SLC3A2 p.Ser342=
c.1026C>G · rs1382490020 · VCV758195
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.077 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.12 | GERP -1.1, phastCons 0.001 |
| Overall | ||
| CADD | 10.86 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,036 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,058 alleles · very rare
exomes 1/1,461,894 · genomes 1/152,164 · joint denominator
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.Ser342=
- Coding
- c.1026C>G
- MANE Select
- NM_001013251
- dbSNP
- rs1382490020
- Type
- single nucleotide variant
- Location
- chr11:62885491 (GRCh38)
- Gene constraint
- LOEUF 0.907 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.01 · 44 PDB
- Residue 342
- an α-helix
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-ser342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown