SLC5A6 p.Pro70=
c.210G>A · rs139747998 · VCV726274
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.361%, eas)
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 -2.7 | GERP -5.2 |
| Overall | ||
| CADD | 5.697 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.361%
East Asian · 162/44,886 alleles
Filtering AF
0.316%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.298%
Overall
0.0282%
455/1,614,174 alleles · rare
exomes 400/1,461,872 · genomes 55/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.361% | 277 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,718 |
| South Asian | 0.0253% | 3,960 |
| European (non-Finnish) | 0.0203% | 4,937 |
| African / African-American | 0.00666% | 15,009 |
| Admixed American | 0.00333% | 30,013 |
| Finnishnot grpmax-eligible | 0.00156% | 64,016 |
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
- SLC5A6
- Protein
- p.Pro70=
- Coding
- c.210G>A
- MANE Select
- NM_021095
- dbSNP
- rs139747998
- Type
- single nucleotide variant
- Location
- chr2:27207441 (GRCh38)
- Gene constraint
- LOEUF 0.609 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 79.99 · 5 PDB
Similar variants
- SLC5A6 p.Pro70Leu Uncertain significance ★ same residue
- SLC5A6 c.393+2T>C Pathogenic/Likely pathogenic ★★ same type
- SLC5A6 p.Arg94Ter Pathogenic ★★ same type
- SLC5A6 p.Ser429Gly Pathogenic/Likely pathogenic ★★ ⚠ same type
- SLC5A6 p.Arg285Cys Uncertain significance ★★ ⚠ same type
- SLC5A6 p.Arg53Gln Uncertain significance ★★ ⚠ same type
- SLC5A6 p.Arg394= Likely benign ★★ same type
- SLC5A6 p.Arg553Gln Likely benign ★★ 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/slc5a6-p-pro70 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown