RAB39B p.Phe164=
c.492C>T · rs782453421 · VCV211977
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0113%, 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 9.7 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 12.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0113%
European (non-Finnish) · 101/895,121 alleles
Filtering AF
0.00944%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0088%
Overall
0.00843%
102/1,209,549 alleles · ultra-rare
exomes 99/1,098,114 · genomes 3/111,435 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0113% | 8,863 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,584 |
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
- RAB39B
- Protein
- p.Phe164=
- Coding
- c.492C>T
- MANE Select
- NM_171998
- dbSNP
- rs782453421
- Type
- single nucleotide variant
- Location
- chrX:155260953 (GRCh38)
- Structure
- AlphaFold pLDDT 88.67 · 1 PDB
- Residue 164
- an α-helix
Similar variants
- RAB39B p.Gly178Arg Uncertain significance ★★ ⚠ same type
- RAB39B p.Ser96Phe Uncertain significance ★★ ⚠ same type
- RAB39B p.Thr129Ile Uncertain significance ★★ ⚠ same type
- RAB39B c.*1347C>T Benign ★★ same type
- RAB39B c.*1656= Benign ★★ same type
- RAB39B p.Gly31= Benign/Likely benign ★★ same type
- RAB39B p.Gly42= Benign/Likely benign ★★ same type
- RAB39B p.His110= Benign/Likely 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/rab39b-p-phe164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown