DVL1 p.Ser177=
c.531C>T · rs148933527 · VCV779999
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.17%, 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 -2.5 | GERP -5 |
| Overall | ||
| CADD | 0.663 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.17%
European (non-Finnish) · 2,002/1,178,068 alleles
Filtering AF
0.164%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.161%
Overall
0.136%
2,191/1,609,644 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.17% | 588 |
| Remaining individualsnot grpmax-eligible | 0.106% | 945 |
| Admixed American | 0.0636% | 1,573 |
| South Asian | 0.053% | 1,887 |
| African / African-American | 0.028% | 3,573 |
| Finnishnot grpmax-eligible | 0.0256% | 3,910 |
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.Ser177=
- Coding
- c.531C>T
- MANE Select
- NM_001330311
- dbSNP
- rs148933527
- Type
- single nucleotide variant
- Location
- chr1:1341741 (GRCh38)
- Gene constraint
- LOEUF 1.046 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.70 · 3 PDB
- Residue 177
- the 'disordered' region
Similar variants
- 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
- DVL1 p.Arg116Gln Uncertain significance ★★ ⚠ same type
- DVL1 p.Arg128Cys 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-ser177 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown