TSC1 p.Arg786fs
c.2356del · rs2538609351 · VCV2697849
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 18 of 23 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 1.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- TSC1
- Protein
- p.Arg786fs
- Coding
- c.2356del
- MANE Select
- NM_000368
- dbSNP
- rs2538609351
- Type
- Deletion
- Location
- chr9:132902640 (GRCh38)
- Gene constraint
- LOEUF 0.227 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 63.55 · 5 PDB
- Residue 786
- the 'mediates interaction with wdr45b' region; an α-helix; a UniProt-annotated variant site (in tsc1)
Disease context
tuberous sclerosis 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Tuberous sclerosis complex (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- All ages
- Prevalence
- 1-9 / 100 000 (Taiwan, Province of China)
Similar variants
- TSC1 p.Arg786Ter Pathogenic ★★ same residue
- TSC1 p.Arg786Gly Uncertain significance ★★ same residue
- TSC1 p.Arg786Leu Uncertain significance ★★ ⚠ same residue
- TSC1 p.Arg786= Likely benign ★★ same residue
- TSC1 p.Arg786Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- TSC1 p.Ala283fs Pathogenic/Likely pathogenic ★★ same condition
- TSC1 p.Ala398fs Pathogenic/Likely pathogenic ★★ same condition
- TSC1 p.Arg429fs 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/tsc1-p-arg786fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown