Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000548.5(TSC2):c.133C>A(p.Leu45Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L45P) has been classified as Uncertain significance.
TSC2 (HGNC:12363): (TSC complex subunit 2) This gene is a tumor suppressor gene that encodes the growth inhibitory protein tuberin. Tuberin interacts with hamartin to form the TSC protein complex which functions in the control of cell growth. This TSC protein complex negatively regulates mammalian target of rapamycin complex 1 (mTORC1) signaling which is a major regulator of anabolic cell growth. Mutations in this gene have been associated with tuberous sclerosis and lymphangioleiomyomatosis. [provided by RefSeq, May 2022]
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
BP4
?
BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (MetaRNN=0.2737669).
Loss of catalytic residue at L45 (P = 0.0018);Loss of catalytic residue at L45 (P = 0.0018);Loss of catalytic residue at L45 (P = 0.0018);Loss of catalytic residue at L45 (P = 0.0018);Loss of catalytic residue at L45 (P = 0.0018);Loss of catalytic residue at L45 (P = 0.0018);Loss of catalytic residue at L45 (P = 0.0018);Loss of catalytic residue at L45 (P = 0.0018);Loss of catalytic residue at L45 (P = 0.0018);Loss of catalytic residue at L45 (P = 0.0018);Loss of catalytic residue at L45 (P = 0.0018);Loss of catalytic residue at L45 (P = 0.0018);Loss of catalytic residue at L45 (P = 0.0018);Loss of catalytic residue at L45 (P = 0.0018);.;