UBA1 p.Phe320=
c.960C>T · rs1556788530 · VCV517807
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000112%, nfe)
Conditions
1
Inborn genetic diseases
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 -10 | GERP -3.4 |
| Overall | ||
| CADD | 0.004 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000112%
European (non-Finnish) · 1/894,946 alleles
Overall
8.26e-05%
1/1,210,761 alleles · very rare
exomes 1/1,096,904 · genomes 0/113,857 · 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
- UBA1
- Protein
- p.Phe320=
- Coding
- c.960C>T
- MANE Select
- NM_003334
- dbSNP
- rs1556788530
- Type
- single nucleotide variant
- Location
- chrX:47202408 (GRCh38)
- Structure
- AlphaFold pLDDT 92.71 · 11 PDB
- Residue 320
- the '2 approximate repeats' region; an α-helix
Similar variants
- UBA1 p.Ala391Thr Uncertain significance ★★ ⚠ same condition
- UBA1 p.Arg288His Uncertain significance ★★ ⚠ same condition
- UBA1 p.Arg450His Uncertain significance ★★ ⚠ same condition
- UBA1 p.Arg699Gln Uncertain significance ★★ ⚠ same condition
- UBA1 p.Arg917Leu Uncertain significance ★★ ⚠ same condition
- UBA1 p.Asn351Ser Uncertain significance ★★ ⚠ same condition
- UBA1 p.Asn757Ser Uncertain significance ★★ ⚠ same condition
- UBA1 p.Gln338Arg Uncertain significance ★★ ⚠ same condition
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/uba1-p-phe320 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown