UROD p.Phe108=
c.324C>T · rs2522917340 · VCV1900530
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.361 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.007 | GERP -0.6, phastCons 0.72 |
| Overall | ||
| CADD | 7.934 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,022 alleles
Overall
6.84e-05%
1/1,461,860 alleles · very rare
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.Phe108=
- Coding
- c.324C>T
- MANE Select
- NM_000374
- dbSNP
- rs2522917340
- Type
- single nucleotide variant
- Location
- chr1:45013641 (GRCh38)
- Gene constraint
- LOEUF 0.914 · pLI <0.01 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 96.90 · 19 PDB
Similar variants
- 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
- UROD p.Glu314= 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-phe108 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown