Is TSC2 p.Pro670Ser (c.2008C>T) pathogenic?

TSC2 p.Pro670Ser (c.2008C>T) is classified Uncertain significance in TSC2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-11-06). AlphaMissense: likely benign (0.0622); Very rare (popmax 0.00233%, eas); Associated with hereditary neoplastic syndrome.

What condition is associated with TSC2 p.Pro670Ser (c.2008C>T)?

TSC2 p.Pro670Ser (c.2008C>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is TSC2 p.Pro670Ser (c.2008C>T) in the general population?

TSC2 p.Pro670Ser (c.2008C>T) is very rare (popmax 0.00233%, eas) (gnomAD).

What do computational predictors say about TSC2 p.Pro670Ser (c.2008C>T)?

AlphaMissense predicts likely benign (score 0.0622) — an in-silico prediction, not a clinical call.

TSC2 p.Pro670Ser

c.2008C>T · rs1338802781 · VCV1784358

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0622 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00233%, eas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.0622	likely benign
REVEL	0.478	indeterminate
SaProt	LLR -6.19	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.12	GERP -3.1
Regional constraint	o/e 1.00	unconstrained · MANE · 37 kb · p 0.88 · regional, not allelic
Overall
CADD	8.602	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00233% East Asian · 1/42,994 alleles

Overall 6.32e-05% 1/1,581,566 alleles · very rare exomes 1/1,429,518 · genomes 0/152,048 · 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: TSC2
Protein: p.Pro670Ser
Coding: c.2008C>T
MANE Select: NM_000548
dbSNP: rs1338802781
Type: single nucleotide variant
Location: chr16:2071845 (GRCh38)
Gene constraint: LOEUF 0.203 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 68.81 · 2 PDB
Residue 670: 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

Similar variants

TSC2 p.Pro670Ala Uncertain significance ★★ ⚠ same residue
TSC2 p.Pro670His Uncertain significance ★ ⚠ same residue
TSC2 p.Pro670Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
TSC2 p.Pro670= Likely benign ★ same residue
TSC2 c.1443+2T>C Pathogenic/Likely pathogenic ★★ same condition
TSC2 c.1443+5G>C Pathogenic/Likely pathogenic ★★ same condition
TSC2 c.1599+1G>A Pathogenic ★★ same condition
TSC2 c.1716+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-pro670ser (accessed [today's date]).

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