ClinVar Genomic variation as it relates to human health

The MYL2 Ala13Thr variant has been identified in multiple unrelated cases of HCM (see references) and was absent in over 350 normal chromosomes (Poetter et al., 1996; Anderson et al., 2001). It is also observed in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/) with an allele frequency of 0.03% (37 alleles). Evidence of MYL2 Ala13Thr segregation with disease has been weak. Li et al, (2017) describes a HCM family consisting of 3 affected family members, 3 variants were identified in the proband, including MYL2 Ala13Thr, but unlike the other 2 variants, it did not segregate to all 3 affected. Anderson et al. (2001) observed this variant in one HCM family: 3 carriers (2 affected, 1 clinically unaffected 10yr-old); 1 genotype-negative individual had left ventricular hypertrophy which may be due to hypertension and obesity. The disease in this same family was later suspected to be due to another variant (MYH7 Asn1327Lys) but this did not segregate in 1 clinically affected individual who met diagnostic criteria for HCM (Hougs et al., 2004). Additionally, MYL2 Ala13Thr was found not to segregate with disease in an additional HCM family identified by LMM, they harboured an MYBPC3 variant (Ball et al., 2012). Further, it failed to segregate in one LVNC family (Klassen S, et al., 2008). Two of the HCM families described above were Ashekenazi Jewish (Anderson et al., 2001; Ball et al., 2012), interestingly genome screening in 44 Ashkenazi Jewish centenarians identified MYL2 A13T in 2 people over the age of 94yrs, suggesting that this variant is a common polymorphism in this sub-population (Fraundenberg-Hua Y, et al., 2014). Functional studies including cell models suggest that MYL2 Ala13Thr may alter contractile function (Szczesna-Cordary D, et al., 2001; Roopnarine O, 2003; Szczesna-Cordary et al., 2004) and actin filament velocity (Farman GP, et al., 2014) in cardiac cells. A transgenic mouse model published by Kazmierczak et al., (2012) showed abnormal remodelling of the heart. However, it is noted that these studies may not accurately represent the biological system, in fact the amino acid at this position is not conserved in rats or mice. We have identified the MYL2 Ala13Thr variant in 2 HCM probands, both of North West European descent. Neither proband has a family history of HCM or sudden cardiac death. We note that additional variants have been identified in one proband which may contribute to the disease phenotype (MYH7 Asp1652Tyr; DSG2 Asp535Glu). Although there is reasonable supportive evidence for the pathogenicty of MYL2 Ala13Thr, based on the lack of segregation reported and a population frequency greater 0.02%, we classify this variant as "likely benign".

The MYL2 c.37G>A; p.Ala13Thr variant (rs104894363) is reported in the literature in individuals and families affected with hypertrophic cardiomyopathy, but does not segregate with disease in all affected family members (Ball 2012, Hougs 2005, Klaassen 2008, Li 2017, Mook 2013). This variant is also reported in ClinVar (Variation ID: 14064), and is found in the Ashkenazi Jewish population with an allele frequency of 0.54% (56/10360 alleles) in the Genome Aggregation Database. The alanine at codon 13 is moderately conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.532). Functional studies of the variant protein show this variant may affect contractile function and actin filament velocity in cardiac cells (Farman 2014, Roopnarine 2003, Szczesna 2001, Szczesna-Cordary 2004). Due to conflicting information, the clinical significance of this variant is uncertain at this time. References: Ball MP et al. A public resource facilitating clinical use of genomes. Proc Natl Acad Sci U S A. 2012 Jul 24;109(30):11920-7. PMID: 22797899. Farman GP, Muthu P, Kazmierczak K, Szczesna-Cordary D, Moore JR. Impact of familial hypertrophic cardiomyopathy-linked mutations in the NH2 terminus of the RLC on beta-myosin cross-bridge mechanics. J Appl Physiol (1985). 2014 Dec 15;117(12):1471-7. PMID: 25324513. Hougs L et al. One third of Danish hypertrophic cardiomyopathy patients with MYH7 mutations have mutations in MYH7 rod region. Eur J Hum Genet. 2005 Feb;13(2):161-5. PMID: 15483641. Klaassen S et al. Mutations in sarcomere protein genes in left ventricular noncompaction. Circulation. 2008 Jun 3;117(22):2893-901. PMID: 18506004. Li L et al. A Potential Oligogenic Etiology of Hypertrophic Cardiomyopathy: A Classic Single-Gene Disorder. Circ Res. 2017 Mar 31;120(7):1084-1090. PMID: 28223422. Mook OR et al. Targeted sequence capture and GS-FLX Titanium sequencing of 23 hypertrophic and dilated cardiomyopathy genes: implementation into diagnostics. J Med Genet. 2013 Sep;50(9):614-26. PMID: 23785128. Roopnarine O. Mechanical defects of muscle fibers with myosin light chain mutants that cause cardiomyopathy. Biophys J. 2003 Apr;84(4):2440-9. PMID: 12668451. Szczesna D et al. Familial hypertrophic cardiomyopathy mutations in the regulatory light chains of myosin affect their structure, Ca2+ binding, and phosphorylation. J Biol Chem. 2001 Mar 9;276(10):7086-92. PMID: 11102452. Szczesna-Cordary D, Guzman G, Ng SS, Zhao J. Familial hypertrophic cardiomyopathy-linked alterations in Ca2+ binding of human cardiac myosin regulatory light chain affect cardiac muscle contraction. J Biol Chem. 2004 Jan 30;279(5):3535-42. PMID: 14594949.

The p.Ala13Thr variant in MYL2 has been reported in 6 individuals with HCM and segregated with disease in 3 affected relatives from 2 families (Poetter 1996, Andersen 2001, Hougs 2005, Klaassen 2008, Mook 2013, LMM data). However, 2 additional relatives with cardiomyopathy from 2 families did not carry the p.Ala13Thr variant (2 non-segregations; Andersen 2001, LMM data). It has also been identified in 0.05% (34/66444) of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs104894363). Functional studies examining effects of this mutation on protein function were not conclusive (Szczesna 2001, Szczesna-Cordary 2004, Farman 2014). Transgenic mice with the p.Ala13Thr variant have left ventricular hypertrophy (Kazmierczak 2012). However, this study may not accurately represent biological function. In summary, due to conflicting information, the clinical significance of the p.Ala13Thr variant is uncertain.

The p.Ala13Thr variant in the MYL2 gene has been previously reported in 3 unrelated individuals with hypertrophic cardiomyopathy and 1 unrelated asymptotic individual; this variant co-segregated with disease in at least 1 affected relative and failed to segregate with disease in at least 1 affected relative (Andersen et al., 2001; Ball et al., 2012; Li et al., 2017; Poetter et al., 1996). This variant has also been identified in 56/10,360 Ashkenazi Jewish and 29/129,136 European chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). This allele frequency is greater than would be expected to be disease-causing for hypertrophic cardiomyopathy. Functional studies of the p.Ala13Thr variant are supportive of a deleterious effect to the protein; however, it is unclear if this would be sufficient to be disease-causing (Kazmierczak et al., 2012). Computational tools predict that this variant is deleterious; however, the accuracy of in silico algorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, the significance of the p.Ala13Thr variant is uncertain. Additional information is needed to resolve the significance of this variant. [ACMG evidence codes used: PS3_supporting; PP3; BS1]

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

Identified independently and in conjunction with additional cardiogenetic variants in individuals referred for cardiomyopathy at GeneDx and in published literature (PMID: 8673105, 11748309, 15483641, 22958901, 18506004, 28223422); Did not segregate with HCM phenotype in one affected relative tested at GeneDx and segregation data in the literature is not definitive (PMID: 15483641, 18506004, 28223422); Published functional studies demonstrate a damaging effect (PMID: 12668451, 11102452, 14594949, 22091967, 26664906); nevertheless, it is unclear how these studies may translate to a pathogenic role in human disease; In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 14594949, 23785128, 23299917, 26074085, 30605904, 24055113, 23861362, 25637381, 25333069, 11102452, 25324513, 11748309, 27153395, 26385864, 27084718, 28510043, 26664906, 28223422, 23197161, 24111713, 26272908, 28518168, 23365102, 28467684, 22958901, 25351510, 31019283, 18506004, 30706179, 33232181, 31980526, 22091967, 22797899, 8673105, 35653365, 15483641, 12668451, 37652022)