SLC5A2 p.Pro277=
c.831C>T · VCV4929662
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000424%, 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 -9.8 | GERP -3.7 |
| Overall | ||
| CADD | 1.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000424%
European (non-Finnish) · 5/1,179,948 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.00031%
5/1,613,072 alleles · very rare
exomes 5/1,460,702 · genomes 0/152,370 · joint denominator
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.Pro277=
- Coding
- c.831C>T
- MANE Select
- NM_003041
- Type
- single nucleotide variant
- Location
- chr16:31487705 (GRCh38)
- Gene constraint
- LOEUF 1.21 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.32 · 12 PDB
Similar variants
- SLC5A2 c.1280+1G>A Likely pathogenic ★★ same type
- SLC5A2 p.Arg368Trp Likely pathogenic ★★ ⚠ same type
- SLC5A2 p.Lys321Arg Pathogenic/Likely pathogenic ★★ same type
- SLC5A2 c.469-3A>T Uncertain significance ★★ same type
- SLC5A2 p.Ala102Val Uncertain significance ★★ ⚠ same type
- SLC5A2 p.Ala549Thr Uncertain significance ★★ ⚠ same type
- SLC5A2 p.Ala549Val Uncertain significance ★★ ⚠ same type
- SLC5A2 p.Arg130His 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/slc5a2-p-pro277 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown