SLC13A3 p.Pro24=
c.72G>C · VCV4701680
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0217%, 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 -0.56 | GERP -3.1, phastCons 0.063 |
| Overall | ||
| CADD | 12.89 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0217%
East Asian · 8/36,886 alleles
Filtering AF
0.0108%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0078%
Overall
0.000595%
9/1,513,236 alleles · ultra-rare
exomes 7/1,360,910 · genomes 2/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0217% | 4,611 |
| Remaining individualsnot grpmax-eligible | 0.00171% | 58,648 |
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
- SLC13A3
- Protein
- p.Pro24=
- Coding
- c.72G>C
- MANE Select
- NM_022829
- Type
- single nucleotide variant
- Location
- chr20:46651350 (GRCh38)
- Gene constraint
- LOEUF 0.898 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.62 · 6 PDB
- Residue 24
- an α-helix
Similar variants
- SLC13A3 p.Ala476Thr Uncertain significance ★★ ⚠ same type
- SLC13A3 p.Arg110Trp Uncertain significance ★★ same type
- SLC13A3 p.Arg317Thr Uncertain significance ★★ ⚠ same type
- SLC13A3 p.Arg359Gln Uncertain significance ★★ same type
- SLC13A3 p.Arg359Trp Uncertain significance ★★ ⚠ same type
- SLC13A3 p.Arg546Gln Uncertain significance ★★ ⚠ same type
- SLC13A3 p.Arg546Trp Uncertain significance ★★ ⚠ same type
- SLC13A3 p.Asn564Thr 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/slc13a3-p-pro24 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown