SLC52A2 p.Val53=
c.159G>C · rs782644724 · VCV2024905
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00988%, sas)
Conditions
1
Brown-Vialetto-van Laere syndrome 2
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 6.6 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 7.141 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00988%
South Asian · 9/91,090 alleles
Filtering AF
0.00514%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00375%
Overall
0.000682%
11/1,613,778 alleles · very rare
exomes 10/1,461,596 · genomes 1/152,182 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00988% | 10,121 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,478 |
| European (non-Finnish) | 8.47e-05% | 1,179,974 |
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
- SLC52A2
- Protein
- p.Val53=
- Coding
- c.159G>C
- MANE Select
- NM_001363118
- dbSNP
- rs782644724
- Type
- single nucleotide variant
- Location
- chr8:144359651 (GRCh38)
- Gene constraint
- LOEUF 0.955 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.50 · 1 PDB
- Residue 53
- an α-helix
Similar variants
- SLC52A2 p.Val53Leu Uncertain significance ★ ⚠ same residue
- SLC52A2 c.131-1G>C Likely pathogenic ★★ same condition
- SLC52A2 p.Ala420Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
- SLC52A2 p.Cys325Gly Likely pathogenic ★★ ⚠ same condition
- SLC52A2 p.Gln270Ter Pathogenic/Likely pathogenic ★★ same condition
- SLC52A2 p.Gly306Arg Pathogenic ★★ same condition
- SLC52A2 p.Gly306Glu Likely pathogenic ★★ same condition
- SLC52A2 p.Leu312Pro Pathogenic/Likely pathogenic ★★ same condition
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-val53 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown