SLC2A9 p.Arg294=
c.882C>T · VCV3709825
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00466%, nfe)
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 -9.6 | GERP -4.2 |
| Overall | ||
| CADD | 0.062 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00466%
European (non-Finnish) · 55/1,180,052 alleles
Filtering AF
0.00367%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00329%
Overall
0.00372%
60/1,614,070 alleles · very rare
exomes 53/1,461,826 · genomes 7/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00466% | 21,455 |
| South Asian | 0.00329% | 30,365 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,245 |
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.Arg294=
- Coding
- c.882C>T
- MANE Select
- NM_020041
- Type
- single nucleotide variant
- Location
- chr4:9920505 (GRCh38)
- Gene constraint
- LOEUF 1.022 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.79 · 7 PDB
- Residue 294
- a UniProt-annotated variant site (no effect on urate transport activity; no effect on protein expression; no effect on glucose transport); an α-helix
Similar variants
- SLC2A9 p.Arg294His Benign ★★ same residue
- SLC2A9 c.681+1G>T Likely pathogenic ★★ same type
- SLC2A9 p.Leu75Arg Pathogenic/Likely pathogenic ★★ same type
- SLC2A9 p.Thr125Met Likely pathogenic ★★ ⚠ same type
- SLC2A9 p.Arg380Gln Uncertain significance ★★ ⚠ same type
- SLC2A9 p.Arg447Trp Uncertain significance ★★ ⚠ same type
- SLC2A9 p.Asn144Ser Uncertain significance ★★ ⚠ same type
- SLC2A9 p.Ile149Val Uncertain significance ★★ ⚠ 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/slc2a9-p-arg294 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown