ClinVar Genomic variation as it relates to human health

Located at the last nucleotide of the exon and predicted to result in abnormal splicing leading to an in-frame deletion of the adjacent exon; Published functional studies demonstrate a damaging effect: cell lines containing this variant were able to form colonies and lost contact inhibition; they also showed the ability to form tumors when introduced to mice (Li 2016); Not observed at significant frequency in large population cohorts (Lek 2016); This variant is associated with the following publications: (PMID: 32978145, 28068329, 27617404, 27862945)

ACMG classification criteria: PS3 supporting, PS4 supporting, PM2 moderated, PP1 supporting, PP3 supporting

This sequence change affects codon 1423 of the NF1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the NF1 protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with neurofibromatosis type 1 (PMID: 21520333, 27862945, 28068329). ClinVar contains an entry for this variant (Variation ID: 423536). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of 27 bp, but is expected to preserve the integrity of the reading-frame (PMID: 28068329). This variant disrupts the c.4269G nucleotide in the NF1 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 18546366). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

The c.4269G>A variant (also known as p.K1423K), located in coding exon 31 of the NF1 gene, results from a G to A substitution at nucleotide position 4269. This nucleotide substitution does not change the at codon 1423. However, this change occurs in the last base pair of coding exon 31, which makes it likely to have some effect on normal mRNA splicing. This alteration was reported in individuals who either had a clinical diagnosis of neurofibromatosis type 1(NF1) or had some clinical features of NF1 (Sites ER et al. Am J Med Genet A, 2017 Mar;173:647-653; Pemov A et al. Oncogene, 2017 Jun;36:3168-3177). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site; however, direct evidence is insufficient at this time (Ambry internal data). Based on the majority of available evidence to date, this variant is likely to be pathogenic.

Variant summary: NF1 c.4269G>A (p.Lys1423Lys) alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: One predicts the variant abolishes a 5' splicing donor site. Two predict the variant weakens a 5' donor site. However, these predictions have yet to be confirmed by functional studies. The frequency data for this variant in gnomAD is considered unreliable, as metrics indicate poor data quality at this position. c.4269G>A has been reported in the literature in individuals affected with Neurofibromatosis Type 1 (Pemov_2017, Wei_2020, Lin_2021, Martorana_2023), including at least one de novo case. These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 37090834, 37751797, 28068329, 32978145). ClinVar contains an entry for this variant (Variation ID: 423536). Based on the evidence outlined above, the variant was classified as likely pathogenic.