DVL1 p.Val349=
c.1047C>T · rs150917044 · VCV718892
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.63%, afr)
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 0.17 | GERP -5.5, phastCons 0.83 |
| Overall | ||
| CADD | 2.236 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.63%
African / African-American · 1,218/74,948 alleles
Filtering AF
1.55%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.52%
Overall
0.0951%
1,529/1,607,284 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.63% | 62 |
| Remaining individualsnot grpmax-eligible | 0.167% | 598 |
| Admixed American | 0.126% | 796 |
| Middle Eastern | 0.0828% | 1,208 |
| European (non-Finnish) | 0.0104% | 9,644 |
| South Asian | 0.00442% | 22,633 |
| East Asian | 0.00224% | 44,658 |
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
- DVL1
- Protein
- p.Val349=
- Coding
- c.1047C>T
- MANE Select
- NM_001330311
- dbSNP
- rs150917044
- Type
- single nucleotide variant
- Location
- chr1:1339589 (GRCh38)
- Gene constraint
- LOEUF 1.046 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.70 · 3 PDB
Similar variants
- DVL1 p.Val349Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
- DVL1 p.Val349dup Uncertain significance ★ same residue
- DVL1 p.Ala125Val Uncertain significance ★★ ⚠ same type
- DVL1 p.Ala288Val Uncertain significance ★★ ⚠ same type
- DVL1 p.Ala361Thr Uncertain significance ★★ ⚠ same type
- DVL1 p.Ala368Val Uncertain significance ★★ ⚠ same type
- DVL1 p.Ala667Pro Uncertain significance ★★ ⚠ same type
- DVL1 p.Arg108Trp 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/dvl1-p-val349 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown