ClinVar Genomic variation as it relates to human health

Canonical splice site variant predicted to result in an in-frame deletion/insertion of a critical region; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 12807981, 25525159, 21354044, 18546366, 19061981, 26056819, 25541118, 29415745, 23913538, 30908848, 33877690, 33057194, 35982159)

The NF1 c.204+1G>A variant (rs886039548), also known as IVS2+1G>A, is reported in the literature in multiple individuals affected with neurofibromatosis type I (Ars 2003, Pros 2008, Zhang 2015). This variant is reported as pathogenic by multiple laboratories in ClinVar (Variation ID: 265442), and is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. This variant disrupts the canonical splice donor site of intron 2, which is likely to negatively impact gene function. Based on available information, this variant is considered to be pathogenic. References: Ars E et al. Recurrent mutations in the NF1 gene are common among neurofibromatosis type 1 patients. J Med Genet. 2003 40(6):e82. Pros E et al. Nature and mRNA effect of 282 different NF1 point mutations: focus on splicing alterations Hum Mutat. 2008 Sep;29(9):E173-93. Zhang J et al. Molecular Characterization of NF1 and Neurofibromatosis Type 1 Genotype-Phenotype Correlations in a Chinese Population. Sci Rep. 2015 5:11291.

ACMG classification criteria: PVS1 strong, PS4 moderated, PM2 moderated, PM6 moderated

The splice site variant c.204+1G>A in NF1 gene has been reported in the literature in individuals affected with neurofibromatosis type 1 (Zhang J et.al.,2015). This variant has been reported to the ClinVar database as Pathogenic. The c.204+1G>A variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. The variant affects an invariant splice nucleotide and is expected to cause loss of function .Donor and acceptor splice site variants typically lead to a loss of protein function and loss-of-function variants in NF1 are known to be pathogenic (Fahsold R et.al.,2000). For these reasons, this variant has been classified as Pathogenic.

This sequence change affects a donor splice site in intron 2 of the NF1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in the loss of 35 amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with neurofibromatosis type 1 (NF1) (PMID: 12807981, 18546366, 21520333, 26056819). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 265442). Studies have shown that disruption of this splice site results in the activation of a cryptic splice site in exon 2 (Invitae). This variant disrupts a region of the NF1 protein in which other variant(s) (p.Leu43Pro) have been determined to be pathogenic (PMID: 28529006, 31370276; Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

The c.204+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 2 of the NF1 gene. This mutation has been identified in multiple individuals with a clinical diagnosis of neurofibromatosis type 1 (Zhang J et al. Sci Rep. 2015 Jun;5:11291; Leskelä HV et al. Bone. 2009 Feb;44:243-50; Ambry internal data). In addition, RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Another alteration impacting the same donor site (c.204+1G>T) has been detected in multiple individuals with neurofibromatosis type 1 and reported to result in aberrant splicing (Fahsold R et al. Am J Hum Genet, 2000 Mar;66:790-818; Wimmer K et al. Hum Mutat, 2007 Jun;28:599-612; Pros E et al. Hum Mutat, 2008 Sep;29:E173-93). c.204+1G>A is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.