UMOD p.Pro102=
c.306C>G · VCV4799532
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0027%, afr)
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 -5 | GERP -4.7 |
| Overall | ||
| CADD | 0.325 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0027%
African / African-American · 2/74,106 alleles
Filtering AF
0.000448%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000168%
Overall
0.000317%
5/1,578,156 alleles · very rare
exomes 2/1,425,904 · genomes 3/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0027% | 37,053 |
| South Asian | 0.00115% | 86,626 |
| European (non-Finnish) | 0.000172% | 581,058 |
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.Pro102=
- Coding
- c.306C>G
- MANE Select
- NM_003361
- Type
- single nucleotide variant
- Location
- chr16:20348995 (GRCh38)
- Gene constraint
- LOEUF 1.241 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.00 · 10 PDB
- Residue 102
- the egf-like 2; calcium-binding domain
Similar variants
- UMOD p.Pro102Leu Uncertain significance ★ ⚠ same residue
- UMOD p.Ala285Glu Pathogenic ★★ same type
- UMOD p.Ala461Glu Likely pathogenic ★★ same type
- UMOD p.Arg185Cys Pathogenic ★★ same type
- UMOD p.Arg204Gly Pathogenic/Likely pathogenic ★★ same type
- UMOD p.Cys106Tyr Pathogenic/Likely pathogenic ★★ same type
- UMOD p.Cys112Tyr Pathogenic/Likely pathogenic ★★ same type
- UMOD p.Cys120Arg 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/umod-p-pro102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown