TSC2 p.Gln613=
c.1839G>A · rs1555505208 · VCV1475831
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 | Δ0.39 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.32 | loss · gain 0.26 · SpliceAI calls gain · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 22.4 | 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.Gln613=
- Coding
- c.1839G>A
- MANE Select
- NM_000548
- dbSNP
- rs1555505208
- Type
- single nucleotide variant
- Location
- chr16:2070578 (GRCh38)
- Gene constraint
- LOEUF 0.203 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.81 · 2 PDB
- Residue 613
- an α-helix
Disease context
tuberous sclerosis 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: hereditary neoplastic syndrome
For Tuberous sclerosis complex (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- All ages
- Prevalence
- 1-9 / 100 000 (Taiwan, Province of China)
Similar variants
- TSC2 p.Gln613Arg Uncertain significance ★★ ⚠ same residue
- TSC2 p.Gln613His Pathogenic ★ ⚠ same residue
- TSC2 p.Gln613Ter Pathogenic ★ 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
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-gln613 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown