UBE2A p.Ala22=
c.66C>T · rs766410122 · VCV2703157
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00348%, 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 -5.8 | GERP -3.9 |
| Overall | ||
| CADD | 7.145 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00348%
African / African-American · 2/57,494 alleles
Filtering AF
0.000577%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000216%
Overall
0.000826%
10/1,210,732 alleles · very rare
exomes 7/1,098,030 · genomes 3/112,702 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00348% | 28,747 |
| South Asian | 0.00176% | 56,921 |
| European (non-Finnish) | 0.000782% | 127,881 |
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.Ala22=
- Coding
- c.66C>T
- MANE Select
- NM_003336
- dbSNP
- rs766410122
- Type
- single nucleotide variant
- Location
- chrX:119574922 (GRCh38)
- Structure
- AlphaFold pLDDT 94.25 · 5 PDB
- Residue 22
- the ubc core domain
Similar variants
- UBE2A p.Arg135Trp Uncertain significance ★★ ⚠ same type
- UBE2A p.Arg95Cys 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
- UBE2A c.125+1G>T Likely pathogenic ★ 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-ala22 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown