ClinVar Miner

Submissions for variant NM_000391.4(TPP1):c.293C>T (p.Thr98Met) (rs140726254)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000118653 SCV000153067 uncertain significance not provided 2014-02-27 criteria provided, single submitter clinical testing
GeneDx RCV000186669 SCV000169039 benign not specified 2013-07-03 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV000118653 SCV000284806 benign not provided 2020-12-04 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000509378 SCV000373335 uncertain significance Ceroid lipofuscinosis neuronal 2 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Ambry Genetics RCV000717754 SCV000848613 uncertain significance Seizures 2018-02-12 criteria provided, single submitter clinical testing The p.T98M variant (also known as c.293C>T), located in coding exon 4 of the TPP1 gene, results from a C to T substitution at nucleotide position 293. The threonine at codon 98 is replaced by methionine, an amino acid with similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000186669 SCV000859381 likely benign not specified 2018-02-10 criteria provided, single submitter clinical testing
Nilou-Genome Lab RCV000509378 SCV001737172 uncertain significance Ceroid lipofuscinosis neuronal 2 2021-05-18 criteria provided, single submitter clinical testing
GenomeConnect, ClinGen RCV000509378 SCV000607046 not provided Ceroid lipofuscinosis neuronal 2 no assertion provided phenotyping only GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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