TOR1A p.Pro308=
c.924C>T · VCV4904896
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00329%, sas)
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 3.5 | GERP 0.37, phastCons 1 |
| Overall | ||
| CADD | 11.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,080 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000186%
3/1,614,068 alleles · very rare
exomes 3/1,461,888 · genomes 0/152,180 · joint denominator
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
- TOR1A
- Protein
- p.Pro308=
- Coding
- c.924C>T
- MANE Select
- NM_000113
- Type
- single nucleotide variant
- Location
- chr9:129814047 (GRCh38)
- Gene constraint
- LOEUF 0.84 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.82 · 3 PDB
- Residue 308
- a UniProt-annotated variant site (in amc5); the 'interaction with klc1' region; a β-strand
Similar variants
- TOR1A p.Pro308Arg Uncertain significance ★ ⚠ same residue
- TOR1A p.Arg282Ter Likely pathogenic ★★ same type
- TOR1A p.Arg288Ter Pathogenic/Likely pathogenic ★★ same type
- TOR1A c.-4G>C Uncertain significance ★★ same type
- TOR1A p.Ala239Thr Uncertain significance ★★ ⚠ same type
- TOR1A p.Ala239Val Uncertain significance ★★ ⚠ same type
- TOR1A p.Arg213Gly Uncertain significance ★★ ⚠ same type
- TOR1A p.Arg260Trp Uncertain significance ★★ ⚠ 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/tor1a-p-pro308 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown