ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.3870G>C (p.Lys1290Asn)

dbSNP: rs1555615497
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000547778 SCV000628551 likely pathogenic Neurofibromatosis, type 1 2023-04-05 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change results in activation of a cryptic splice site and introduces a premature termination codon (Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 457672). This missense change has been observed in individual(s) with clinical features of neurofibromatosis, type 1 (Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces lysine, which is basic and polar, with asparagine, which is neutral and polar, at codon 1290 of the NF1 protein (p.Lys1290Asn). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product.

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