SLC52A2 p.Phe197=
c.591C>T · rs1554854078 · VCV798560
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 2.2 | GERP 0.32, phastCons 1 |
| Overall | ||
| CADD | 8.633 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,886 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000136%
Overall
0.000186%
3/1,613,004 alleles · very rare
exomes 3/1,460,670 · genomes 0/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,886 |
| South Asian | 0.0022% | 45,543 |
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.Phe197=
- Coding
- c.591C>T
- MANE Select
- NM_001363118
- dbSNP
- rs1554854078
- Type
- single nucleotide variant
- Location
- chr8:144360083 (GRCh38)
- Gene constraint
- LOEUF 0.955 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.50 · 1 PDB
- Residue 197
- an α-helix
Similar variants
- SLC52A2 p.Phe197del 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-phe197 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown