SLC16A2 p.Pro37=
c.111T>C · rs762215475 · VCV2902598
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00277%, nfe)
Conditions
1
Spastic paraplegia
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 -0.71 | GERP -2.1, phastCons 0.012 |
| Overall | ||
| CADD | 4.625 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00277%
European (non-Finnish) · 24/865,271 alleles
Filtering AF
0.00188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00158%
Overall
0.00217%
25/1,152,757 alleles · very rare
exomes 24/1,041,430 · genomes 1/111,327 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00277% | 36,053 |
| Remaining individualsnot grpmax-eligible | 0.00219% | 45,655 |
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
- SLC16A2
- Protein
- p.Pro37=
- Coding
- c.111T>C
- MANE Select
- NM_006517
- dbSNP
- rs762215475
- Type
- single nucleotide variant
- Location
- chrX:74421748 (GRCh38)
- Structure
- AlphaFold pLDDT 79.48 · 7 PDB
- Residue 37
- 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-pro37 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown