ClinVar Genomic variation as it relates to human health

c.665+1 G>A: IVS6+1 G>A in intron 6 of the CLN6 gene (NM_017882.2). The c.665+1 G>A splice site mutation in the CLN6 gene destroys the canonical splice donor site in intron 6. This mutation is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. Although this mutation has not been previously reported to our knowledge, homozygosity for this mutation is consistent with a diagnosis of neuronal ceroid lipofuscinosis (NCL). The variant is found in EPILEPSY panel(s).

The homozygous c.665+1G>A variant in CLN6 was identified by our study in two siblings with neuronal ceroid lipofuscinosis. The c.665+1G>A variant in CLN6 has been previously reported in one individual with neuronal ceroid lipofuscinosis 6A (PMID: 34849271), but has been identified in 0.0009% (1/113632) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs796052356). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar (Variation ID: 205171) and has been interpreted as pathogenic by GeneDx and as likely pathogenic by Invitae. The affected individual previously reported was a homozygote (PMID: 34849271), and the two siblings identified by our study were also homozygotes, which increases the likelihood that the c.665+1G>A variant is pathogenic. A different nucleotide change that also results in a splice donor variant at the same site, c.665+1G>T (ClinVar Variation ID: 1027501) has been previously reported likely pathogenic, and the variant being assessed here, c.665+1G>A, is predicted by SpliceAI to have a similar effect on splicing. This variant is located in the 5' splice region. Computational tools predict a splicing impact, though this information is not predictive enough to determine pathogenicity. There is an in-frame cryptic splice site 123 bases from the intron-exon boundary, providing evidence that this variant may delete 41 amino acids instead of causing loss of function. However, this information is not predictive enough to determine pathogenicity. Loss of function of the CLN6 gene is an established disease mechanism in autosomal recessive neuronal ceroid lipofuscinosis. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic for autosomal recessive neuronal ceroid lipofuscinosis. ACMG/AMP Criteria applied: PVS1_Strong, PS1_Supporting, PM2_Supporting, PM3 (Richards 2015).

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. This variant disrupts the p.Met241 amino acid residue in CLN6. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 12815591, 18811591, 20430023; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 205171). This variant has not been reported in the literature in individuals affected with CLN6-related conditions. This variant is present in population databases (rs796052356, gnomAD 0.0009%). This sequence change affects a donor splice site in intron 6 of the CLN6 gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product.