UROD p.Val90=
c.270A>G · VCV4972129
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0637%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.04 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.24 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 2 | GERP -0.66, phastCons 1 |
| Overall | ||
| CADD | 8.71 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0637%
South Asian · 58/91,088 alleles
Filtering AF
0.0505%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0458%
Overall
0.00471%
76/1,614,110 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0637% | 1,570 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,500 |
| European (non-Finnish) | 0.00102% | 98,336 |
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
- UROD
- Protein
- p.Val90=
- Coding
- c.270A>G
- MANE Select
- NM_000374
- Type
- single nucleotide variant
- Location
- chr1:45013348 (GRCh38)
- Gene constraint
- LOEUF 0.914 · pLI <0.01 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 96.90 · 19 PDB
- Residue 90
- an α-helix
Similar variants
- UROD p.Val90del Likely pathogenic ★ same residue
- UROD c.636+1G>C Pathogenic ★★ same type
- UROD p.Ala80Ser Pathogenic/Likely pathogenic ★★ ⚠ same type
- UROD p.Arg142Ter Pathogenic/Likely pathogenic ★★ same type
- UROD p.Arg144Ter Pathogenic ★★ same type
- UROD p.Arg193Pro Likely pathogenic ★★ same type
- UROD p.Gln116Ter Pathogenic ★★ same type
- UROD p.Gln206Ter Pathogenic/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/urod-p-val90 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown