DVL1 p.Ser575=
c.1725C>T · rs370626248 · VCV1154165
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0028%, 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 7.4 | GERP -0.73, phastCons 1 |
| Overall | ||
| CADD | 7.619 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0028%
African / African-American · 2/71,398 alleles
Filtering AF
0.000465%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000174%
Overall
0.00131%
2/152,242 alleles · very rare
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.Ser575=
- Coding
- c.1725C>T
- MANE Select
- NM_001330311
- dbSNP
- rs370626248
- Type
- single nucleotide variant
- Location
- chr1:1336505 (GRCh38)
- Gene constraint
- LOEUF 1.046 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.70 · 3 PDB
- Residue 575
- 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-ser575 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown