SLC5A2 p.Ser78=
c.234T>C · VCV4929655
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.83%, afr)
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 -6.3 | GERP -3.7 |
| Overall | ||
| CADD | 3.998 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.83%
African / African-American · 1,377/75,078 alleles
Filtering AF
1.75%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.72%
Overall
0.095%
1,533/1,614,092 alleles · low-frequency
exomes 781/1,461,700 · genomes 752/152,392 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.83% | 55 |
| Remaining individualsnot grpmax-eligible | 0.128% | 781 |
| Admixed American | 0.0849% | 1,177 |
| Middle Eastern | 0.033% | 3,031 |
| European (non-Finnish) | 0.00186% | 53,638 |
| South Asian | 0.0011% | 91,084 |
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.Ser78=
- Coding
- c.234T>C
- MANE Select
- NM_003041
- Type
- single nucleotide variant
- Location
- chr16:31484854 (GRCh38)
- Gene constraint
- LOEUF 1.21 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.32 · 12 PDB
- Residue 78
- an α-helix
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-ser78 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown