Is SLC2A9 p.Phe117= (c.351C>T) pathogenic?

SLC2A9 p.Phe117= (c.351C>T) is classified Benign/Likely benign in SLC2A9 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-26). Rare (popmax 0.127%, nfe); Associated with hypouricemia, renal, 2.

What condition is associated with SLC2A9 p.Phe117= (c.351C>T)?

SLC2A9 p.Phe117= (c.351C>T) is associated with hypouricemia, renal, 2 (ClinVar).

How common is SLC2A9 p.Phe117= (c.351C>T) in the general population?

SLC2A9 p.Phe117= (c.351C>T) is rare (popmax 0.127%, nfe) (gnomAD).

SLC2A9 p.Phe117=

c.351C>T · rs148002726 · VCV350239

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.127%, nfe)

Conditions

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 -2.3	GERP -3
Overall
CADD	9.477	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.127% European (non-Finnish) · 1,502/1,180,016 alleles

Filtering AF 0.122% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.12%

Overall 0.111% 1,789/1,614,164 alleles · rare exomes 1,668/1,461,842 · genomes 121/152,322 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.192%	521
European (non-Finnish)grpmax	0.127%	786
Remaining individualsnot grpmax-eligible	0.115%	868
Admixed American	0.112%	896
African / African-American	0.0306%	3,263
East Asian	0.00223%	44,884
South Asian	0.0011%	91,072

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Phe117=
Coding: c.351C>T
MANE Select: NM_020041
dbSNP: rs148002726
Type: single nucleotide variant
Location: chr4:9996840 (GRCh38)
Gene constraint: LOEUF 1.022 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.79 · 7 PDB
Residue 117: an α-helix

Full SLC2A9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hypouricemia, renal, 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-phe117 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown