RAB39B p.Asp90=
c.270C>T · rs370262046 · VCV1695328
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0088%, 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 9.9 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 13.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0088%
African / African-American · 5/56,850 alleles
Filtering AF
0.0034%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00216%
Overall
0.000414%
5/1,207,909 alleles · very rare
exomes 2/1,096,685 · genomes 3/111,224 · 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
- RAB39B
- Protein
- p.Asp90=
- Coding
- c.270C>T
- MANE Select
- NM_171998
- dbSNP
- rs370262046
- Type
- single nucleotide variant
- Location
- chrX:155261175 (GRCh38)
- Structure
- AlphaFold pLDDT 88.67 · 1 PDB
- Residue 90
- a β-strand
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-asp90 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown