UROD p.Val90del
c.264TGT[1] · rs1463137951 · VCV2733888
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00801%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 20.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,924 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.00062%
10/1,614,100 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00801% | 12,487 |
| East Asian | 0.00223% | 44,906 |
| Admixed American | 0.00167% | 60,000 |
| European (non-Finnish) | 0.000169% | 590,030 |
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.Val90del
- Coding
- c.264TGT[1]
- MANE Select
- NM_000374
- dbSNP
- rs1463137951
- Type
- Microsatellite
- Location
- chr1:45013341 (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.Val90= Likely benign ★ same residue
- UROD p.Ile83del Uncertain significance ★★ same type
- UROD c.636+10GA[5] Likely benign ★ 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-val90del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown