Variant classification summary

NM_000368.4:c.682C>T

TSC1 · NP_000359.1:p.(Arg228Ter) · NM_000368.4

GRCh37: chr9:135796805 G>A · GRCh38: chr9:132921418 G>A

Gene: TSC1 Transcript: NM_000368.4

Final call

Pathogenic

PVS1 very strong PS4 moderate PM2 moderate PP1 supporting PP5 supporting

Variant details

Gene

TSC1

Transcript

NM_000368.4

Protein

NP_000359.1:p.(Arg228Ter)

gnomAD AF

6.195441394222132e-07 (v4.1)

ClinVar

Pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000368.4:c.682C>T (p.Arg228Ter) is a nonsense variant in exon 8 of 23 exons of TSC1 predicted to result in nonsense-mediated decay and complete loss of hamartin protein function.

2

The variant is effectively absent from population databases (gnomAD v4.1: 1/1,614,090 alleles, AF = 6.2e-07), meeting PM2 at moderate strength.

3

The variant has been reported in multiple unrelated individuals with Tuberous Sclerosis Complex, including two affected siblings in family HOU-21 (Rose et al. 1999), and has been classified as Pathogenic by 10 independent clinical diagnostic laboratories in ClinVar (VariationID: 49083).

4

Cosegregation with disease was observed in two affected siblings in family HOU-21, with the variant absent in unaffected parents and siblings.

5

Under generic ACMG/AMP 2015 classification rules (Richards et al. 2015), this variant meets criteria for Pathogenic classification: PVS1 (very_strong) + PM2 (moderate) + PS4 (moderate) + PP1 (supporting) + PP5 (supporting).

Final determination: Generic ACMG/AMP 2015 fallback rules support a Pathogenic classification based on the observed combination of very strong, strong, moderate, and supporting pathogenic criteria.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Met	NM_000368.4:c.682C>T is a nonsense variant (p.Arg228Ter) in exon 8 of 23 exons of TSC1. Loss-of-function is an established disease mechanism for Tuberous Sclerosis Complex, and nonsense-mediated decay is predicted for this early truncation at codon 228 of 1164. Under the generic PVS1 decision framework (PMC6185798), this null variant qualifies for PVS1 at the very-strong level.	pvs1_generic_framework pvs1_gene_context pvs1_variant_assessment PMID:10090883
PS1	N/A	PS1 applies when the identical amino acid change arises from a different nucleotide change that is already established as pathogenic. No such comparator nucleotide change was identified for p.Arg228Ter.
PS2	Not met	No confirmed de novo observation with proven maternity and paternity was identified. PMID:10090883 reports two affected siblings in family HOU-21 with unaffected parents, attributed to maternal germline mosaicism rather than a confirmed de novo event. The Victorian Clinical Genetics Services submission mentions de novo cases, but no independently verifiable de novo data with established parentage is available.	PMID:10090883
PS3	Not met	No variant-specific functional data were identified for NM_000368.4:c.682C>T (p.Arg228Ter). The OncoKB-indexed publications (PMID:23485365, PMID:24529379) discuss general TSC1/TSC2 pathway biology and mTORC1 regulation but do not test this specific variant. No systematic functional characterization (e.g., saturation mutagenesis, tiling screen) spanning codon 228 was identified. PMID:21510812 was indexed as a candidate PS3 source but no full text is available to verify variant-specific functional data.
PS4	Met	This variant has been reported in multiple individuals with Tuberous Sclerosis Complex. PMID:10090883 reports two affected siblings in family HOU-21 harboring this variant. In ClinVar, 10 clinical diagnostic laboratories have independently classified this variant as Pathogenic, indicating observation in numerous affected individuals. The variant is effectively absent from the general population (gnomAD v4.1: 1/1,614,090 alleles, AF = 6.2e-07). The prevalence in affected individuals significantly exceeds the population frequency.	PMID:10090883 clinvar gnomad_v4
PS5	Not met	No independently confirmed de novo observation for this variant by a different group in a laboratory with established parentage testing. The PS2 criterion was not met; PS5 similarly requires evidence of a de novo observation that is not available.
PM1	Not met	Codon 228 in TSC1 is not located in a statistically significant mutational hotspot (cancerhotspots.org negative) or in a specific well-established critical functional domain at the residue level. While the nonsense variant truncates the protein before the coiled-coil domain (aa 719-998) and TSC2-binding regions, PM1 requires the variant to be located within a defined functional domain, not merely upstream of it. The truncating effect is already captured by PVS1.
PM2	Met	This variant is effectively absent from large population databases. It is absent from gnomAD v2.1 and present at an extremely low frequency in gnomAD v4.1 (1/1,614,090 alleles, AF = 6.2e-07, 0 homozygotes), far below the 0.1% threshold for PM2. It is also absent from gnomAD-Canada v1.0.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	NM_000368.4:c.682C>T is a nonsense variant producing a premature termination codon (p.Arg228Ter). The PM5 criterion assesses missense changes at the same residue where a different pathogenic missense change has been previously reported. No same-residue missense comparator was identified, and the variant type (nonsense) does not align with the classic PM5 semantics.	pm5_candidates
PM6	Not met	No confirmed de novo observation with established maternity and paternity was identified. PM6 requires a de novo observation with confirmed parentage, which is not available for this variant.
PP1	Met	PMID:10090883 reports two affected siblings in family HOU-21 who both carry the C682T (R228X) variant while unaffected parents and unaffected siblings do not. The variant co-segregates with disease in this sibship. Additionally, the Labcorp/Invitae ClinVar submission (SCV000284736) notes segregation with disease in related individuals. Although the family structure is small and the inheritance reflects germline mosaicism, the observation of the variant in multiple affected family members and its absence in unaffected relatives supports pathogenicity.	PMID:10090883
PP2	N/A	PP2 applies to missense variants in genes with a low rate of benign missense variation where missense changes are a common disease mechanism. NM_000368.4:c.682C>T is a nonsense (truncating) variant, not a missense change.
PP3	N/A	PP3 evaluates in silico prediction of deleteriousness for missense and splice variants. NM_000368.4:c.682C>T is a nonsense variant whose protein-truncating effect is directly observable. The deleterious impact is established by the variant type, making in silico predictions redundant. SpliceAI predicts no significant splice impact (max delta = 0.17), consistent with a coding effect rather than a splicing defect.	spliceai bayesdel
PP4	Not assessed	PP4 requires that the patient's phenotype or family history is highly specific for the disease with a single genetic etiology. Insufficient phenotype data is available for the index case to assess this criterion.
PP5	Met	This variant is reported as Pathogenic in ClinVar (VariationID: 49083) by 10 independent clinical diagnostic laboratories. Although the aggregate review status is 'criteria provided, single submitter' (1-star) and no expert panel review has been performed, the consistent pathogenic classification across multiple reputable clinical laboratories supports pathogenicity at the supporting evidence level.	clinvar
BA1	Not met	The variant is not common in any population. gnomAD v4.1 maximum population allele frequency is 8.5e-07 in European (non-Finnish), far below the 1% BA1 threshold.	gnomad_v4
BS1	Not met	The variant is essentially absent from population databases. gnomAD v4.1 total AF = 6.2e-07, far below the 0.3% BS1 threshold for a dominant disorder.	gnomad_v4
BS2	Not assessed	BS2 requires observation of the variant in a healthy adult individual for a fully penetrant dominant disorder. No such observation is documented for this variant. The one gnomAD v4.1 allele carrier is of unknown phenotype.
BS3	Not met	No functional studies demonstrate a neutral or benign effect for this variant. No well-established in vitro or in vivo functional data are available to show that this variant does not impair protein function.
BS4	Not assessed	BS4 requires lack of segregation of the variant with disease in multiple affected family members. No such data are available; the only available segregation data (PMID:10090883) shows co-segregation with disease, not lack of segregation.
BP1	N/A	BP1 applies to missense variants in genes where primarily truncating variants cause disease. NM_000368.4:c.682C>T is itself a truncating (nonsense) variant, making BP1 inapplicable.
BP2	Not assessed	BP2 requires observation of the variant in trans with a known pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant in a recessive disorder. No such data are available.
BP4	Not met	BP4 requires multiple lines of computational evidence suggesting no impact on gene or gene product. NM_000368.4:c.682C>T is a nonsense variant that introduces a premature termination codon, unequivocally impacting the protein product. SpliceAI predicts no significant splice alteration (max delta = 0.17), but this does not constitute evidence of a benign effect for a truncating variant. BayesDel score (0.65) is in the deleterious range, not consistent with a benign prediction.	spliceai bayesdel
BP5	Not assessed	BP5 requires that the variant be found in a case with an alternate molecular basis for disease. No alternative molecular diagnosis has been documented for individuals carrying this variant.
BP6	Not met	BP6 applies when a reputable source reports the variant as benign. ClinVar (VariationID: 49083) reports this variant as Pathogenic by 10 clinical laboratories, which directly contradicts BP6.	clinvar
BP7	N/A	BP7 applies to synonymous variants with no predicted splice impact. NM_000368.4:c.682C>T is a nonsense variant producing a premature termination codon (p.Arg228Ter), not a synonymous change.
BP3	N/A	BP3 applies to in-frame indels in repetitive regions without a known function. This variant is a single-nucleotide substitution, not an in-frame indel.
PM3	N/A	PM3 applies to recessive disorders where the variant is detected in trans with a pathogenic variant. TSC is an autosomal dominant disorder; PM3 is not applicable.
PM4	N/A	PM4 applies to in-frame deletions/insertions or stop-loss variants. NM_000368.4:c.682C>T is a single-nucleotide substitution producing a premature stop codon (nonsense), not an in-frame indel or stop-loss variant.

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