ClinVar Genomic variation as it relates to human health

The FLCN c.250-2A>G variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant is alternatively referred to as IVS4-2A>G in the literature. This variant was reported in individuals with Birt-Hogg-Dubé syndrome (Table 1, Toro et al. 2008. PubMed ID: 18234728; Figure 2, Sattler et al. 2020. PubMed ID: 31958439; Truong et al. 2021. PubMed ID: 34654685). This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/17-17129638-T-C). It is interpreted as likely pathogenic and pathogenic in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/96481/). Variants that disrupt the consensus splice acceptor site in FLCN are expected to be pathogenic. This variant is interpreted as pathogenic.

This sequence change affects an acceptor splice site in intron 4 of the FLCN gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (rs398124533, gnomAD 0.0009%). Disruption of this splice site has been observed in individuals with Birt-Hogg-Dubé syndrome (PMID: 18234728). This variant is also known as IVS4-2A>G. ClinVar contains an entry for this variant (Variation ID: 96481). Studies have shown that disruption of this splice site results in activation of a cryptic splice site, and produces a non-functional protein and/or introduces a premature termination codon (internal data). For these reasons, this variant has been classified as Pathogenic.

This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function.

The FLCN c.250-2A>G variant disrupts a canonical splice-acceptor site and interferes with normal FLCN mRNA splicing. This variant has been reported in the published literature in several affected individuals and families with Birt-Hogg-Dubé syndrome (PMIDs: 18234728 (2008), 31958439 (2020), and 35639097 (2022)). It has also been reported in early onset renal cell carcinoma (PMID: 34654685 (2021)) and rhabdomyoma (PMID: 25610687 (2014)). Based on the available information, this variant is classified as pathogenic.

The c.250-2A>G intronic pathogenic mutation results from an A to G substitution two nucleotides upstream from coding exon 2 in the FLCN gene. This alteration was previously identified in 13 individuals from four unrelated families affected with perifollicular fibromas, trichodiscomas, renal tumors, lung cysts and spontaneous pneumothorax (Toro J et al. J Med Genet. 2008 Jun;45(6):321-31). This alteration has been observed in multiple individuals with a personal and/or family history that is consistent with FLCN-related disease (Ambry internal data). RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation.

Variant summary: FLCN c.250-2A>G, also referred to as IVS4-2A>G in the literature, is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4e-06 in 251292 control chromosomes (gnomAD). c.250-2A>G has been reported in the literature in many individuals from multiple unrelated families affected with Birt-Hogg-Dube Syndrome (e.g. Toro_2008, Mikesell_2014, Sattler_2020). These data indicate that the variant is very likely to be associated with disease. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

Canonical splice site variant expected to result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown; Deletions involving coding exons of this gene are a known mechanism of disease (HGMD); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 19802896, 29357828, 18234728, 25610687, 21937013, 25525159, 31958439, 34654685)