Is TSC2 p.Pro1771= (c.5313G>A) pathogenic?

TSC2 p.Pro1771= (c.5313G>A) is classified Benign/Likely benign in TSC2 (ClinVar, Multiple submitters, 9 submitters; last evaluated 2025-11-18). Ultra-rare (popmax 0.0165%, mid); Associated with hereditary neoplastic syndrome.

What condition is associated with TSC2 p.Pro1771= (c.5313G>A)?

TSC2 p.Pro1771= (c.5313G>A) is associated with hereditary neoplastic syndrome, tuberous sclerosis, tuberous sclerosis 2 (ClinVar).

How common is TSC2 p.Pro1771= (c.5313G>A) in the general population?

TSC2 p.Pro1771= (c.5313G>A) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

TSC2 p.Pro1771=

c.5313G>A · rs765607686 · VCV413716

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.34 · evaluated, not missing
Constraint at this position
Conservation	phyloP -4.5	GERP -3.1
Overall
CADD	0.188	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,062 alleles

Filtering AF 0.00223% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00198%

Overall 0.00291% 47/1,612,740 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,062
East Asian	0.00446%	22,437
Admixed American	0.00333%	30,003
South Asian	0.00329%	30,359
European (non-Finnish)	0.00305%	32,777
African / African-American	0.00267%	37,501
Finnishnot grpmax-eligible	0.00159%	62,738

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.Pro1771=
Coding: c.5313G>A
MANE Select: NM_000548
dbSNP: rs765607686
Type: single nucleotide variant
Location: chr16:2088499 (GRCh38)
Gene constraint: LOEUF 0.203 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 68.81 · 2 PDB
Residue 1771: the 'disordered' region

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.Pro1771Ser Uncertain significance ★★ ⚠ same residue
TSC2 p.Pro1771Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
TSC2 p.Pro1771Gln Uncertain significance ★ ⚠ same residue
TSC2 p.Pro1771Thr Uncertain significance ★ ⚠ same residue
TSC2 p.Pro1771fs 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

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-pro1771 (accessed [today's date]).

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