SLC2A9 p.Ser41=
c.123T>C · rs112581525 · VCV725274
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.02%, afr)
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 0.017 | GERP -2.1 |
| Overall | ||
| CADD | 2.476 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.02%
African / African-American · 766/74,796 alleles
Filtering AF
0.964%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.94%
Overall
0.0614%
991/1,613,372 alleles · low-frequency
exomes 556/1,461,698 · genomes 435/151,674 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.02% | 98 |
| Remaining individualsnot grpmax-eligible | 0.118% | 844 |
| Admixed American | 0.0734% | 1,363 |
| Middle Eastern | 0.0338% | 2,957 |
| European (non-Finnish) | 0.00848% | 11,799 |
| South Asian | 0.00549% | 18,200 |
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.Ser41=
- Coding
- c.123T>C
- MANE Select
- NM_020041
- dbSNP
- rs112581525
- Type
- single nucleotide variant
- Location
- chr4:10021307 (GRCh38)
- Gene constraint
- LOEUF 1.022 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.79 · 7 PDB
Similar variants
- 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
- SLC2A9 p.Phe471Leu 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-ser41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown