ClinVar Miner

Submissions for variant NM_000268.4(NF2):c.1490G>C (p.Ser497Thr) (rs900545157)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000455655 SCV000539889 uncertain significance not specified 2016-06-23 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Reported in 1 paper
Invitae RCV000804584 SCV000944501 uncertain significance Neurofibromatosis, type 2 2019-12-12 criteria provided, single submitter clinical testing This sequence change replaces serine with threonine at codon 497 of the NF2 protein (p.Ser497Thr). The serine residue is moderately conserved and there is a small physicochemical difference between serine and threonine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in an individual with clinical features of neurofibromatosis type 2 (PMID: 15684865). ClinVar contains an entry for this variant (Variation ID: 403231). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.
Ambry Genetics RCV001011871 SCV001172249 uncertain significance Hereditary cancer-predisposing syndrome 2019-05-03 criteria provided, single submitter clinical testing The p.S497T variant (also known as c.1490G>C), located in coding exon 14 of the NF2 gene, results from a G to C substitution at nucleotide position 1490. The serine at codon 497 is replaced by threonine, an amino acid with similar properties. This alteration has been reported in a cohort of 271 patient samples, however authors note that only a minority of these samples meet the full National Institutes of Health (NIH) criteria for Neurofibromatosis type 2 (NF2) because many requests were from patients in whom NF2 was a differential diagnosis (Wallace AJ et al. Genet. Test., 2004;8:368-80). This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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