Final classification

VUS

PS2BS2BS3BS4

TSC2

c.2476C>A

p.Leu826Met

missense · exon 22

Gene context NCBI Gene ↗ OncoKB ↗

TSC2 is a tumor suppressor gene that encodes tuberin, a growth-inhibitory protein. Tuberin teams up with hamartin to form the TSC protein complex, which keeps cell growth in check by dampening mTORC1 signaling. Mutations in TSC2 cause tuberous sclerosis, a disorder featuring benign and occasionally malignant tumors, and are also linked to lymphangioleiomyomatosis. Loss-of-function changes in TSC2 are seen in some cancers, such as liver and endometrial cancers, and can make tumors sensitive to mTOR-inhibiting drugs.

This variant

TSC2 is a tumor suppressor whose loss of function causes tuberous sclerosis, and a VUS means current evidence neither confirms nor rules out pathogenicity for this variant. Functional studies show p.Leu826Met retains normal tuberin activity and it was inherited from an unaffected father, yet one confirmed de novo occurrence in a sporadic TSC patient keeps it from being classified benign.

Transcript

NM_000548.5

HGVS · transcript:coding

NM_000548.5:c.2476C>A

GRCh38

chr16:2074320 C>A

GRCh37

chr16:2124321 C>A

VUS: with no TSC2-specific VCEP framework available, generic ACMG/AMP 2015 rules were applied, and strong pathogenic PS2 evidence conflicting with benign BS3 (strong) and BS2/BS4 (supporting) resolves to VUS.

Classification rationale

PS2 BS2BS3BS4 VUS

TSC2 c.2476C>A missense · exon 22

PS2 (Strong): confirmed de novo occurrence of c.2476C>A in sporadic TSC patient S19-01, with both parents tested. BS3 (Strong): the exact p.L826M substitution preserved normal tuberin function in orthogonal assays, comparable to wild type and distinct from damaging comparators. BS2 (Supporting): the variant was identified in a clinically unaffected father who transmitted it to both children. BS4 (Supporting): non-segregation with TSC, as both children inherited L826M from their clinically unaffected father. Overall: VUS, produced by the generic ACMG/AMP 2015 combination rule when strong pathogenic evidence conflicts with strong and supporting benign evidence.

PS2 + BS2 + BS3 + BS4 → VUS

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.

Gene diagram · NM_000548.5 · variants mapped to exon structure

TSC2 NM_000548.5

Fetching transcript structure from UCSC…

Applied criteria · 4 applied · 18 assessed

MetEvidence satisfies this criterion.

Not metEvaluated against available evidence; threshold not reached.

Not assessedApplies in principle, but no evidence was found to evaluate it.

N/ADoesn't apply to this variant type.

Applied · 4

Strength Supporting Moderate Strong Very strong

PS2 strong Pathogenic

Met (strong): confirmed de novo occurrence in sporadic TSC patient S19-01, with both parents tested negative.

PMID:9829910 reports c.2476C>A in exon 21 as a missense mutation in sporadic patient S19-01.PMID:9829910 states that all 11 mutations in sporadic individuals were tested in the respective parents and that none of the parents carried the TSC2 mutations except for the separate S12 familial deletion; it then states that the de novo origin of the 10 sporadic mutations was confirmed by testing both parents.Generic ACMG/AMP PS2 was used because no TSC2-specific VCEP/CSPEC framework was available.

PMID:9829910 ↗PMID:25741868 ↗

BS2 supporting review Benign

Met (supporting): the variant was found in a clinically unaffected father who transmitted it to both children. Flagged for human review: the reports lack detailed age, examination, and penetrance data for the carrier.

PMID:17120248 reports: 'In Family B, both children also inherited a TSC2 L826M polymorphism from their unaffected father.' The paper also states that this polymorphism has no effect on TSC2 protein function.PMID:15483652 identifies L826M in an unaffected relative of a TSC patient and describes it as a nonpathogenic substitution after tuberin-hamartin interaction, signaling, and rheb GTPase assays.The exact case variant is NM_000548.5:c.2476C>A, normalized as NP_000539.2:p.(Leu826Met); the papers use the equivalent L826M notation.

PMID:17120248 ↗PMID:15483652 ↗

BS3 strong Benign

Met (strong): the exact p.L826M substitution preserved tuberin function, with binding, mTOR suppression, and rheb GAP activity comparable to wild type.

PMID:15483652 identified L826M as a nonpathogenic change found in an unaffected relative and experimentally showed preserved tuberin-hamartin interaction, normal inhibition of S6K T389 and S6 phosphorylation, and retained stimulation of rheb GTPase activity.PMID:15483652 provides assay controls and calibration: wild-type tuberin retained activity, mock/untransfected controls established baseline signaling, pathogenic variants showed impaired readouts, L826M was tested in multiple independent experiments, and the normal-function findings were concordant across protein interaction, downstream mTOR signaling, and biochemical GAP activity assays.PMID:17120248 reports that both children in Family B inherited TSC2 L826M from their clinically unaffected father and states that the polymorphism had no effect on TSC2 protein function. The paper itself cites prior functional work rather than presenting a new L826M assay, so it is corroborative and not the primary assay evidence.

PMID:15483652 ↗PMID:17120248 ↗

BS4 supporting Benign

Met (supporting): non-segregation with TSC, as both children in Family B inherited L826M from their clinically unaffected father.

PMID:17120248 reports inheritance of L826M by both children from their unaffected father and states that the polymorphism had no effect on TSC2 protein function.PMID:15483652 reports L826M among nonpathogenic substitutions identified in unaffected relatives of TSC patients.These observations provide lack-of-segregation evidence for the disease phenotype and support BS4.

PMID:17120248 ↗PMID:15483652 ↗PMID:25741868 ↗

Assessed · not applied · 12 not met · 6 not assessed

Pathogenic

PS1 Not met: no distinct nucleotide change producing p.Leu826Met was found; the exact c.2476C>A was reported instead.

PS3 Not met: functional studies of the exact substitution showed preserved tuberin function, with binding, mTOR suppression, and rheb activity comparable to wild type.

PS4 Not assessed: the variant appeared once among 20 sporadic TSC cases with no case-control analysis, so enrichment could not be established.

PM1 Not met: no authoritative VCEP domain list applies, and the N-terminal TSC1-binding region is not established as a critical domain lacking benign variation.

PM2 Not met: gnomAD v4.1 overall allele frequency is 0.13527%, above the <0.1% PM2 threshold.

PM5 Not met: the same-residue p.Leu826Pro comparator (PMID:22903760) has no functional result and is not established as pathogenic.

PP1 Not met: L826M was inherited from a clinically unaffected father by both children in Family B, inconsistent with disease segregation.

PP2 Not met: evidence does not show pathogenic missense is common and benign missense rare in TSC2; the variant itself has benign functional evidence.

PP3 Not met: REVEL score 0.638 is below the ClinGen-calibrated supporting PP3 threshold of 0.773.

PP4 Not assessed: no proband phenotype was available, so phenotype specificity for TSC2-related disease could not be evaluated.

PP5 Not assessed: ClinVar has no expert-panel pathogenic or likely pathogenic assertion for this exact variant.

Benign

BA1 Not met: the highest observed allele frequency, 0.17372% (gnomAD v4.1 European non-Finnish), is far below the >1% BA1 threshold.

BS1 Not met: the highest observed allele frequency, 0.17372% (gnomAD v4.1 European non-Finnish), is below the >0.3% BS1 threshold.

BP1 Not met: TSC2 has a substantial, experimentally documented missense disease mechanism, so it is not a primarily truncating gene for BP1.

BP2 Not assessed: the record does not show L826M in trans with a known pathogenic variant, so the required phase is unestablished.

BP4 Not met: REVEL score 0.638 is above the ClinGen-calibrated supporting BP4 threshold of 0.290.

BP5 Not assessed: no evidence of an alternate molecular diagnosis fully explaining the phenotype was available.

BP6 Not assessed: ClinVar has no expert-panel benign or likely benign assertion for this exact variant.

N/A · 6 PVS1 · PM3 · PM4 · PM6 · BP3 · BP7

Research & evidence

Population frequency

gnomAD v4.1

gnomAD v2.1

v4.1

This variant is present in gnomAD v4.1 (AF= 0.0013527; MAF= 0.13527%, 2182/1613066 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00173723; MAF= 0.17372%, 2050/1180042 alleles, homozygotes = 0); grpmax FAF= 0.00167402.

v2.1

This variant is present in gnomAD v2.1 (AF= 0.000649079; MAF= 0.06491%, 183/281938 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.0011274; MAF= 0.11274%, 145/128614 alleles, homozygotes = 0); grpmax FAF= 0.00103684.

🇨🇦 CA

This variant is present in gnomAD-Canada v1.0 (AF= 0.0002714146129627619, 5/18422 alleles, homozygotes = 0).

Allele frequency by ancestry

three datasets · side by side

gnomAD v4.1

0.14% · 2182 / 1,613,066
0 hom · FAF 0.17%

European (non-Finnish) 2050 / 1,180,042	0.17%
Middle Eastern 6 / 6,046	0.099%
Remaining individuals 48 / 62,486	0.077%
Admixed American 43 / 60,032	0.072%
South Asian 18 / 91,082	0.02%
African/African American 11 / 75,064	0.015%
European (Finnish) 6 / 62,904	0.0095%

+ 3 not observed (Amish, East Asian, Ashkenazi Jewish)

gnomAD v2.1

0.065% · 183 / 281,938
0 hom · FAF 0.1%

European (non-Finnish) 145 / 128,614	0.11%
Admixed American 25 / 35,428	0.071%
Remaining individuals 4 / 7,214	0.055%
South Asian 5 / 30,616	0.016%
European (Finnish) 3 / 24,866	0.012%
African/African American 1 / 24,916	0.004%

+ 2 not observed (Ashkenazi Jewish, East Asian)

gnomAD Canada 🇨🇦

0.027% · 5 / 18,422
0 hom

Latino/Admixed American 1 / 838	0.12%
European (non-Finnish) 4 / 11,742	0.034%

+ 7 not observed (African/African American, Ashkenazi Jewish, East Asian, European (Finnish), Middle Eastern, Remaining individuals, South Asian)

gnomAD v4 ↗ gnomAD v2 ↗ gnomAD 🇨🇦 ↗

ClinVar

This variant has been reported in ClinVar as Likely benign (10 clinical laboratories) and as Benign (8 clinical laboratories) and as Uncertain significance (1 clinical laboratory). (ClinVarID = 41732)

ClinVar ↗

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.638. BayesDel score = 0.0342033.

SpliceAI ↗

Functional Likely Oncogenic

OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. TSC2, a GTPase-activating protein, is altered by mutation in various cancers, including endometrial and colorectal cancer.

OncoKB ↗

COSMIC

Cancer hotspots

Somatic evidence Not in COSMIC / hotspots

COSMIC

This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV104375750, n = 2 times).

Hotspots

This variant does not lie in a statistically significant hotspot.

COSMIC ↗ Hotspots ↗

Literature · how each cited paper was used

4papers cited

Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 5 further PMIDs triaged but not cited — see Sources & references.

Distinct effects of single amino-acid changes to tuberin on the function of the tuberin-hamartin complex.

PMID 15483652 ↗ · Nellist M et al. · 2005 Jan CLINVAR · case observation

Searched

TSC2 c.2476C>ANP_000539.2:p.(L826M)L826M

Found

The paper explicitly studied the TSC2 L826M tuberin substitution. L826M was identified in an unaffected relative of a person with TSC. In the reported functional assays, L826M did not affect the tuberin-hamartin interaction, inhibited S6K T389 and S6 phosphorylation similarly to wild-type tuberin, and increased rheb GTPase activity. The authors reported no evidence that L826M disrupted tuberin function.

Variant

✓ Names this variant — characterised directly

Applied to

→BS2 supporting

The variant was identified in an unaffected relative, supporting observation in an unaffected adult.

→BS3 strong

Direct exact-variant functional evidence shows preserved tuberin function across interaction, downstream signaling, and rheb GAP activity assays.

→BS4 supporting

Reports L826M in unaffected relatives of TSC patients, supporting lack of segregation with disease.

The R367Q, A607T and L826M substitutions are nonpathogenic changes identified in unaffected relatives of TSC patients (Hodges et al13; O. Sancak, manuscript in preparation).

Location Results, first paragraph; Discussion, second paragraph; Table 1 · Context Site-directed mutagenesis of full-length TSC2 followed by assays of tuberin-hamartin interaction, PKB-dependent tuberin phosphorylation, inhibition of S6K T389 and S6 phosphorylation in transfected cells, and in-vitro rheb GTPase activity; L826M was reported in an unaffected relative of a TSC patient. · full text

Unusually mild tuberous sclerosis phenotype is associated with TSC2 R905Q mutation.

PMID 17120248 ↗ · Jansen AC et al. · 2006 Nov CLINVAR · functional

Searched

TSC2 c.2476C>ANP_000539.2:p.(L826M)L826Munaffected father

Found

In Family B, both children inherited the TSC2 L826M polymorphism from their clinically unaffected father. The paper states that this polymorphism had no effect on TSC2 protein function.

Variant

✓ Names this variant — characterised directly

Applied to

→BS2 supporting

The exact L826M variant was inherited from a clinically unaffected father to both children, providing unaffected-adult observation evidence.

→BS3 strong

Corroborates absence of functional effect for L826M, while the primary BS3 evidence comes from PMID:15483652.

→BS4 supporting

Documents inheritance of L826M from a clinically unaffected father to both children, supporting lack of segregation with TSC.

In Family B, both children also inherited a TSC2 L826M polymorphism from their unaffected father. This polymorphism has no effect on the TSC2 protein function.

Location Results, Additional Families · Context Family-based clinical and molecular study of TSC2 codon 905 missense families, with clinical and molecular data from additional TSC families. · full text

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

PMID 25741868 ↗ CLINVAR · functional

Found

Structured finding pending for this record — see source link.

Applied to

→PS2 strong

→BS4 supporting

Exon scanning of the entire TSC2 gene for germline mutations in 40 unrelated patients with tuberous sclerosis.

PMID 9829910 ↗ · Beauchamp RL et al. · 1998 CLINVAR · splicing rna

Searched

c.2476C>ANP_000539.2:p.(L826M)

Found

The paper reports c.2476C>A in TSC2 as a missense mutation in exon 21 in sporadic patient S19-01, describing the resulting amino-acid change as Leu825Met under its numbering. It states that parental testing was performed for sporadic cases and none of the parents carried the TSC2 mutations; it also reports that none of the six missense mutations was observed in at least 80 CEPH control chromosomes. The supplied protein normalization is NP_000539.2:p.(L826M), whereas the paper uses Leu825Met.

Variant

✓ Names this variant — characterised directly

Applied to

→PS2 strong

Reports the exact c.2476C>A variant in a sporadic TSC patient and confirmed absence from both parents in the de novo sporadic cohort.

Among the 20 sporadic cases, we identified 11 mutations (55%) (Table 1) including three missense mutations in E11(Tyr407Asp), E21(Leu825-Met), and E37(Tyr1650Cys)

Location Results, Identification and Characterization of Mutations; Table 1, patient S19-01 · Context Screening of exons 1-41 of TSC2 in 40 unrelated tuberous sclerosis patients, including 20 sporadic cases, using SSCP analysis followed by direct genomic sequencing; parental testing was performed for sporadic cases and a CEPH control panel of at least 80 chromosomes was assessed. · full text

Sources & reference links

8Sources

ClinVar

gnomAD v2.1

gnomAD v4.1

gnomAD-Canada

SpliceAI

OncoKB

COSMIC

Cancer hotspots

Triaged references · 5 PMIDs not cited in assessment

22903760 ↗ Functional assessment of TSC2 variants identified in individuals with tuberous sclerosis complex. ONCOKB

15798777 ↗ Mutational analysis of the TSC1 and TSC2 genes in a diagnostic setting: genotype--phenotype correlations and comparison of diagnostic DNA techniques in Tuberous Sclerosis Complex. CLINVAR

21309039 ↗ Functional assessment of variants in the TSC1 and TSC2 genes identified in individuals with Tuberous Sclerosis Complex. CLINVAR

24033266 ↗ A systematic approach to assessing the clinical significance of genetic variants. CLINVAR

28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR

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