SLC2A9 p.Pro222=
c.666C>T · rs139449249 · VCV350234
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.14%, eas)
Conditions
1
hypouricemia, renal, 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.8 | GERP -4.1 |
| Overall | ||
| CADD | 0.756 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.14%
East Asian · 962/44,862 alleles
Filtering AF
2.03%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.99%
Overall
0.0628%
1,014/1,614,106 alleles · low-frequency
exomes 964/1,461,838 · genomes 50/152,268 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 2.14% | 47 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,251 |
| Admixed American | 0.0133% | 7,503 |
| South Asian | 0.00549% | 18,215 |
| European (non-Finnish) | 0.00237% | 42,143 |
| African / African-American | 0.00133% | 75,034 |
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
- SLC2A9
- Protein
- p.Pro222=
- Coding
- c.666C>T
- MANE Select
- NM_020041
- dbSNP
- rs139449249
- Type
- single nucleotide variant
- Location
- chr4:9980607 (GRCh38)
- Gene constraint
- LOEUF 1.022 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.79 · 7 PDB
- Residue 222
- a turn
Similar variants
- SLC2A9 p.Pro222Arg Uncertain significance ★ ⚠ same residue
- SLC2A9 p.Leu75Arg Pathogenic/Likely pathogenic ★★ same condition
- SLC2A9 p.Thr125Met Likely pathogenic ★★ ⚠ same condition
- SLC2A9 p.Arg447Trp Uncertain significance ★★ ⚠ same condition
- SLC2A9 p.Ile207Val Uncertain significance ★★ ⚠ same condition
- SLC2A9 p.Ile335Thr Uncertain significance ★★ ⚠ same condition
- SLC2A9 p.Ile375Thr Uncertain significance ★★ ⚠ same condition
- SLC2A9 p.Leu17Arg Uncertain significance ★★ ⚠ 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/slc2a9-p-pro222 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown