Is SLC5A2 p.Val343= (c.1029G>A) pathogenic?

SLC5A2 p.Val343= (c.1029G>A) is classified Uncertain significance in SLC5A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-26). Very rare (popmax 0.00133%, afr); Associated with familial renal glucosuria.

What condition is associated with SLC5A2 p.Val343= (c.1029G>A)?

SLC5A2 p.Val343= (c.1029G>A) is associated with familial renal glucosuria (ClinVar).

How common is SLC5A2 p.Val343= (c.1029G>A) in the general population?

SLC5A2 p.Val343= (c.1029G>A) is very rare (popmax 0.00133%, afr) (gnomAD).

How is Familial renal glucosuria inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

SLC5A2 p.Val343=

c.1029G>A · VCV3580324

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Conditions

familial renal glucosuria

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 2.9	GERP -0.18, phastCons 1
Overall
CADD	15.15	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/74,938 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000372% 6/1,611,320 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00133%	74,938
South Asian	0.0011%	91,000
European (non-Finnish)	0.000339%	294,958

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: SLC5A2
Protein: p.Val343=
Coding: c.1029G>A
MANE Select: NM_003041
Type: single nucleotide variant
Location: chr16:31488390 (GRCh38)
Gene constraint: LOEUF 1.21 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.32 · 12 PDB
Residue 343: a disulfide bond; a turn

Full SLC5A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

For Familial renal glucosuria (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: All ages

Similar variants

SLC5A2 c.1280+1G>A Likely pathogenic ★★ same condition
SLC5A2 p.Arg368Trp Likely pathogenic ★★ ⚠ same condition
SLC5A2 p.Lys321Arg Pathogenic/Likely pathogenic ★★ same condition
SLC5A2 c.469-3A>T Uncertain significance ★★ same condition
SLC5A2 p.Ala102Val Uncertain significance ★★ ⚠ same condition
SLC5A2 p.Ala549Thr Uncertain significance ★★ ⚠ same condition
SLC5A2 p.Ala549Val Uncertain significance ★★ ⚠ same condition
SLC5A2 p.Arg130His 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/slc5a2-p-val343 (accessed [today's date]).

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