UBE2A p.Arg95=
c.285T>C · rs958346644 · VCV752138
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00524%, afr)
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 -2.7 | GERP -4.2 |
| Overall | ||
| CADD | 4.172 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00524%
African / African-American · 3/57,292 alleles
Filtering AF
0.00139%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000685%
Overall
0.000331%
4/1,209,054 alleles · very rare
exomes 1/1,096,645 · genomes 3/112,409 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00524% | 19,097 |
| European (non-Finnish) | 0.000112% | 894,238 |
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
- UBE2A
- Protein
- p.Arg95=
- Coding
- c.285T>C
- MANE Select
- NM_003336
- dbSNP
- rs958346644
- Type
- single nucleotide variant
- Location
- chrX:119582631 (GRCh38)
- Structure
- AlphaFold pLDDT 94.25 · 5 PDB
- Residue 95
- the ubc core domain
Similar variants
- UBE2A p.Arg95Cys Uncertain significance ★★ ⚠ same residue
- UBE2A p.Arg95His Conflicting classifications of pathogenicity ★ ⚠ same residue
- UBE2A p.Arg135Trp Uncertain significance ★★ ⚠ same type
- UBE2A p.Ile57Val Uncertain significance ★★ ⚠ same type
- UBE2A c.125+14C>T Benign/Likely benign ★★ same type
- UBE2A c.44+8G>A Likely benign ★★ same type
- UBE2A c.45-5C>T Benign/Likely benign ★★ same type
- UBE2A p.Thr107= 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/ube2a-p-arg95 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown