SLC1A2 p.Asp486=
c.1458C>T · rs1591402683 · VCV765033
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.433 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.37 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -0.45, phastCons 1 |
| Overall | ||
| CADD | 6.637 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,746 alleles
Overall
6.84e-05%
1/1,461,540 alleles · very rare
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.Asp486=
- Coding
- c.1458C>T
- MANE Select
- NM_004171
- dbSNP
- rs1591402683
- Type
- single nucleotide variant
- Location
- chr11:35265722 (GRCh38)
- Gene constraint
- LOEUF 0.569 · pLI 0.84 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.64 · 7 PDB
- Residue 486
- a binding site; 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-asp486 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown