VPS33B p.Phe298=
c.894T>C · rs2040592605 · VCV3061668
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
VPS33B-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.58 | GERP -0.45 |
| Overall | ||
| CADD | 8.728 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- VPS33B
- Protein
- p.Phe298=
- Coding
- c.894T>C
- MANE Select
- NM_018668
- dbSNP
- rs2040592605
- Type
- single nucleotide variant
- Location
- chr15:91006018 (GRCh38)
- Gene constraint
- LOEUF 0.971 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.82
Disease context
VPS33B-related disorder
Similar variants
- VPS33B p.Phe298fs Likely pathogenic same residue
- VPS33B p.Arg93Ter Pathogenic/Likely pathogenic ★★ same condition
- VPS33B p.Ala606Thr Uncertain significance ★★ ⚠ same condition
- VPS33B p.Arg109His Uncertain significance ★★ ⚠ same condition
- VPS33B p.Thr451Ala Uncertain significance ★★ ⚠ same condition
- VPS33B c.357+1G>A Likely pathogenic ★ same condition
- VPS33B c.1480-1G>A Likely pathogenic same condition
- VPS33B p.Asp319Gly Uncertain significance ⚠ same condition
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/vps33b-p-phe298 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown