rs3218716

Description

Low GERP score may suggest that this variant may belong in a lower pathogenicity class

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000042901, PMID:7581410, PS1_S). The variant was co-segregated with Cardiomyopathy, hypertrophic, 1 in multiple affected family members with additional meioses meeting strong evidence levels (PMID: 10521296, 17125710, 23233322, 24111713, 19880069, 22857948, 23283745, 16858239, 24093860, 20031618, PP1_S). A different missense change at the same codon has been reported to be associated with MYH7 related disorder (PMID:17125710, PM5_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000024, PM2_M). The variant is located in a well-established functional domain or exonic hotspot, where pathogenic variants have frequently reported (PM1_M).Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 797 of the MYH7 protein (p.Ala797Thr). This variant is present in population databases (rs3218716, gnomAD 0.007%). This missense change has been observed in individuals with hypertrophic cardiomyopathy (PMID: 10521296, 16858239, 17125710, 19880069, 20031618, 22857948, 23233322, 23283745, 24093860, 24111713). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 42901). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant is found within a region of MYH7 between codons 181 and 937 that contains the majority of the myosin head domain. Missense variants in this region have been shown to be significantly overrepresented in individuals with hypertrophic cardiomyopathy (PMID: 27532257). For these reasons, this variant has been classified as Pathogenic.

Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. p.Ala797Thr (c.2389 G>A) in the MYH7 gene. We classify it as likely disease causing, based on the data reviewed below. The variant has been observed in 14 families with HCM thought to originate from the same founder and an additional 20 presumably unrelated patients with HCM. There is strong segregation data within the founder families and moderate segregation data in other cases. The variant was first published by Moolman-Smook et al in 1995. They reported one Caucasian South African family in which the variant segregated with cardiomyopathy in four first degree relatives. They subsequently identified the variant in several other families and reported that haplotype analysis was consistent with a founder effect (Moolman-Smook et al 2000). This same group published a review that notes that they have observed p.Ala797Thr in 14 families with 80 carriers of this variant (Bink et al 2009). In studying these kindreds the authors have observed that this variant is associated with age-dependent penetrance, with only 2/3 of carriers having hypertrophy by age 35. The variant was also correlated with reduced diastolic dysfunction. This variant has also been observed in patients with HCM outside of South Africa. Van Driest et al (2004) observed the variant in 2 of 389 patients with HCM, ancestry not reported. The variant was reported in a paper from Carolyn Ho's group on echo and MRI phenotyping in sarcomere variant carriers who do not yet have a diagnosis of HCM (Valente et al 2013). Presumably the variant was first identified in a patient with HCM, though that is not explicitly stated in the paper. Kassen et al (2013) observed the variant in 1 of 192 HCM patients in their Egyptian cohort. Nunez et al (2013) observed the variant in 2 of 104 HCM patients in their Spanish cohort. One of the patients also carried p.Arg1022Pro in MYBPC3. Multiple disease associated variants have been reported at either the same or nearby codons (p.Ala797Pro and p. Lue796Phe) (CardioGenomics http://genepath.med.harvard.edu). Conservation analysis indicates that Alanine is partially conserved at this position across species. In silico analysis predicts the variant to be tolerated (SIFT) or benign (polyphen). In total the variant has been seen in ~5/7402 published controls and individuals from publicly available population datasets. The variant was recently reported online in 1 of 2206 African-American individuals and 0 of 4300 Caucasian individuals in the NHLBI Exome Sequencing Project dataset (as of December 19th, 2013). The phenotype of that individual is not publicly available, however the cohorts that were merged to create this dataset were all either general population samples or samples recruited for common cardiovascular disease such as hypertension. Note that other variants with strong evidence for pathogenicity have been seen at similar frequencies in this dataset so this does not necessarily rule out pathogenicity (Pan et al 2012). It is also listed in dbSNP (rs3218716) with the following frequencies in the relevant HapMap samples: 0/60 Caucasians, 1/43 Chinese individuals, 1/86 Japanese individuals, 0/60 African individuals, 1/46 Mexican individuals, 1/88 Italian individuals. The inconsistency between the ESP Caucasian data and the HapMap Caucasian data is curious. We would most likely put more weight on the ESP data. The variant was not observed in the following published control samples: Moolman et al (1995) did not identify the variant in 56 Caucasian and 54 mixed ancestry controls. Van Driest et al (2004) did not observe the variant in 100 African American and 100 Caucasian control samples from Coriell. Nunez et al (2013) did not obs

In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 29300372, 27532257, 26582918, 33297573, 30755392, 33673806, 31589614, 31447099, 30291343, 32233023, 32420109, 31006259, 11186938, 16858239, 19880069, 20031618, 22857948, 23283745, 23782526, 24111713, 25351510, 25937619, 28408708, 29687901, 28615295, 28420666, 28790153, 21310275, 28606303, 28971120, 28138913, 27831900, 27247418, 24793961, 26969327, 27737317, 28166811, 24093860, 19287818, 10521296, 15358028, 23233322, 7581410, 25031304, 23299917, 25637381, 18029407, 17125710, 29260236, 26743238)

MYH7 Ala797Thr has previously been described in HCM patients from at least 11 centres (Moolman., et al 1995; Van Driest., et al 2004; Laredo., et al 2007; Revera., et al 2008; Kaski., et al 2009; Brito., et al 2012; Marsiglia., et al 2013; Kassem., et al 2013; Berge & Leren., et al 2014; Walsh., et al 2017). Strong co-segregation of this variant with disease has been demonstrated in unrelated families (Moolman., et al 1995; Laredo., et al 2007). The variant is present in the Exome Aggregation Consortium dataset (MAF=0.00003; http://exac.broadinstitute.org/). Moolman et al first identified this variant (1995) and haplotype analysis in subsequent papers led them to suggest it may be a South African founder variant (2000). We have observed the Ala797Thr variant in three unrelated HCM probands, one of these proband also has a second MYH7 variant (p.Arg807His) which was inherited in trans. In a large HCM population study Walsh et al., showed that MYH7 variants identified in HCM cases were found to cluster between amino acids 181- 937 (2017), this implies that variants in this region are likely to cause a HCM phenotype. Based on the adapted ACMG guidelines (Kelly MA, et al., 2018) this variant has been reported in well over 15 HCM probands (PS4), segregates with disease in multiple families (PP1_strong), is located in a known functional domain of MYH7 (PM1) and is rare in the general population (PM2), therefore we classify MYH7 Ala797Thr as "pathogenic".

This missense variant replaces alanine with threonine at codon 797 in the myosin head/motor domain of the MYH7 protein. Alanine at this position is not evolutionarily conserved and occurs in only 7 mammalian species, while all other mammalian species have serine at this position. Computational prediction tools (AGVGD, SIFT, Polyphen and REVEL) indicate that the variant amino acid threonine is likely to be tolerated for protein function. This variant has been reported in many individuals affected with hypertrophic cardiomyopathy (PMID: 7581410, 10521296, 11186938, 11447480, 15358028, 16858239, 17125710, 20031618, 22857948, 23233322, 23283745, 24093860, 24111713, 24793961, 26969327, 27247418, 27532257, 27737317, 27831900, 28138913, 28615295, 28790153, 33297573) and has been shown to segregate with disease in several families (PMID: 11186938, 17125710). This variant is particularly common in the South African individuals affected with hypertrophic cardiomyopathy (PMID: 27841901). This variant has been identified in 6/251468 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, this variant appears to be rare in the general population and has been reported in many affected individuals. The mechanism by which this variant causes disease remains to be investigated. Based on the available evidence, this variant is classified as Likely Pathogenic.

The c.2389G>A;p.(Ala797Thr) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 42901; PMID: 31110529; 23233322; 7581410;18029407;17125710;28606303; 22857948; 28138913; 27831900) - PS4.The variant is located in a mutational hot spot and/or critical and well-established functional domain (IQ) - PM1. The variant is present at low allele frequencies population databases (rs3218716– gnomAD 0.0002629%; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2_supporting. The variant co-segregated with disease in multiple affected family members (PMID: 11186938; 17125710) - PP1_strong. In summary, the currently available evidence indicates that the variant is pathogenic.

PS4, PP1_strong, PM1

This variant was identified in an individual with Wolff-Parkinson-White syndrome

The p.A797T pathogenic mutation (also known as c.2389G>A), located in coding exon 19 of the MYH7 gene, results from a G to A substitution at nucleotide position 2389. The alanine at codon 797 is replaced by threonine, an amino acid with similar properties. This mutation has been reported in association with hypertrophic cardiomyopathy (HCM) and has shown a founder effect in the South African population (Moolman JC et al. Hum Mutat. 1995;6(2):197-8; Moolman-Smook JC et al. Am J Hum Genet. 1999;65(5):1308-20; Revera M et al. Cardiovasc Res. 2008;77(4):687-94; Brito D et al. Rev Port Cardiol. 2012;31(9):577-87; Kassem HSh et al. J Cardiovasc Transl Res. 2013;6(1):65-80; Lopes LR et al. Heart. 2015;01(4):294-301; Walsh R et al. Genet. Med. 2017;19(2):192-203). This alteration has also segregated with disease across several families (Moolman-Smook JC et al. Am J Hum Genet. 1999;65(5):1308-20; Moolman-Smook J et al. J Med Genet. 2000;37(12):951-6; Laredo R et al. Rev Esp Cardiol. 2006;59(10):1008-18). Based on the supporting evidence, p.A797T is interpreted as a disease-causing mutation.

proposed classification - variant undergoing re-assessment, contact laboratory