ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.266C>A (p.Thr89Lys)

dbSNP: rs1555605392
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Human Genetics, Inc, Center for Human Genetics, Inc RCV000659960 SCV000781868 uncertain significance Neurofibromatosis, type 1 2016-11-01 criteria provided, single submitter clinical testing
Invitae RCV000659960 SCV000818167 uncertain significance Neurofibromatosis, type 1 2023-12-11 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with lysine, which is basic and polar, at codon 89 of the NF1 protein (p.Thr89Lys). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with NF1-related conditions. ClinVar contains an entry for this variant (Variation ID: 547565). 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 expected to disrupt NF1 protein function with a positive predictive value of 95%. 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.
Genome-Nilou Lab RCV000659960 SCV002561430 uncertain significance Neurofibromatosis, type 1 2022-03-15 criteria provided, single submitter clinical testing
Ambry Genetics RCV002424562 SCV002743861 uncertain significance Hereditary cancer-predisposing syndrome; Cardiovascular phenotype 2022-10-31 criteria provided, single submitter clinical testing The p.T89K variant (also known as c.266C>A), located in coding exon 3 of the NF1 gene, results from a C to A substitution at nucleotide position 266. The threonine at codon 89 is replaced by lysine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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