TSC1 c.163C>T, p.(Gln55Ter)

Reasoning

NM_000368.5:c.163C>T produces NP_000359.1:p.(Gln55Ter), a nonsense variant located in exon 4 of the TSC1 transcript (23 total coding exons per the gene's published mutational spectrum). The premature termination codon occurs at residue 55 of a 1164-aa protein, far upstream of the final exon-exon junction, so the transcript is predicted to undergo nonsense-mediated decay (NMD) rather than escape it; it is not in the terminal or penultimate exon. No CSPEC/VCEP-specific PVS1 decision tree exists for TSC1 (framework_mode: generic_acmg; no cspec found), so the generic ClinGen SVI PVS1 recommendations (PMC6185798) were applied. Germline loss-of-function is an established disease mechanism for TSC1 (autosomal dominant tuberous sclerosis complex via biallelic/haploinsufficient inactivation of the TSC1-TSC2-TBC1D7 complex, a negative regulator of mTORC1), supported by targeted germline literature review confirming LOF as the causal mechanism. There is no evidence in the case bundle of exon 4 being alternatively spliced/skippable, of the affected region being non-critical, or of population-level enrichment of LoF variants at this exon that would argue for a downgrade. Given confirmed transcript relevance (canonical NM_000368.5), NMD-predicted truncation removing ~95% of the protein, and an established LOF disease mechanism, this variant meets full-strength PVS1 under the generic decision tree.

Rule

PMC6185798 generic PVS1 decision tree, nonsense variant branch: LOF established for gene -> NMD predicted (not last/penultimate exon) -> no evidence of non-critical region or exon-skipping rescue -> PVS1 (Very Strong)

Evidence considered

• pvs1_variant_assessment.json: transcript_hgvs NM_000368.5:c.163C>T, protein_1l NP_000359.1:p.(Q55*), consequence_class 'nonsense', variant_bucket 'nonsense', framework_source PMC6185798, suggested_default_strength 'PVS1'.
• VariantValidator predicted protein alignment: position_first 54, position_last_predicted 55, position_last_original 1165 (i.e. wild-type protein length 1164 aa), confirming the truncation eliminates the vast majority of the protein.
• VariantValidator exonic position mapping places c.163C>T within exon 4 (start_exon/end_exon = '4') for both GRCh37 and GRCh38 coordinates.
• pvs1_gene_context.json: germline_disease_context_found=true, lof_mechanism_supported=true, mechanism_rationale states targeted germline literature review identified disease-focused publications supporting TSC1 loss of function as a germline disease mechanism, so generic PVS1 framework assessment is eligible; pvs1_gene_gate='eligible'.
• pvs1_gene_context.json caution notes: no official CSPEC/VCEP or local explicit PVS1 framework available, so generic PVS1 fallback follows PMC6185798.
• PMID:10227394 abstract snippet states the TSC1 gene 'has 23 exons, spanning 45 kb of genomic DNA, and encoding an 8.6 kb mRNA,' establishing exon 4 as an early, non-terminal exon relative to the 23-exon gene structure, consistent with NMD-predicted decay for the exon-4 nonsense variant.
• case_summary.json normalization: protein_3l NP_000359.1:p.(Gln55Ter) confirms nonsense/stop-gain consequence at codon 55.

Still missing

• No formal gnomAD constraint metrics (pLI/LOEUF) or exon-level population LoF enrichment data were available in the case bundle to explicitly rule out a non-critical/tolerated exon.
• No experimental NMD confirmation (e.g., RNA studies) was available; NMD status is predicted from position (>50bp from final exon-exon junction, exon 4 of 23), not directly measured.

Sources

Reasoning

PM2 is met at moderate strength under the generic ACMG/AMP framework: the exact TSC1 c.163C>T (p.Gln55Ter) variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.

Rule

Generic ACMG/AMP PM2 (moderate): absent from controls (or at extremely low frequency if recessive) in population databases.

Evidence considered

• No TSC1-specific ClinGen VCEP specification or local gene-specific framework was retrieved; generic ACMG/AMP assessment was used.
• The normalized exact variant is NC_000009.11:g.135802635G>A (GRCh37) / NC_000009.12:g.132927248G>A (GRCh38), corresponding to NM_000368.5:c.163C>T, p.(Gln55Ter).
• The variant was reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, with no overall or ancestry-specific allele count or frequency reported.
• Under the generic ACMG/AMP framework, PM2 applies to variants absent from controls or at extremely low frequency when consistent with the disorder; the observed absence satisfies this evidence item.

Sources

Reasoning

BA1 is not met: the exact variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, so no population allele frequency approaches the generic stand-alone benign threshold.

Rule

Generic ACMG/AMP BA1: an allele frequency above the stand-alone benign threshold is required; absent variants do not meet BA1.

Evidence considered

• No TSC1-specific ClinGen VCEP specification or local gene-specific framework was retrieved; generic ACMG/AMP population-frequency assessment was used.
• The normalized exact variant is NC_000009.11:g.135802635G>A (GRCh37) / NC_000009.12:g.132927248G>A (GRCh38), corresponding to NM_000368.5:c.163C>T, p.(Gln55Ter).
• The variant was reported absent in gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; therefore it cannot meet a stand-alone benign frequency threshold.

Sources

Reasoning

BS1 is not met: the exact variant is absent from all three queried population datasets, so there is no allele frequency greater than expected for TSC1-related tuberous sclerosis complex.

Rule

Generic ACMG/AMP BS1: apply only when observed population frequency is greater than expected for the disorder.

Evidence considered

• No TSC1-specific ClinGen VCEP specification or local gene-specific framework was retrieved; generic ACMG/AMP population-frequency assessment was used.
• The variant was absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, with no overall or ancestry-specific allele count or frequency reported.
• An absent allele has no frequency that can exceed the frequency expected for the relevant disease; BS1 is therefore not met.

Sources

Reasoning

No case-level documentation establishes that NM_000368.5:c.163C>T (p.Gln55Ter) occurred de novo in an affected individual with both parents tested and biological parentage confirmed. A ClinVar research submission records de novo origin, but supplies neither parental test results nor phenotype or parentage details; it cannot establish PS2.

Rule

Generic ACMG/AMP 2015 PS2: de novo occurrence in a patient with the disease and no family history, with maternity and paternity confirmed.

Evidence considered

• No TSC1 ClinGen VCEP/cSPEC or local gene-specific framework was retrieved; generic ACMG/AMP evidence assessment is the governing fallback.
• ClinVar lists the exact variant and one research submission with origin recorded as de novo, but the bundle provides no supporting parental genotypes, parentage confirmation, phenotype, or case-level evidence for that assertion.
• PMID:10227394 and PMID:17304050 were reviewed because they were linked to the exact ClinVar record; neither full text mentions c.163C>T, p.Gln55Ter, or a corresponding case, so neither provides de novo evidence for this variant.

Still missing

• Obtain the proband phenotype and diagnostic basis for tuberous sclerosis complex.
• Obtain molecular results for both parents using an assay with adequate sensitivity for parental mosaicism.
• Obtain biological parentage confirmation and the number of independent qualifying de novo observations.

Sources

Reasoning

No variant-specific functional assay data (e.g., minigene splicing assay, TSC1/TSC2 GAP complex activity assay, mTORC1 signaling rescue assay, or other validated well-established functional study) for NM_000368.5:c.163C>T (p.Gln55Ter) was identified in the case bundle or in the retrieved full-text publications. Available TSC1 literature (PMID:23485365, PMID:24529379, PMID:22923433) discusses TSC1/mTORC1 pathway biology and gene-level loss-of-function mechanism generally, or reports other somatic TSC1 mutations, but none report a validated functional assay conducted on this specific variant. No ClinGen VCEP-specific PS3/BS3 functional assay framework is available for TSC1 (cspec.found=false, framework_mode=generic_acmg), so generic ACMG/AMP PS3 criteria requiring a validated assay directly interrogating this variant's effect cannot be met.

Still missing

• No variant-specific functional assay (splicing, protein stability, GAP-domain/mTORC1 activity, or complementation) identified for c.163C>T / p.Gln55Ter
• No ClinGen TSC1/TSC2 VCEP specification available to define validated assay types or PS3 strength calibration
• Full-text review of the six available fulltext_map.json papers did not locate the variant or an assay result for it

Sources

Reasoning

No case-control or other statistically valid enrichment dataset for the exact TSC1 variant was provided. ClinVar submissions and cited cohort leads cannot substitute for a controlled enrichment analysis.

Rule

Generic ACMG/AMP PS4 requires a statistically increased prevalence of the variant in affected individuals compared with controls; reports or assertions without controlled enrichment data are insufficient.

Evidence considered

• ClinVar's exact-variant record contains individual laboratory submissions and literature leads, but the available material provides no case-control counts, odds ratio, or enrichment statistic for p.Gln55Ter.

Still missing

• Case and control counts for NM_000368.5:c.163C>T (p.Gln55Ter), with a prespecified phenotype and statistical analysis.

Sources

Reasoning

The unsupported ClinVar de novo-origin field alone does not provide sufficient case-level evidence to apply assumed de novo evidence. No proband phenotype, parental genotypes, or documentation of which parent(s) were tested is available.

Rule

Generic ACMG/AMP 2015 PM6: assumed de novo occurrence without confirmation of paternity and maternity; case-level phenotype and parental testing information are required to evaluate the observation.

Evidence considered

• No TSC1 ClinGen VCEP/cSPEC or local gene-specific framework was retrieved; generic ACMG/AMP evidence assessment is the governing fallback.
• ClinVar lists one research submission with origin recorded as de novo, but the bundle supplies no case-level details needed to assess an assumed de novo observation.
• PMID:10227394 and PMID:17304050 were reviewed because they were linked to the exact ClinVar record; neither full text mentions c.163C>T, p.Gln55Ter, or a corresponding case.

Still missing

• Obtain the proband phenotype and diagnostic basis for tuberous sclerosis complex.
• Obtain parental molecular testing results; if biological parentage cannot be confirmed, document the tested parents and assay limitations.
• Obtain source case documentation for the de novo-origin assertion.

Sources

Reasoning

No informative family pedigree, affected-relative genotypes, unaffected-relative genotypes, or meiosis count is provided for this variant. Therefore, cosegregation cannot be assessed.

Rule

Generic ACMG/AMP 2015 PP1: cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease.

Evidence considered

• No TSC1 ClinGen VCEP/cSPEC or local gene-specific framework was retrieved; generic ACMG/AMP evidence assessment is the governing fallback.
• The case-evidence bundle contains no variant-specific familial cosegregation data or meiosis counts.
• PMID:10227394 and PMID:17304050 were reviewed because they were linked to the exact ClinVar record; neither full text mentions c.163C>T, p.Gln55Ter, or a corresponding family.

Still missing

• Obtain a pedigree with phenotypes and molecular results for informative relatives.
• Document the number of informative meioses and any non-segregating relatives, accounting for age-dependent or variable expression.

Sources

Reasoning

No proband-level phenotype was supplied for this case. The ClinVar condition labels include tuberous sclerosis and bladder cancer, but they do not document the evaluated individual's phenotype or establish that it is highly specific for a TSC1-related disorder.

Rule

Generic ACMG/AMP PP4 requires a patient phenotype or family history that is highly specific for a disease with a single genetic etiology; condition labels alone do not establish this criterion.

Evidence considered

• The exact-variant ClinVar record lists conditions including tuberous sclerosis 1, tuberous sclerosis syndrome, malignant tumor of urinary bladder, and not provided; no individual-level phenotype is available in the bundle.

Still missing

• Proband-level clinical features, diagnostic evaluation, and differential diagnosis information sufficient to assess phenotype specificity for TSC1-related tuberous sclerosis complex.

Sources

Reasoning

The exact ClinVar record has pathogenic laboratory submissions but no expert-panel submission. Under the requested restricted rule, non-expert pathogenic assertions cannot support PP5.

Rule

Apply PP5 only for an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification.

Evidence considered

• The exact-variant ClinVar submission audit reports zero expert-panel submissions; the pathogenic assertions are single-submitter laboratory or research submissions.

Still missing

• An exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion.

Sources

Reasoning

BS2 cannot be assessed because the variant is absent from the queried population datasets and the supplied evidence contains no observation of this variant in a healthy adult individual, including no homozygote observation.

Rule

Generic ACMG/AMP BS2: requires observation in a healthy adult individual for a disorder expected to be fully penetrant at an early age; absence and unreported homozygotes are insufficient.

Evidence considered

• The exact variant was absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; consequently these data provide neither healthy adult observations nor homozygote observations.
• Absence in population datasets is not evidence for BS2.

Still missing

• No cohort-level evidence documents healthy adult carriers or homozygotes for this exact variant.
• No TSC1-specific BS2 specification defining an eligible unaffected-adult cohort, age threshold, or required observation count was retrieved.

Sources

Reasoning

No variant-specific functional assay data showing normal/wild-type function for NM_000368.5:c.163C>T (p.Gln55Ter) was identified. The variant is a premature termination codon in exon 5 of 23 (well upstream of the final exon), consistent with a predicted loss-of-function mechanism per gene-level literature (PMID:23485365, PMID:24529379), but no direct functional assay result (splicing, protein expression/stability, or TSC-complex/mTORC1 activity) evaluating this exact variant was found, so BS3 cannot be assessed as met or not_met on functional grounds.

Still missing

• No variant-specific functional assay data available to evaluate for a benign/normal-function signal
• No ClinGen TSC1/TSC2 VCEP specification available to define validated assay types or BS3 strength calibration

Sources

Reasoning

No reliable non-segregation observation is provided. The bundle contains no genotype-positive affected relative lacking the variant, nor an appropriately evaluated genotype-positive unaffected relative that could support BS4.

Rule

Generic ACMG/AMP 2015 BS4: lack of segregation in affected members of a family.

Evidence considered

• No TSC1 ClinGen VCEP/cSPEC or local gene-specific framework was retrieved; generic ACMG/AMP evidence assessment is the governing fallback.
• The case-evidence bundle contains no variant-specific familial non-segregation data.
• PMID:10227394 and PMID:17304050 were reviewed because they were linked to the exact ClinVar record; neither full text mentions c.163C>T, p.Gln55Ter, or a corresponding family.

Still missing

• Obtain a pedigree, relative phenotypes, ages, and molecular results to identify informative non-segregation.
• Assess penetrance, variable expression, age-dependent manifestations, and parental mosaicism before considering non-segregation evidence.

Sources

Reasoning

BP2 cannot be assessed because no observation places c.163C>T in trans with a pathogenic/likely pathogenic variant for a dominant disorder, or in cis with a pathogenic/likely pathogenic variant. No phase data or second germline variant are supplied.

Rule

Generic ACMG/AMP BP2: observation in trans with a pathogenic variant for a dominant disorder, or in cis with a pathogenic variant in any inheritance pattern, requires confirmed allelic phase.

Evidence considered

• No TSC1 CSPEC/VCEP framework was retrieved; the case framework specifies generic ACMG/AMP fallback.
• PMID:17304050 establishes the relevant tuberous sclerosis complex context as autosomal dominant; however, it does not provide a qualifying allelic observation for c.163C>T.
• The consolidated case-evidence bundle contains no second germline pathogenic/likely pathogenic variant and no cis/trans phase result for c.163C>T.

Still missing

• Affected-proband genotype showing a second pathogenic/likely pathogenic variant and laboratory-confirmed phase (trans or cis), together with the associated disorder context.

Sources

Reasoning

No evaluated individual, phenotype, or alternative molecular diagnosis is provided. The available ClinVar condition labels cannot demonstrate that the phenotype is fully explained by a separate molecular cause.

Rule

Generic ACMG/AMP BP5 requires a variant identified in an individual with an alternate molecular basis for the disease.

Evidence considered

• The exact-variant ClinVar record provides condition labels but no evidence of a second molecular diagnosis in an evaluated individual.

Still missing

• Proband-level phenotype and a confirmed alternative molecular diagnosis that fully explains that phenotype.

Sources

Reasoning

No exact-variant ClinVar expert-panel Benign or Likely benign assertion is present. Under the requested restricted rule, neither aggregate labels nor non-expert assertions can support BP6.

Rule

Apply BP6 only for an exact-variant ClinVar expert-panel Benign or Likely benign classification.

Evidence considered

• The exact-variant ClinVar submission audit reports zero expert-panel submissions and no Benign or Likely benign submission.

Still missing

• An exact-variant ClinVar expert-panel Benign or Likely benign assertion.

Sources