DVL3 p.Ser596=
c.1788C>T · rs367640106 · VCV734120
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.126%, nfe)
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 -2 | GERP -1 |
| Overall | ||
| CADD | 2.094 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.126%
European (non-Finnish) · 1,477/1,175,972 alleles
Filtering AF
0.12%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.118%
Overall
0.0987%
1,584/1,604,752 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.126% | 796 |
| Remaining individualsnot grpmax-eligible | 0.0854% | 1,170 |
| Admixed American | 0.0324% | 3,091 |
| African / African-American | 0.028% | 3,567 |
| Finnishnot grpmax-eligible | 0.0224% | 4,457 |
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.Ser596=
- Coding
- c.1788C>T
- MANE Select
- NM_004423
- dbSNP
- rs367640106
- Type
- single nucleotide variant
- Location
- chr3:184170392 (GRCh38)
- Gene constraint
- LOEUF 0.536 · pLI 0.70 (gnomAD)
- Structure
- AlphaFold pLDDT 59.50 · 9 PDB
- Residue 596
- the 'disordered' region
Similar variants
- DVL3 p.Ser596Cys 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-ser596 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown