SLC52A2 p.Val366=
c.1098G>T · rs2537248909 · VCV3036525
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
SLC52A2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.35 | donor loss, 3 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.9 | GERP 0.95, phastCons 1 |
| Overall | ||
| CADD | 7.255 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- SLC52A2
- Protein
- p.Val366=
- Coding
- c.1098G>T
- MANE Select
- NM_001363118
- dbSNP
- rs2537248909
- Type
- single nucleotide variant
- Location
- chr8:144360686 (GRCh38)
- Gene constraint
- LOEUF 0.955 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.50 · 1 PDB
- Residue 366
- a turn
Disease context
SLC52A2-related disorder
Similar variants
- SLC52A2 p.Val366Ala Uncertain significance ★ ⚠ same residue
- SLC52A2 c.131-1G>C Likely pathogenic ★★ same condition
- SLC52A2 p.Ala420Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
- SLC52A2 p.Gln270Ter Pathogenic/Likely pathogenic ★★ same condition
- SLC52A2 p.Gly306Arg Pathogenic ★★ same condition
- SLC52A2 p.Leu312Pro Pathogenic/Likely pathogenic ★★ same condition
- SLC52A2 p.Leu339Pro Pathogenic ★★ same condition
- SLC52A2 p.Cys325Gly Likely pathogenic ★★ ⚠ 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/slc52a2-p-val366 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown