UMOD p.Phe354=
c.1062C>T · rs78613713 · VCV318293
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.14%, afr)
Conditions
1
familial juvenile hyperuricemic nephropathy type 1
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 -0.34 | GERP -3.9 |
| Overall | ||
| CADD | 6.192 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.14%
African / African-American · 859/75,060 alleles
Filtering AF
1.08%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.06%
Overall
0.0603%
974/1,614,248 alleles · low-frequency
exomes 467/1,461,886 · genomes 507/152,362 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.14% | 87 |
| Admixed American | 0.0583% | 1,715 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,156 |
| East Asian | 0.0356% | 2,806 |
| South Asian | 0.0274% | 3,644 |
| Middle Eastern | 0.0165% | 6,062 |
| European (non-Finnish) | 0.000763% | 131,116 |
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
- UMOD
- Protein
- p.Phe354=
- Coding
- c.1062C>T
- MANE Select
- NM_003361
- dbSNP
- rs78613713
- Type
- single nucleotide variant
- Location
- chr16:20346246 (GRCh38)
- Gene constraint
- LOEUF 1.241 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.00 · 10 PDB
- Residue 354
- the 'zp-n' region; the zp domain
Similar variants
- UMOD p.Ala285Glu Pathogenic ★★ same condition
- UMOD p.Ala461Glu Likely pathogenic ★★ same condition
- UMOD p.Arg185Cys Pathogenic ★★ same condition
- UMOD p.Arg204Gly Pathogenic/Likely pathogenic ★★ same condition
- UMOD p.Cys106Tyr Pathogenic/Likely pathogenic ★★ same condition
- UMOD p.Cys112Tyr Pathogenic/Likely pathogenic ★★ same condition
- UMOD p.Cys120Arg Likely pathogenic ★★ same condition
- UMOD p.Cys248Trp Pathogenic ★★ 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/umod-p-phe354 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown