val360=
c.1080C>T · rs754076040 · VCV2651382
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00894%, 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 · G>T here scores Δ0.27 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.18 | GERP -3.4, phastCons 0.005 |
| Overall | ||
| CADD | 4.711 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00894%
East Asian · 4/44,754 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.00104%
15/1,445,638 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00894% | 11,188 |
| Remaining individualsnot grpmax-eligible | 0.00323% | 30,970 |
| European (non-Finnish) | 0.000772% | 129,511 |
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
- DARS1
- Protein
- p.Val360=
- Coding
- c.1080C>T
- MANE Select
- NM_001349
- dbSNP
- rs754076040
- Type
- single nucleotide variant
- Location
- chr2:135916252 (GRCh38)
- Gene constraint
- LOEUF 1.023 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.69 · 3 PDB
Similar variants
- DARS1 p.Val360Ile Likely benign ★ ⚠ same residue
- DARS1 p.Ala429Thr Uncertain significance ★★ ⚠ same type
- DARS1 p.Arg197Cys Uncertain significance ★★ ⚠ same type
- DARS1 p.Arg498Gln Uncertain significance ★★ ⚠ same type
- DARS1 p.Arg63His Uncertain significance ★★ ⚠ same type
- DARS1 p.Arg81His Uncertain significance ★★ ⚠ same type
- DARS1 p.Asn233Ser Uncertain significance ★★ ⚠ same type
- DARS1 p.Glu357Lys 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/dars1-p-val360 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown