UBE2A p.Ala5=
c.15T>C · rs2520613818 · VCV2694217
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000112%, 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 0.43 | GERP -4.2, phastCons 1 |
| Overall | ||
| CADD | 13.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000112%
European (non-Finnish) · 1/889,542 alleles
Overall
8.35e-05%
1/1,198,300 alleles · very rare
exomes 1/1,084,289 · genomes 0/114,011 · 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
- UBE2A
- Protein
- p.Ala5=
- Coding
- c.15T>C
- MANE Select
- NM_003336
- dbSNP
- rs2520613818
- Type
- single nucleotide variant
- Location
- chrX:119574726 (GRCh38)
- Structure
- AlphaFold pLDDT 94.25 · 5 PDB
- Residue 5
- the ubc core domain; an α-helix
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-ala5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown