UMPS p.Ser476=
c.1428T>C · VCV4963953
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00924%, nfe)
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 0.49 | GERP 2.7, phastCons 1 |
| Overall | ||
| CADD | 8.963 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00924%
European (non-Finnish) · 109/1,179,974 alleles
Filtering AF
0.00782%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00727%
Overall
0.00675%
109/1,614,084 alleles · very rare
exomes 109/1,461,796 · genomes 0/152,288 · 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
- UMPS
- Protein
- p.Ser476=
- Coding
- c.1428T>C
- MANE Select
- NM_000373
- Type
- single nucleotide variant
- Location
- chr3:124744069 (GRCh38)
- Gene constraint
- LOEUF 0.735 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.36 · 125 PDB
- Residue 476
- the 'ompdecase' region; an α-helix
Similar variants
- UMPS c.*37C>T Uncertain significance ★★ same type
- UMPS p.Ala386= Uncertain significance ★★ same type
- UMPS p.Ala386Val Uncertain significance ★★ ⚠ same type
- UMPS p.Ala4Pro Uncertain significance ★★ ⚠ same type
- UMPS p.Arg230Cys Uncertain significance ★★ same type
- UMPS p.Arg313Trp Uncertain significance ★★ ⚠ same type
- UMPS p.Arg363Gln Uncertain significance ★★ ⚠ same type
- UMPS p.Asp271His Uncertain significance ★★ ⚠ 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/umps-p-ser476 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown