RAB33B p.Ser14=
c.42G>T · rs777789062 · VCV1957990
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000847%, nfe)
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 |
|---|---|---|
| Pangolin | Δ0.30 | gain · loss 0.00 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.52 | GERP -2.6, phastCons 0.71 |
| Overall | ||
| CADD | 7.993 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000847%
European (non-Finnish) · 10/1,179,974 alleles
Filtering AF
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000312%
Overall
0.00062%
10/1,614,082 alleles · very rare
exomes 10/1,461,788 · genomes 0/152,294 · joint denominator
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
- RAB33B
- Protein
- p.Ser14=
- Coding
- c.42G>T
- MANE Select
- NM_031296
- dbSNP
- rs777789062
- Type
- single nucleotide variant
- Location
- chr4:139454237 (GRCh38)
- Gene constraint
- LOEUF 0.774 · pLI 0.39 (gnomAD)
- Structure
- AlphaFold pLDDT 81.55 · 2 PDB
Similar variants
- RAB33B p.Gln134Ter Pathogenic ★★ same type
- RAB33B c.*2355T>A Uncertain significance ★★ same type
- RAB33B p.Asn139Lys Uncertain significance ★★ ⚠ same type
- RAB33B p.Asn185Asp Uncertain significance ★★ ⚠ same type
- RAB33B p.Asn43Ser Uncertain significance ★★ ⚠ same type
- RAB33B p.Ile191Met Uncertain significance ★★ ⚠ same type
- RAB33B p.Ile33Leu Uncertain significance ★★ same type
- RAB33B p.Leu49Val 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/rab33b-p-ser14 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown