DVL3 p.Ser233=
c.699G>A · rs114642851 · VCV1548135
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0516%, nfe)
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 Δ0.63 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -3.4 |
| Overall | ||
| CADD | 1.982 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0516%
European (non-Finnish) · 609/1,179,976 alleles
Filtering AF
0.0482%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0468%
Overall
0.0419%
676/1,613,984 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0516% | 1,938 |
| Remaining individualsnot grpmax-eligible | 0.0512% | 1,953 |
| Admixed American | 0.0283% | 3,529 |
| Middle Eastern | 0.0165% | 6,060 |
| African / African-American | 0.016% | 6,251 |
| South Asian | 0.00329% | 30,358 |
| East Asian | 0.00223% | 44,862 |
| Finnishnot grpmax-eligible | 0.00156% | 63,988 |
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.Ser233=
- Coding
- c.699G>A
- MANE Select
- NM_004423
- dbSNP
- rs114642851
- Type
- single nucleotide variant
- Location
- chr3:184165427 (GRCh38)
- Gene constraint
- LOEUF 0.536 · pLI 0.70 (gnomAD)
- Structure
- AlphaFold pLDDT 59.50 · 9 PDB
- Residue 233
- the 'disordered' region
Similar variants
- 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
- DVL3 p.Arg166Trp 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-ser233 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown