TOR1A p.Ser298=
c.894C>T · rs1189133538 · VCV3048781
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
TOR1A-related disorder
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 |
|---|---|---|
| Pangolin | Δ0.64 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP -0.8, phastCons 0.99 |
| Overall | ||
| CADD | 12.27 | 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
- TOR1A
- Protein
- p.Ser298=
- Coding
- c.894C>T
- MANE Select
- NM_000113
- dbSNP
- rs1189133538
- Type
- single nucleotide variant
- Location
- chr9:129814077 (GRCh38)
- Gene constraint
- LOEUF 0.84 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.82 · 3 PDB
- Residue 298
- a UniProt-annotated variant site (in amc5); the 'interaction with klc1' region; an α-helix
Disease context
TOR1A-related disorder
Similar variants
- TOR1A p.Arg288Ter Pathogenic/Likely pathogenic ★★ same condition
- TOR1A c.748+1G>A Likely pathogenic ★ same condition
- TOR1A p.Gly157= Likely benign same condition
- TOR1A p.Ter333TrpextTer? Uncertain significance ★★ same condition
- TOR1A p.Arg282Ter 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
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-ser298 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown