ClinVar Miner

Submissions for variant NM_207346.3(TSEN54):c.1079C>T (p.Ala360Val)

gnomAD frequency: 0.00019  dbSNP: rs368377822
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics Inc RCV000993357 SCV001146256 likely benign not provided 2019-03-19 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001125686 SCV001284785 uncertain significance Pontoneocerebellar hypoplasia 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.
GeneDx RCV000993357 SCV001756752 likely benign not provided 2020-03-03 criteria provided, single submitter clinical testing
Invitae RCV000993357 SCV002110212 uncertain significance not provided 2022-10-03 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 360 of the TSEN54 protein (p.Ala360Val). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with TSEN54-related conditions. ClinVar contains an entry for this variant (Variation ID: 805689). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TSEN54 protein function. 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.
CeGaT Center for Human Genetics Tuebingen RCV000993357 SCV004144236 likely benign not provided 2022-11-01 criteria provided, single submitter clinical testing TSEN54: BP4

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