ClinVar Genomic variation as it relates to human health

The p.Glu139Glu (NM_017777.3 c.417G>A) variant in MKS1 has been reported in 8 co mpound heterozygous individuals with Meckel syndrome and 1 compound heterozygous individual with Joubert syndrome (Consugar 2007, Khaddour 2007, Frank 2007, Tal lila 2009, Bachmann-Gagescu 2015). This variant is located in the last base of t he exon, which is part of the 5? splice region, and has been demonstrated to imp act splicing in patient cells (Consugar 2007). It has been identified in 31/126, 722 European chromosomes by the Genome Aggregation Database (gnomAD, http://gnom ad.broadinstitute.org; dbSNP rs386834048, rs370514840). Although this variant ha s been seen in the general population, its frequency is low enough to be consist ent with a recessive carrier frequency. Biallelic loss of function of the MKS1 g ene is associated with Meckel syndrome and Joubert syndrome. In summary, the p. Glu139Glu variant is likely pathogenic for Meckel syndrome in an autosomal reces sive manner based on its occurrence in affected individuals and demonstrated imp act on splicing.

Variant summary: MKS1 c.417G>A (p.Glu139Glu) 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: Two predict the variant abolishes the canonical 5' splicing donor site. At least one publication reports experimental evidence that this variant indeed affects mRNA splicing, leading to the skipping of exon 4 which results in an in-frame deletion (p.Phe88_Glu139del) (Consugar_2007). The variant allele was found at a frequency of 0.00013 in 249574 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in MKS1 causing Meckel Syndrome Type 1 (0.00013 vs 0.0011), allowing no conclusion about variant significance. c.417G>A has been reported in the literature as a biallelic genotype in multiple individuals affected with Meckel Syndrome Type 1, including one homozygote and at least three cases where it was found in trans with a pathogenic variant (e.g. Frank_2007, Consugar_2007, Khaddour_2007, Meier_2019). The variant has also been reported in at least one individual affected with Joubert syndrome (e.g. Bachmann-Gagescu_2015). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 26092869, 17377820, 17437276, 17397051, 30679815, 26490104, 28497568, 19466712). Eight submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as either pathogenic (n=2)/likely pathogenic (n=4) or VUS (n=2). Based on the evidence outlined above, the variant was classified as pathogenic.

The c.417G>A (p.E139E) alteration is located in coding exon 4 of the MKS1 gene. This alteration consists of a G to A substitution at nucleotide position 417. This nucleotide substitution does not change the glutamic acid at codon 139. However, this change occurs in the last base pair of coding exon 4, which makes it likely to have some effect on normal mRNA splicing. This variant has been identified in individuals with Meckel syndrome as well as Joubert syndrome in conjunction with a second MKS1 variant (Frank, 2007; Khaddour, 2007; Consugar, 2007; Bachmann-Gagescu, 2015; Summers, 2017). RT-PCR of fibroblasts from an individual with Meckel syndrome and this variant demonstrated exon skipping (Consugar, 2007). In silico splice site analysis predicts that this alteration may weaken the native splice donor site. Based on the available evidence, this alteration is classified as likely pathogenic.

The MKS1 c.417G>A (p.Glu139Glu) variant has been reported in three studies in probands with Meckel syndrome (MKS) in which it is found in a total of four individuals, all in a compound heterozygous state with a second pathogenic variant (Consugar et al. 2007; Khaddour et al. 2007; Frank et al. 2007). The p.Glu139Glu variant was absent from 410 control chromosomes but is reported at a frequency of 0.000394 in the Ashkenazi Jewish population of the Genome Aggregation Database. The p.Glu139Glu variant is a synonymous variant that affects the last nucleotide of exon four and is predicted to destroy the splice donor site. RT-PCR and sequence analysis of proband fibroblasts showed a smaller abnormal band which when sequenced, confirmed that the variant results in skipping of exon 4 (Consugar et al. 2007). Aberrant splicing is a known mechanism in MKS. Based on the evidence, the p.Glu139Glu variant is classified as likely pathogenic for Meckel syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

This sequence change affects codon 139 of the MKS1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the MKS1 protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs386834048, gnomAD 0.04%). This variant has been observed in individual(s) with Meckel syndrome or Joubert syndrome (PMID: 17377820, 17397051, 17437276, 26092869, 26490104, 28497568). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 1392). 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 exon 4, but is expected to preserve the integrity of the reading-frame (PMID: 17377820). For these reasons, this variant has been classified as Pathogenic.

Converted during submission to Likely pathogenic.

The MKS1 c.417G>A is a noncoding alteration. This variant is predicted to alter splicing based on available splicing prediction programs (SpliceAI, Jaganathan et al. 2019. PubMed ID: 30661751). This variant has been reported in individuals with Joubert syndrome (Table S5, Bachmann-Gagescu et al. 2015. PubMed ID: 26092869; Supplemental Table II, Summers et al. 2017. PubMed ID: 28497568) and Meckel syndrome (Consugar et al. 2007. PubMed ID: 17377820; Meier et al. 2019. PubMed ID: 30679815). mRNA studies in affected individual's fibroblasts confirmed that this variant results in the skipping of exon 4 (Consugar et al. 2007. PubMed ID: 17377820). This variant is reported in 0.039% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. This variant is interpreted as likely pathogenic.