VAPB p.Ser58fs
c.172del · rs2516033050 · VCV1810152
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 6 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 4 | GERP 2.8, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- VAPB
- Protein
- p.Ser58fs
- Coding
- c.172del
- MANE Select
- NM_004738
- dbSNP
- rs2516033050
- Type
- Deletion
- Location
- chr20:58418324 (GRCh38)
- Gene constraint
- LOEUF 0.699 · pLI 0.52 (gnomAD)
- Structure
- AlphaFold pLDDT 77.45 · 3 PDB
- Residue 58
- a β-strand; the msp domain
Similar variants
- VAPB p.Ser58= Likely benign ★★ same residue
- VAPB p.Asn39fs Uncertain significance ★★ same type
- VAPB p.Cys53fs Uncertain significance ★ same type
- VAPB c.315+220del Benign ★ same type
- VAPB c.316-3del Benign ★ same type
- VAPB c.396+21_396+23del Likely benign ★ same type
- VAPB c.-149del Likely benign ★ same type
- VAPB c.*200_*201del Benign ★ 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/vapb-p-ser58fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown