ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.366CTT[1] (p.Phe124del)

dbSNP: rs1342475885
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000644181 SCV000765871 uncertain significance Tuberous sclerosis 2 2024-04-15 criteria provided, single submitter clinical testing This variant, c.369_371del, results in the deletion of 1 amino acid(s) of the TSC2 protein (p.Phe124del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with TSC2-related conditions. ClinVar contains an entry for this variant (Variation ID: 535946). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. RNA analysis performed to evaluate the impact of this variant on mRNA splicing indicates it does not significantly alter splicing (Invitae). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx RCV002245065 SCV002513164 uncertain significance not provided 2022-05-06 criteria provided, single submitter clinical testing In silico analysis supports a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 18466115)
Ambry Genetics RCV002343305 SCV002621423 uncertain significance Hereditary cancer-predisposing syndrome 2024-06-17 criteria provided, single submitter clinical testing The c.369_371delCTT variant (also known as p.F124del) is located in coding exon 4 of the TSC2 gene. This variant results from an in-frame CTT deletion at nucleotide positions 369 to 371. This results in the in-frame deletion of a phenylalanine at codon 124. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
All of Us Research Program, National Institutes of Health RCV004004010 SCV004825732 uncertain significance Tuberous sclerosis syndrome 2023-08-15 criteria provided, single submitter clinical testing This variant is a deletion of one amino acid at position 124 of the TSC2 protein. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with TSC2-related disorders in the literature. This variant has been identified in 1/31396 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV002245065 SCV005622705 uncertain significance not provided 2023-10-16 criteria provided, single submitter clinical testing

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