ClinVar Genomic variation as it relates to human health

NM_000071.2(CBS):c.430G>A(E144K) is a missense variant classified as likely pathogenic in the context of homocystinuria, CBS-related. E144K has been observed in cases with relevant disease (PMID: 14722927, 12124992, 11359213, 7611293, 33057012). Functional assessments of this variant are available in the literature (PMID: 25331909, 22267502, 20506325, 20490928). E144K has been observed in population frequency databases (gnomAD: SAS 0.01%). In summary, NM_000071.2(CBS):c.430G>A(E144K) is a missense variant that has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.

Variant summary: CBS c.430G>A (p.Glu144Lys) results in a conservative amino acid change located in the pyridoxal-phosphate dependent enzyme (IPR001926) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.8e-05 in 250114 control chromosomes (gnomAD). c.430G>A has been reported in the literature as a compound heterozygous genotype in trans with other pathogenic alleles in multiple individuals affected with Homocystinuria (e.g. Shih_1995, Gordon_1998, Janosik_2001, Guastadnes_2002,Kozich_2010). These data indicate that the variant is very likely to be associated with disease. In some of these cases, the variant has been reported to co-occur in cis with another variant which has conflicting interpretations of pathogenicity (i.e. c.463G>A, p.A155T in Janosik_2001). Multiple publications report contrasting experimental evidence evaluating an impact on protein function. The variant was found to result in significantly reduced enzyme activity in yeast and bacterial cell lines (e.g. Gordon_1998, Kozich_2010, Mayfield_2012) but had no significant damaging effect in experiments in a mammalian cell line (Melenovska_2014). The following publications have been ascertained in the context of this evaluation (PMID: 12124992, 10215408, 11359213, 20506325, 22267502, 25331909, 7611293). Six submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic (n=5)/likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as pathogenic.

The p.Glu144Lys variant in CBS has been reported in at least 10 individuals with homocystinuria (Shih 1995 PMID: 7611293, Gordon 1998 PMID: 10215408, Gaustadnes 2002 PMID: 12124992, Kaur 2020 PMID: 33057012). It has also been identified in 0.0036% (2/55574) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant has also been reported in ClinVar (Variation ID 122). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In vitro functional studies support an impact on protein function as the expression of enzymatic activity was found to be <1% of wild type in E. Coli and yeast (Gordon 1998 PMID: 10215408, Mayfield 2012 PMID: 22267502). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive homocystinuria. ACMG/AMP Criteria applied: PM3_VeryStrong, PM2_Supporting, PP3, PS3_Supporting. (This variant did not meet the variant calling quality criteria, and was included because it has been previously reported as a clinically significant variant.)

Published functional studies demonstrate a damaging effect through decreased enzyme levels (Kozich et al., 2010); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 15365998, 14722927, 22267502, 9156316, 31301157, 7611293, 11748855, 11359213, 25331909, 12124992, 20567906, 10215408, 20506325, 33057012)

This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 144 of the CBS protein (p.Glu144Lys). This variant is present in population databases (rs121964966, gnomAD 0.01%). This missense change has been observed in individual(s) with homocystinuria (PMID: 7611293, 10215408, 12124992, 33057012). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 122). 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 expected to disrupt CBS protein function. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on CBS function (PMID: 20506325, 22267502, 25331909). For these reasons, this variant has been classified as Pathogenic.

The CBS c.430G>A variant is predicted to result in the amino acid substitution p.Glu144Lys. This variant has been reported in the heterozygous state with a second causative or likely causative variant in multiple patients with cystathionine beta-synthase deficiency (e.g., Shih et al. 1995. PubMed ID: 7611293; Janosík et al. 2001. PubMed ID: 11359213; Gaustadnes et al. 2002. PubMed ID: 12124992; Kaur et al. 2020. PubMed ID: 33057012). Functional studies have shown that the p.Glu144Lys change essentially abolishes CBS activity in E. coli and yeast cells (Kozich et al. 2010. PubMed ID: 20506325; Mayfield et al. 2012. PubMed ID: 22267502), although studies using CHO-K1 cells were conflicting (Melenovská et al. 2014. PubMed ID: 25331909). This variant is reported in 0.0098% of alleles in individuals of South Asian descent in gnomAD. Taken together, this variant is interpreted as likely pathogenic.