SLC16A3 p.Pro89=
c.267C>T · rs200551682 · VCV716780
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.108%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.7 |
| Overall | ||
| CADD | 0.425 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.108%
South Asian · 98/91,082 alleles
Filtering AF
0.0903%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0839%
Overall
0.0178%
287/1,608,884 alleles · rare
exomes 278/1,456,562 · genomes 9/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.108% | 929 |
| Middle Eastern | 0.0497% | 2,012 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,461 |
| European (non-Finnish) | 0.0134% | 7,467 |
| Admixed American | 0.01% | 10,004 |
| African / African-American | 0.00933% | 10,721 |
| East Asian | 0.00223% | 44,866 |
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
- SLC16A3
- Protein
- p.Pro89=
- Coding
- c.267C>T
- MANE Select
- NM_004207
- dbSNP
- rs200551682
- Type
- single nucleotide variant
- Location
- chr17:82236772 (GRCh38)
- Gene constraint
- LOEUF 1.402 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.62
Similar variants
- SLC16A3 p.Ala15Val Benign ★★ same type
- SLC16A3 p.Ala127Val Uncertain significance ★ ⚠ same type
- SLC16A3 p.Ala235Thr Uncertain significance ★ ⚠ same type
- SLC16A3 p.Ala277Thr Uncertain significance ★ same type
- SLC16A3 p.Ala281Val Uncertain significance ★ ⚠ same type
- SLC16A3 p.Ala308Ser Uncertain significance ★ ⚠ same type
- SLC16A3 p.Ala308Val Uncertain significance ★ ⚠ same type
- SLC16A3 p.Ala380Gly 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/slc16a3-p-pro89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown