SLC3A2 p.Glu2=
c.6G>A · rs114958414 · VCV3164749
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.137%, afr)
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 -1.1 | GERP -4.4 |
| Overall | ||
| CADD | 0.97 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.137%
African / African-American · 103/75,048 alleles
Filtering AF
0.116%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.108%
Overall
0.00683%
110/1,611,026 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.137% | 729 |
| Remaining individualsnot grpmax-eligible | 0.00802% | 12,467 |
| Admixed American | 0.00167% | 59,896 |
| European (non-Finnish) | 8.49e-05% | 1,177,523 |
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
- SLC3A2
- Protein
- p.Glu2=
- Coding
- c.6G>A
- MANE Select
- NM_001013251 · reported on NM_001012662
- dbSNP
- rs114958414
- Type
- single nucleotide variant
- Location
- chr11:62856275 (GRCh38)
- Gene constraint
- LOEUF 0.907 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.01 · 44 PDB
- Residue 2
- the 'disordered' region; a modified residue (n-acetylserine); a modified residue (phosphoserine)
Similar variants
- SLC3A2 c.301+3G>A Benign ★★ same type
- SLC3A2 p.Arg338Met Likely benign ★★ ⚠ same type
- SLC3A2 p.Leu435= Benign ★★ same type
- SLC3A2 p.Lys491Gln Benign ★★ same type
- SLC3A2 p.Pro415Ser Benign/Likely benign ★★ same type
- SLC3A2 p.Ala346Ser Uncertain significance ★ ⚠ same type
- SLC3A2 p.Ala346Thr Uncertain significance ★ ⚠ same type
- SLC3A2 p.Ala492Gly 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/slc3a2-p-glu2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown