Is TSC2 p.Ser1698= (c.5094C>T) pathogenic?

TSC2 p.Ser1698= (c.5094C>T) is classified Benign/Likely benign in TSC2 (ClinVar, Multiple submitters, 12 submitters; last evaluated 2026-06-01). Ultra-rare (popmax 0.0285%, sas); Associated with hereditary neoplastic syndrome.

What condition is associated with TSC2 p.Ser1698= (c.5094C>T)?

TSC2 p.Ser1698= (c.5094C>T) is associated with hereditary neoplastic syndrome, tuberous sclerosis, tuberous sclerosis 2 (ClinVar).

How common is TSC2 p.Ser1698= (c.5094C>T) in the general population?

TSC2 p.Ser1698= (c.5094C>T) is ultra-rare (popmax 0.0285%, sas) (gnomAD).

TSC2 p.Ser1698=

c.5094C>T · rs45514196 · VCV137748

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 12 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0285%, sas)

Conditions

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 -9.5	GERP -3.2
Overall
CADD	2.55	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0285% South Asian · 26/91,084 alleles

Filtering AF 0.0199% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0171%

Overall 0.00533% 86/1,612,710 alleles · ultra-rare exomes 80/1,460,518 · genomes 6/152,192 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0285%	3,503
Remaining individualsnot grpmax-eligible	0.016%	6,247
East Asian	0.00446%	22,445
European (non-Finnish)	0.0039%	25,653
Admixed American	0.00167%	60,006
African / African-American	0.00133%	74,912

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: TSC2
Protein: p.Ser1698=
Coding: c.5094C>T
MANE Select: NM_000548
dbSNP: rs45514196
Type: single nucleotide variant
Location: chr16:2088073 (GRCh38)
Gene constraint: LOEUF 0.203 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 68.81 · 2 PDB
Residue 1698: the rap-gap domain

Full TSC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: tuberous sclerosis tuberous sclerosis 2

Similar variants

TSC2 p.Ser1698Thr Uncertain significance ★★ ⚠ same residue
TSC2 p.Ser1698Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
TSC2 p.Ser1698Gly 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

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-ser1698 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown