SLC13A3 p.Phe22=
c.66C>T · rs1011834868 · VCV1550847
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00476%, 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 -0.12 | GERP -4.2 |
| Overall | ||
| CADD | 11.76 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00476%
European (non-Finnish) · 54/1,134,150 alleles
Filtering AF
0.00373%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00334%
Overall
0.0039%
59/1,514,524 alleles · very rare
exomes 58/1,362,300 · genomes 1/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00476% | 21,003 |
| Admixed American | 0.0042% | 23,818 |
| Remaining individualsnot grpmax-eligible | 0.00341% | 29,338 |
| African / African-American | 0.00143% | 69,710 |
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.Phe22=
- Coding
- c.66C>T
- MANE Select
- NM_022829
- dbSNP
- rs1011834868
- Type
- single nucleotide variant
- Location
- chr20:46651356 (GRCh38)
- Gene constraint
- LOEUF 0.898 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.62 · 6 PDB
- Residue 22
- 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-phe22 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown