DVL3 p.Ala93=
c.279T>G · rs779764964 · VCV744744
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, mid)
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 · T>A here scores Δ0.23 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP 0.69 |
| Overall | ||
| CADD | 6.282 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,084 alleles
Filtering AF
0.00724%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00676%
Overall
0.00743%
120/1,614,046 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,042 |
| European (non-Finnish) | 0.00864% | 11,569 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,497 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,801 |
| South Asian | 0.00659% | 15,182 |
| Admixed American | 0.00333% | 29,997 |
| African / African-American | 0.00133% | 74,930 |
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
- DVL3
- Protein
- p.Ala93=
- Coding
- c.279T>G
- MANE Select
- NM_004423
- dbSNP
- rs779764964
- Type
- single nucleotide variant
- Location
- chr3:184164314 (GRCh38)
- Gene constraint
- LOEUF 0.536 · pLI 0.70 (gnomAD)
- Structure
- AlphaFold pLDDT 59.50 · 9 PDB
- Residue 93
- the 'disordered' region
Similar variants
- DVL3 p.Ala93Thr Uncertain significance ★ ⚠ same residue
- DVL3 c.1715-1G>A Pathogenic/Likely pathogenic ★★ same type
- DVL3 p.Ala359Thr Uncertain significance ★★ ⚠ same type
- DVL3 p.Ala565Val Uncertain significance ★★ ⚠ same type
- DVL3 p.Ala593Val Uncertain significance ★★ ⚠ same type
- DVL3 p.Ala629Thr Uncertain significance ★★ ⚠ same type
- DVL3 p.Arg145Gln Uncertain significance ★★ ⚠ same type
- DVL3 p.Arg157Gln 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/dvl3-p-ala93 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown