TSC2 p.Val892=
c.2676C>A · rs2089318045 · VCV2825188
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
tuberous sclerosis 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.23 | acceptor loss, 36 bp away · masked 0 · deltas |
|---|---|---|
| Pangolin | Δ0.27 | loss · gain 0.04 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -0.002 | GERP -1.8, phastCons 0.79 |
| Overall | ||
| CADD | 4.303 | 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
- TSC2
- Protein
- p.Val892=
- Coding
- c.2676C>A
- MANE Select
- NM_000548
- dbSNP
- rs2089318045
- Type
- single nucleotide variant
- Location
- chr16:2076104 (GRCh38)
- Gene constraint
- LOEUF 0.203 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.81 · 2 PDB
- Residue 892
- an α-helix
Disease context
tuberous sclerosis 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: tuberous sclerosis
For Tuberous sclerosis complex (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- All ages
- Prevalence
- 1-9 / 100 000 (Taiwan, Province of China)
Similar variants
- TSC2 p.Val892Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
- TSC2 p.Val892Phe Uncertain significance ★ ⚠ same residue
- TSC2 c.1257+1G>A Pathogenic ★★ same condition
- TSC2 c.1258-2A>G Pathogenic ★★ same condition
- TSC2 c.1361+1G>A Pathogenic/Likely pathogenic ★★ same condition
- TSC2 c.1361+1G>T Pathogenic/Likely pathogenic ★★ same condition
- TSC2 c.1362-1G>A Pathogenic ★★ same condition
- TSC2 c.138+2T>C 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/tsc2-p-val892 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown