UBA7 p.Val438=
c.1314G>A · rs141890605 · VCV3055621
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.428%, afr)
Conditions
1
UBA7-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.23 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.12 | GERP -2.1, phastCons 0.93 |
| Overall | ||
| CADD | 15.52 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.428%
African / African-American · 321/75,038 alleles
Filtering AF
0.389%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.374%
Overall
0.0222%
358/1,614,084 alleles · rare
exomes 210/1,461,782 · genomes 148/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.428% | 234 |
| Middle Eastern | 0.0825% | 1,212 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,472 |
| Admixed American | 0.0183% | 5,456 |
| European (non-Finnish) | 0.000254% | 393,321 |
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
- UBA7
- Protein
- p.Val438=
- Coding
- c.1314G>A
- MANE Select
- NM_003335
- dbSNP
- rs141890605
- Type
- single nucleotide variant
- Location
- chr3:49810670 (GRCh38)
- Gene constraint
- LOEUF 0.883 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.36 · 6 PDB
- Residue 438
- the '2 approximate repeats' region; a β-strand; a UniProt-annotated variant site (found in a small consanguineous family with learning disability; uncertain significance)
Disease context
UBA7-related disorder
Similar variants
- UBA7 p.Gln433Ter Uncertain significance ★ same condition
- UBA7 c.2910-9C>T Likely benign same condition
- UBA7 p.Ala391= Likely benign same condition
- UBA7 p.Ala88= Benign same condition
- UBA7 p.Arg414His Likely benign ⚠ same condition
- UBA7 p.Arg839Pro Benign ⚠ same condition
- UBA7 p.Leu512= Likely benign same condition
- UBA7 p.Thr151= Likely benign 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/uba7-p-val438 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown