ClinVar Genomic variation as it relates to human health

The c.5326A>G (p.Ser1776Gly) variant in MYH7 has been reported in 12 individuals with hypertrophic cardiomyopathy (PMID:27532257; PMID:11861413; PMID:21239446; Partners LMM ClinVar SCV000203861.4; SHaRe consortium, PMID: 30297972) but has also been identified in 0.02% (2/8654) of East Asian chromosomes by ExAC (http://exac.broadinstitute.org). Since the MYH7 specifications state that PS4 is only applicable if the variant is absent or rare in large population studies, PS4 criterion was not applied (PMID:29300372). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as uncertain significance for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PP3

In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 16918501, 29300372, 21239446, 11861410, 25961035, 27247418, 23074333, 27532257, 24510615, 29121657, 28518168, 30297972, 31493341, 32420109, 30847666, 37652022, 34542152, 34136434, 34137518, 11861413)

The p.Ser1776Gly variant in MYH7 has been identified in at least 12 individuals with HCM (Blair 2002, Fokstuen 2010, Homburger 2016, Walsh 2017, Kelly 2018, Ho 2018, LMM data) and segregated with disease in 1 affected family member (Blair 2 002). It has also been identified in 0.03% (6/19954) of East Asian and 0.02% (5/ 24968) of African chromosomes by gnomAD (http://gnomad.broadinstitute.org). Comp utational prediction tools and conservation analysis suggest that this variant m ay impact the protein, though this information is not predictive enough to deter mine pathogenicity. Moreover, this variant was classified as a variant of uncert ain significance on December 15, 2016 by the ClinGen-approved Inherited Cardiomy opathy expert panel (SCV000564457.2). In summary, the clinical significance of t he p.Ser1776Gly variant is uncertain due to conflicting evidence. ACMG/AMP Crite ria applied: PP3.

This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 1776 of the MYH7 protein (p.Ser1776Gly). This variant is present in population databases (rs369437262, gnomAD 0.03%). This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 11861413, 27247418, 27532257, 28518168, 29121657). ClinVar contains an entry for this variant (Variation ID: 177629). 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 MYH7 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change does not substantially affect MYH7 function (PMID: 16918501). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

This missense variant replaces serine with glycine at codon 1776 of the MYH7 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). A functional study has shown that this variant does not affect cMyBP-C attachment to the thick filament (PMID: 16918501). This variant has been reported in two related individuals affected with hypertrophic cardiomyopathy (PMID: 11861413) and in four unrelated individuals with hypertrophic cardiomyopathy (PMID: 27247418, 27532257, 29121657, 31493341, 33495597). This variant has been identified in 13/282892 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

This missense variant replaces serine with glycine at codon 1776 of the MYH7 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). A functional study has shown that this variant does not affect cMyBP-C attachment to the thick filament (PMID: 16918501). This variant has been reported in two related individuals affected with hypertrophic cardiomyopathy (PMID: 11861413) and in four unrelated individuals with hypertrophic cardiomyopathy (PMID: 27247418, 27532257, 29121657, 31493341, 33495597). This variant has been identified in 13/282892 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

The p.S1776G variant (also known as c.5326A>G), located in coding exon 35 of the MYH7 gene, results from an A to G substitution at nucleotide position 5326. The serine at codon 1776 is replaced by glycine, an amino acid with similar properties. This variant has been detected in hypertrophic cardiomyopathy cohorts, although, in some cases, clinical details were limited or it co-occurred with other variants (Fokstuen S et al. J Med Genet. 2011;48(8):572-6; Homburger JR et al. Proc Natl Acad Sci U.S.A. 2016 06;113(24):6701-6; Viswanathan SK et al. PLoS ONE. 2017;12(11):e0187948; Walsh R et al. Genet Med. 2017 02;19(2):192-203). In one study, this variant co-segregated with disease in two affected siblings (Blair E et al. Circ Res. 2002;90(3):263-9). This variant has also been seen in an exome cohort, a control cohort, and a biobank cohort but cardiovascular history was not provided (Pan S et al. Circ Cardiovasc Genet. 2012 5(6):602-10; Kapplinger JD et al. J Cardiovasc Transl Res. 2014;7(3):347-61; Park J et al. Hum Mol Genet. 2022 03;31(5):827-837). This variant is located in the LMM protein domain, involved in thick filament assembly supporting contractile function. One in vitro functional study indicated this variant did not disrupt binding to myosin binding protein C, but may affect thick filament structure and stability; however, the physiological relevance of this finding is unclear (Flashman E et al. Biochem J. 2007;401(1):97-102). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear.

The inherited c.5326A>G (p.Ser1776Gly) variant identified in the MYH7 gene substitutes a very well conserved Serine for Glycine at amino acid 1776/1936 (exon 37/40). This variant is found with low frequency in gnomAD(v3.1.1)(8 heterozygotes, 0 homozygotes; allele frequency: 5.256e-5) suggesting that it is not a common benign variant in the populations represented in that database. In silico algorithms predict this variant to be Damaging (SIFT; score:0.001) and Pathogenic (REVEL; score:0.776) to the function of the canonical transcript. This variant has been reviewed by ClinGen's Cardiomyopathy Variant Curation Expert Panel classified as a Variant of Uncertain Significance in ClinVar (VarID:177629). The c.5326A>G (p.Ser1776Gly) variant has been reported in multiple individuals with hypertrophic cardiomyopathy [PMID:11861413, 21239446, 31199839, others], and segregated with disease in one set of siblings [PMID:11861413]. However, this variant has also been detected in control populations [PMID:24510615], and functional studies suggest it does not alter the ability to bind myosin-binding protein C[PMID:16918501], although additional studies are needed to confirm this finding. Given conflicting evidence regarding its pathogenicity, the inheritedc.5326A>G (p.Ser1776Gly) variant identified in the MYH7 gene is reported as a Variant of Uncertain Significance.

Variant summary: MYH7 c.5326A>G (p.Ser1776Gly) results in a non-conservative amino acid change located in the Myosin tail domain of 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 3.2e-05 in 251494 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.5326A>G has been reported in the literature in individuals affected with HCM (Blair_2002, Fokstuen_2011, Homburger_2017, Walsh_2017, Viswanathan_2017, Kelly_2018, Daoud_2019, vanLint_2019, AlShafai_2021) including reports of co-occurrences of this variant with other pathogenic variants. One study showed limited evidence indicating this variant may segregate with disease (Blair_2002). However, these reports do not provide unequivocal conclusions about association of the variant with HCM. One in vitro study showed that this variant does not affect cMyBP-C attachment to the thick filament, showing no damaing effect of this variant in this context (Flashman_2007). The following publications have been ascertained in the context of this evaluation (PMID: 34137518, 11861413, 30731207, 16918501, 21239446, 27247418, 34136434, 29300372, 31199839, 29121657, 27532257, 30847666). Fourteen clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, with all laboratories classifying the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

The p.Ser1776Gly variant in the MYH7 gene has been previously reported in several unrelated individuals with hypertrophic cardiomyopathy (Fokstuen et al., 2011; Viswanathan et al., 2017; Walsh et al., 2017; van Lint et al., 2019) and segregated with disease in two affected individuals from one family (Blair et al., 2002). However, in many cases another potentially causative variant was identified. Additionally, this variant has been reported at a high frequency in affected individuals of Asian/Pacific Islander ancestry, a population that is insufficiently represented in population databases. This variant has been identified in 6/19,954 East Asian chromosomes (13/282,892 chromosomes overall) by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Although this variant has been seen in the general population, it has not been observed at a high enough frequency to rule out pathogenicity. One in vitro study suggested that this variant does not disrupt binding to myosin binding C protein (Flashman et al., 2007) The serine at position 1776 is highly conserved. Computational tools predict that the p.Ser1776Gly 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.Ser1776Gly variant is uncertain. Additional information is needed to resolve the significance of this variant. [ACMG evidence codes used: PP3]

The p.Ser1776Gly variant in the MYH7 gene has been previously reported in several unrelated individuals with hypertrophic cardiomyopathy (Fokstuen et al., 2011; Viswanathan et al., 2017; Walsh et al., 2017; van Lint et al., 2019) and segregated with disease in two affected individuals from one family (Blair et al., 2002). However, in many cases another potentially causative variant was identified. Additionally, this variant has been reported at a high frequency in affected individuals of Asian/Pacific Islander ancestry, a population that is insufficiently represented in population databases. This variant has been identified in 6/19,954 East Asian chromosomes (13/282,892 chromosomes overall) by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Although this variant has been seen in the general population, it has not been observed at a high enough frequency to rule out pathogenicity. •One in vitrostudy suggested that this variant does not disrupt binding to myosin binding C protein (Flashman et al., 2007). The serine at position 1776 is highly conserved. Computational tools predict that the p.Ser1776Gly variant is deleterious; however, the accuracy of in silicoalgorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, the significance ofthe p.Ser1776Glyvariant is uncertain. Additional information is needed to resolve the significance of this variant. [ACMG evidence codes used: PP3]

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.Ser1776Gly (AGC>GGC): c.5326 A>G in exon 37 of the MYH7 gene (NM_000257.2) We first reviewed this variant in 2011. We re-reviewed them October 15th, 2014 and then again February 20th, 2015. Given the high frequency of Filipino cases and lack of ancestry matched controls we consider this a variant of uncertain significance. The variant has been seen in two published cases of HCM and at least 15 unpublished cases (not including the patient). Ancestry is only available for 11 cases (including this patient); 5 are Asian, 6 are Filipino of those are Asian, as is this patient. At least 4 of 16 total cases (including ours) have another sarcomere variant. This variant has been reported previously in two unrelated cases of HCM (Blair et al 2002, Fokstuen et al 2010). In the family reported by Blair et al (2002) the variant was present in two affected siblings and absent in an unaffected sibling (ancestry not reported). The proband underwent analysis of MYH7, MYBPC3, TNNT2, ACTC2, MYL2 and had no variants in those genes. Cases were recruited in the UK and South Africa.Fokstuen et al (2010) observed the variant in 1 of 122 unrelated HCM patients recruited in Switzerland. They did not provide segregation data. Subjects underwent sequencing of MYH7, MYBPC3, TNNT2, TPM1, TNNI3, MYL3, MYL2, CSRP3, PLN, ACTC1, TNNC1, PRKAG2, however the authors do not report if any cases had multiple variants. We have seen the variant in one other patient with HCM in our center who is Fillipino. This is a semi conservative amino acid change with a polar Serine replaced with a nonpolar Glycine at codon 1776 of MYH7 gene. The Serine at position 1776 is conserved across mammals and myosin isoforms. Given that this amino acid change is located in a core position of the myosin rod, where a Glycine is expected to be energetically unfavorable, Blair et al (2002) hypothesized that this variant would disrupt the normal coiled-coil structure of myosin. However, this variant did not interfere with binding to myosin binding protein C (Flasshman et al 2007). Variants in nearby codons have been reported in association with cardiomyopathy: p.Glu1768Lys (van Driest et al 2003), p.Thr1775Ile (Bos et al 2014), p.Ala1777Thr (Richard et al 2003, Bos et al 2014), p.His1778Tyr (Alfares et al 2015), . The variant was reported online in 4 of 60705 individuals in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/), which currently includes variant calls on ~64,000 individuals of European, African, Latino and Asian descent (as of February 23rd, 2015). Specifically, the variant was observed in 2 of 4327 East Asians and 2 of 5203 Africans, . The phenotype of those individuals is not publicly available. The dataset is comprised of multiple cohorts, some of which were recruited from the general population, others were enriched for common cardiovascular disease. Note that other variants with strong evidence for pathogenicity have been seen at similar frequencies in datasets like this so this does not necessarily rule out pathogenicity (Pan et al 2012). Blair et al (2002) report they did not observe the variant in 200 presumably healthy control individuals. Fokstuen et al (2010) did not analyze teh variant in controls.

The MYH7 c.5326A>G variant is predicted to result in the amino acid substitution p.Ser1776Gly. This variant has been reported in several individuals with hypertrophic cardiomyopathy (HCM) (Blair et al. 2002. PubMed ID: 11861413; Table S4, Kelly et al. 2018. PubMed ID: 29300372; Table S1B, Walsh et al. 2016. PubMed ID: 27532257). It has been reported to segregate with HCM in a family (Blair et al. 2002. PubMed ID: 11861413). This variant has also been found in control individuals in large cohort studies looking at gene burden and penetrance (Dataset S1, Homburger et al. 2016. PubMed ID: 27247418; Table S6, Park et al. 2022. PubMed ID: 34542152). In vitro experimental studies show this variant does not impact cMyBP-C-myosin binding (Flashman et al. 2007. PubMed ID: 16918501); however, protein modeling studies indicate this variant likely affects the coiled-coil structure and filament assembly (Blair et al. 2002. PubMed ID: 11861413). This variant is interpreted as uncertain by the ClinGen Cardiomyopathy Variant Curation Expert Panel in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/177629/). This variant is reported in 0.030% of alleles in individuals of East Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.