ClinVar Genomic variation as it relates to human health

The L277P variant in the MKKS gene has been reported previously in two unrelated individuals with Bardet-Biedl syndrome who each also harbored a loss-of-function variant in MKKS (Katsanis et al., 2000; Moore et al., 2005). The L277P variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The L277P variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position where amino acids with similar properties to Leucine are tolerated across species. Functional studies demostrated that L277P could not rescue the morphant phenotype in zebrafish embryos, suggesting that L277P has a damaging effect on the MKKS protein (Zaghloul et al., 2010). We interpret L277P as a pathogenic variant.

Variant summary: MKKS c.830T>C (p.Leu277Pro) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 6.4e-05 in 251158 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in MKKS causing Bardet-Biedl Syndrome (6.4e-05 vs 0.00076), allowing no conclusion about variant significance. c.830T>C has been reported in the literature in both compound heterozygous and homozygous individuals affected with Bardet-Biedl Syndrome and has been reported to segregate with disease in related individuals (e.g., Katsanis_2000, Pereiro_2011, Groopman_2019). These data indicate that the variant is likely to be associated with disease. Several publications report experimental evidence evaluating an impact on protein function, finding that the variant behaved a a null allele in a zebrafish model of gastrulation phenotypes (Zaghloul_2010) and greatly disrupted MKKS protein interactions (e.g., Rachel_2012, Seo_1010). Five ClinVar submitters (evaluation after 2014) have cited the variant with conflicting assessments; four submitters classified the variant as pathogenic/likely pathogenic, and one classified it as uncertain significance. Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 277 of the MKKS protein (p.Leu277Pro). This variant is present in population databases (rs74315398, gnomAD 0.009%). This missense change has been observed in individual(s) with Bardet-Biedl syndrome (PMID: 10973251). 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: 5314). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt MKKS protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects MKKS function (PMID: 20498079, 22446187). For these reasons, this variant has been classified as Pathogenic.

The MKKS c.830T>C variant is predicted to result in the amino acid substitution p.Leu277Pro. This variant has been reported in the compound heterozygous state in at least one individual affected with Bardet-Biedl syndrome, and segregated with disease in the family (Katsanis et al. 2000. PubMed ID: 10973251; Moore et al. 2005. PubMed ID: 15637713). Functional studies revealed that this variant causes disruption of the MKKS-BBS12 interaction and could not rescue the morphant phenotype in zebrafish (Seo et al. 2010. PubMed ID: 20080638; Zaghloul et al. 2010. PubMed ID: 20498079, Supplementary Table 5; Hulleman et al. 2016. PubMed ID: 26900326). At PreventionGenetics, we identified this variant in the heterozygous state, along with a second heterozygous pathogenic variant, in an affected patient (internal data). Based on these observations, this variant is classified as pathogenic.