SLC1A2 p.Ser487=
c.1461T>A · rs375515105 · VCV1545889
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.024%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.038 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.47 | GERP -4.9 |
| Overall | ||
| CADD | 4.538 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.024%
African / African-American · 18/74,936 alleles
Filtering AF
0.0155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0128%
Overall
0.00124%
20/1,613,850 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.024% | 4,163 |
| Admixed American | 0.00167% | 60,004 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,476 |
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
- SLC1A2
- Protein
- p.Ser487=
- Coding
- c.1461T>A
- MANE Select
- NM_004171
- dbSNP
- rs375515105
- Type
- single nucleotide variant
- Location
- chr11:35265719 (GRCh38)
- Gene constraint
- LOEUF 0.569 · pLI 0.84 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.64 · 7 PDB
- Residue 487
- an α-helix
Similar variants
- SLC1A2 p.Pro289Arg Pathogenic/Likely pathogenic ★★ same type
- SLC1A2 c.562-2A>G Uncertain significance ★★ same type
- SLC1A2 p.Ala210Thr Uncertain significance ★★ ⚠ same type
- SLC1A2 p.Ala293Thr Uncertain significance ★★ ⚠ same type
- SLC1A2 p.Ala349Thr Uncertain significance ★★ ⚠ same type
- SLC1A2 p.Ala349Val Uncertain significance ★★ ⚠ same type
- SLC1A2 p.Ala362Thr Uncertain significance ★★ ⚠ same type
- SLC1A2 p.Ala394Thr 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/slc1a2-p-ser487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown