TSC2 p.Val199fs
c.595del · rs2151061858 · VCV1686276
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 6 of 42 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | 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
- TSC2
- Protein
- p.Val199fs
- Coding
- c.595del
- MANE Select
- NM_000548
- dbSNP
- rs2151061858
- Type
- Deletion
- Location
- chr16:2055514 (GRCh38)
- Gene constraint
- LOEUF 0.203 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.81 · 2 PDB
- Residue 199
- an α-helix; the 'required for interaction with tsc1' region
Disease context
lymphangioleiomyomatosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Perivascular epithelioid cell neoplasm (Orphanet):
- Onset
- Adolescent, Adult, Childhood, Elderly
Similar variants
- TSC2 p.Val199Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- TSC2 c.5252_5259+19del Pathogenic/Likely pathogenic ★★ same condition
- TSC2 p.Arg1032_Tyr1033insTer Pathogenic ★★ same condition
- TSC2 p.Asp1126fs Pathogenic ★★ same condition
- TSC2 p.Asp702fs Pathogenic ★★ same condition
- TSC2 p.His1746_Arg1751del Pathogenic/Likely pathogenic ★★ same condition
- TSC2 p.Val1492fs Pathogenic ★★ same condition
- TSC2 p.Gly1086del 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/tsc2-p-val199fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown