TSC1 p.Arg692=
c.2074C>A · rs118203631 · VCV1785438
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Conditions
1
hereditary neoplastic syndrome
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 |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 8.6 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 12.85 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,070 alleles
Overall
6.2e-05%
1/1,613,868 alleles · very rare
exomes 0/1,461,688 · genomes 1/152,180 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- TSC1
- Protein
- p.Arg692=
- Coding
- c.2074C>A
- MANE Select
- NM_000368
- dbSNP
- rs118203631
- Type
- single nucleotide variant
- Location
- chr9:132903785 (GRCh38)
- Gene constraint
- LOEUF 0.227 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 63.55 · 5 PDB
- Residue 692
- the 'mediates interaction with wdr45b' region; an α-helix; a UniProt-annotated variant site (in tsc1)
Similar variants
- TSC1 p.Arg692Pro Uncertain significance ★★ ⚠ same residue
- TSC1 p.Arg692Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- TSC1 p.Arg692Leu Uncertain significance ★ ⚠ same residue
- TSC1 c.1029+1G>A Pathogenic/Likely pathogenic ★★ same condition
- TSC1 c.1997+2T>G Pathogenic/Likely pathogenic ★★ same condition
- TSC1 c.1998-1G>T Pathogenic/Likely pathogenic ★★ same condition
- TSC1 c.2042-5A>G Pathogenic/Likely pathogenic ★★ same condition
- TSC1 c.2208+2T>A Pathogenic/Likely 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-arg692 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown