ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.1491del (p.Glu498fs)

dbSNP: rs137854346
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine RCV003388570 SCV004100659 likely pathogenic Tuberous sclerosis 2 criteria provided, single submitter clinical testing The frameshift deletion p.E498Rfs*37 in TSC2 (NM_000548.5) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.E498Rfs*37 variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant is predicted to cause loss of normal protein function through protein truncation caused a frameshift mutation. The frame shifted sequence continues 37 residues until a stop codon is reached. The gene TSC2 has a low rate of benign loss of function variants as indicated by a high LoF variants Z-Score of 7.28. The p.E498Rfs*37 variant is a loss of function variant in the gene TSC2, which is intolerant of Loss of Function variants, as indicated by the presence of existing pathogenic loss of function variant NP_000539.2:p.T5Qfs*7 and 472 others. There are 306 downstream pathogenic loss of function variants, with the furthest variant being 1311 residues downstream of the variant p.E498Rfs*37. For these reasons, this variant has been classified as Likely Pathogenic.
Tuberous sclerosis database (TSC2) RCV000042898 SCV000066694 not provided Tuberous sclerosis syndrome no assertion provided curation

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