SLC16A2 p.Pro49=
c.147C>T · VCV3624976
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Spastic paraplegia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Overall | ||
| CADD | 3.531 | 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
- SLC16A2
- Protein
- p.Pro49=
- Coding
- c.147C>T
- MANE Select
- NM_006517
- Type
- single nucleotide variant
- Location
- chrX:74421784 (GRCh38)
- Structure
- AlphaFold pLDDT 79.48 · 7 PDB
- Residue 49
- the 'disordered' region
Similar variants
- SLC16A2 c.1399+1G>A Pathogenic ★★ same condition
- SLC16A2 c.576-1G>A Pathogenic/Likely pathogenic ★★ same condition
- SLC16A2 p.Arg171Ter Pathogenic ★★ same condition
- SLC16A2 p.Gln16Ter Pathogenic ★★ same condition
- SLC16A2 p.Gln52Ter Pathogenic ★★ same condition
- SLC16A2 p.Gly327Arg Pathogenic/Likely pathogenic ★★ same condition
- SLC16A2 p.Asn471Lys Uncertain significance ★★ ⚠ same condition
- SLC16A2 p.Asp521Glu Uncertain significance ★★ ⚠ 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/slc16a2-p-pro49 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown