ClinVar Genomic variation as it relates to human health

The NM_000257.4(MYH7):c.2606G>A (p.Arg869His) variant has been identified in >30 individuals with HCM, including at least 2 individuals with an additional variant in another gene that may contribute to their disease (PS4; Van Driest 2004 PMID: 15358028; Girolami 2006 PMID: 16858239; Cecchi 2006 PMID: 17180650; Olivotto 2008 PMID: 18533079; Girolami 2010 PMID: 20359594; Olivotto 2011 PMID: 21835430; Witjas-Paalberends 2013 PMID: 23674513; Marsiglia 2013 PMID: 24093860; Bos 2014 PMID: 24793961; Coppini 2014 PMID: 25524337; Adalsteinsdottir 2014 PMID: 25078086; Homburger 2016 PMID: 27247418; Viswanathan 2017 PMID: 29121657; Walsh 2017 PMID: 2753225; Ho 2018 PMID: 30297972; Ambry pers. comm.; Centenary Institute Sydney pers. comm.; CHEO pers. comm.; GeneDx pers. comm.; Invitae pers. comm.; LMM pers. comm.; OMGL pers. comm.). This variant also segregated in 6 affected relatives with HCM from at least two families (PP1_Moderate; Girolami 2010 PMID: 20359594; GeneDx pers. comm.). Additionally, this variant has also been reported in 1 individual with DCM with an additional variant in another gene that may contribute to their disease, 1 individual with LVH and suspected HCM, 1 individual with LVNC, 1 individual with septal hypertrophy with AV conduction defect, and 4 individuals with unspecified heart disease (Ambry pers. comm.; GenDx pers. comm.). This variant was identified in 0.002% (FAF 95% CI; 2/16254) of African chromosomes by gnomAD v2.1.1 (https://gnomad.broadinstitute.org), but has also been identified in a greater number of African chromosomes in gnomAD v.3.1. Therefore, the PM2 criterion was downgraded to PM2_supporting. This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be associated with HCM (PM1; Walsh 2017 PMID:27532257). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In summary, this variant meets criteria to be classified as likely pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. ACMG/AMP Criteria applied: PS4, PP1_Moderate, PM2_Supporting, PM1.

The p.Arg869His variant in MYH7 has been reported in >15 individuals with HCM and segregated with disease in one affected relative (Song 2005, Olivotto 2008, Girolami 2010, Adalsteinsdottir 2014, Bos 2014, Homburger 2016, Viswanathan 2017, Walsh 2017, LMM data). It has been identified in 6/251440 chromosomes by gnomAD (http://gnomad.broadinstitute.org). Computational prediction tools and conservation analysis suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In addition, this variant lies in the head region of the protein and missense variants in this region are statistically more likely to be disease-associated (Walsh 2016). In summary, this variant meets criteria to be classified as likely pathogenic for autosomal dominant HCM. ACMG/AMP Criteria applied: PS4, PM1, PM2, PP3.

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 869 of the MYH7 protein (p.Arg869His). This variant is present in population databases (rs202141173, gnomAD 0.01%). This missense change has been observed in individuals with hypertrophic cardiomyopathy (PMID: 16858239, 17180650, 18533079, 20359594, 22763267, 23674513, 24093860, 25078086, 27247418, 27532257, 29121657). ClinVar contains an entry for this variant (Variation ID: 177667). 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%. This variant disrupts the p.Arg869 amino acid residue in MYH7. Other variant(s) that disrupt this residue have been observed in individuals with MYH7-related conditions (PMID: 30588760, 32380161), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.

The p.R869H pathogenic mutation (also known as c.2606G>A), located in coding exon 20 of the MYH7 gene, results from a G to A substitution at nucleotide position 2606. The arginine at codon 869 is replaced by histidine, an amino acid with highly similar properties. This alteration is located in the myosin head domain, which contains a statistically significant clustering of pathogenic missense variants (Homburger JR et al. Proc Natl Acad Sci U S A, 2016 06;113:6701-6; Walsh R et al. Genet Med, 2017 02;19:192-203; Ambry internal data). This alteration has been reported in numerous individuals with hypertrophic cardiomyopathy (HCM), although clinical details were limited in some cases (Van Driest SL et al. J. Am. Coll. Cardiol., 2004 Aug;44:602-10; Olivotto I et al. Mayo Clin. Proc., 2008 Jun;83:630-8; Girolami F et al. J. Am. Coll. Cardiol., 2010 Apr;55:1444-53; Witjas-Paalberends ER et al. Cardiovasc. Res., 2013 Aug;99:432-41; Adalsteinsdottir B et al. Circulation, 2014 Sep;130:1158-67; Lopes LR et al. Heart, 2015 Feb;101:294-301; Ambry internal data). This variant was also reported to segregate with disease in multiple affected family members (Maurizi N et al. JAMA Cardiol, 2018 Jun;3:520-525; external communication). In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this variant is interpreted as a disease-causing mutation.

This c.2606G>A (p.Arg869His) variant in the MYH7 gene has been reported in several patients with hypertrophic cardiomyopathy [PMID 18533079, 20359594, 24793961, 14676227, 27247418, 25078086]. Cosegregation has been reported but no detailed information was available for review [PMID 18533079]. This variant was also reported in a patient with hypertrophic cardiomyopathy diagnosed at 18 years of age [PMID 20359594 ]. The patient carries a frameshift variant in TNNI3 and a missense in MYBPC3, both inherited from the father; and this variant in MYH7, inherited from the mother. The mother had mild asymmetric septal hypertrophy. Additional patients have been reported with a change affecting the same amino acid position (Arg869Cys, Arg869Gly). While not validated for clinical use, computer-based algorithms yield discrepant results regarding the deleterious effect of this p.Arg869His change. However, this variant is highly conserved in mammal. This variant has been observed in 6 heterozygous individuals in the gnomAD database (http://gnomad.broadinstitute.org/variant/14-23894051-C-T). This variant is thus classified as likely pathogenic.

PS4, PM1

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: 25078086, 22763267, 24093860, 25351510, 20359594, 25524337, 9172070, 31112422, 30297972, 22958901, 10024460, 18533079, 15358028, 21835320, 24793961, 27247418, 26332594, 27532257, 23674513, 29121657, 29875424, 31447099, 32894683)

This missense variant replaces arginine with histidine at codon 869 in the neck and hinge (S2) domain of the MYH7 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). This variant is found within a highly conserved region of the myosin head domain. Missense variants in this region have been shown to be significantly overrepresented in individuals with hypertrophic cardiomyopathy (PMID: 27532257). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in over 40 individuals affected with hypertrophic cardiomyopathy (PMID: 15358028, 16858239, 18533079, 20359594, 23674513, 24093860, 24793961, 25078086, 27532257, 29121657, 30297972). Several of these individuals also carried pathogenic variants in the MYBPC3 and TNNI3 genes (PMID: 18533079, 20359594). It has been shown that this variant segregates with disease in several affected individuals across two families (PMID: 20359594; ClinVar SCV001976466.1). This variant has also been reported in an individual affected with dilated cardiomyopathy (PMID: 36203036). This variant has been identified in 6/251440 chromosomes in the general population by the Genome Aggregation Database (gnomAD). A different variant affecting the same codon, p.Arg869Cys, is considered to be disease-causing (ClinVar variation ID: 181196), suggesting that arginine at this position is important for MYH7 protein function. Based on the available evidence, this variant is classified as Likely Pathogenic.

This missense variant replaces arginine with histidine at codon 869 in the neck and hinge (S2) domain of the MYH7 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). This variant is found within a highly conserved region of the myosin head domain. Missense variants in this region have been shown to be significantly overrepresented in individuals with hypertrophic cardiomyopathy (PMID: 27532257). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in over 40 individuals affected with hypertrophic cardiomyopathy (PMID: 15358028, 16858239, 18533079, 20359594, 23674513, 24093860, 24793961, 25078086, 27532257, 29121657, 30297972). Several of these individuals also carried pathogenic variants in the MYBPC3 and TNNI3 genes (PMID: 18533079, 20359594). It has been shown that this variant segregates with disease in several affected individuals across two families (PMID: 20359594; ClinVar SCV001976466.1). This variant has also been reported in an individual affected with dilated cardiomyopathy (PMID: 36203036). This variant has been identified in 6/251440 chromosomes in the general population by the Genome Aggregation Database (gnomAD). A different variant affecting the same codon, p.Arg869Cys, is considered to be disease-causing (ClinVar variation ID: 181196), suggesting that arginine at this position is important for MYH7 protein function. Based on the available evidence, this variant is classified as Likely Pathogenic.

Variant Summary: MYH7 c.2606G>A (p.Arg869His) results in a non-conservative amino acid change located in the Myosin tail domain (IPR002928). Five of five in-silico tools predict a damaging effect of the variant on protein function (ACMG PP3, PP2). The variant allele was found at a frequency of 2.4e-05 in 251440 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.2606G>A has been reported in the literature in several well phenotyped individuals affected with and meeting established clinical criteria for Hypertrophic Cardiomyopathy (HCM) (e.g. Witjas-Paalberends_2013, Adalsteinsdottir_2014, Olivotto_2011, Girolami_2010, Walsh_2017, Ho_2018). Though the variant was reported to co-occur with other pathogenic MYBPC3 variants in two different families, the double heterozygous patients showed an earlier onset of HCM, a more rapid disease progression with a more severe phenotype than heterozygous variant carriers, which might be consistent with an additive effect for the co-occurring variants (Girolami_2010, Olivotto_2011). A recent study reported that the allele frequency of this variant in a cohort of HCM patients is much higher (0.0076; i.e. 42/5526 alleles) than that in controls (6/251440 in gnomAD), suggesting this variant could be associated with HCM (Ho_2018) (ACMG PS4). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five ClinVar submissions (evaluation after 2014) cite the variant: four times as likely pathogenic and once as uncertain significance. In addition, other variants affecting the same codon, R869C, R869G, R869L, have been reported in HGMD in association with HCM (ACMG PM1). Based on the evidence outlined above the variant was re-classified as likely pathogenic.

The MYH7:Arg869His variant has been implicated in HCM in several studies (Van Driest et al, 2004; Girolami et al., 2006, Olivotto et al., 2008; Girolami et al., 2010; Witjas-Paalberens et al., 2013; Marsiglia et al., 2013; Adalsteinsdottir et al., 2014; Bos et al., 2014; Mazzarotto & Girolami et al., 2018). This variant is sufficiently rare in the gnomAD population database (MAF 2.39E-5) to activate the PM2 moderate criteria for rarity as per the ACMG/AMP variant interpretation guidelines adapted for MYH7 variants in cardiomyopathy (Kelly et al., 2018). The Arg869His variant alters a residue within the myosin head, which constitutes a large hotspot for variants with a high prior likelihood of pathogenicity in HCM characterised by etiological fraction >0.95 (Kelly et al., 2018 defines ita s between residues 181-937; Walsh et al., 2019 as 167-931), causing the activation of the PM1 criteria (Kelly et al., 2018). Furthermore, we found evidence of co-segregation with HCM in a large Italian pedigree comprising 7 affected carriers and 1 deceased obligate carrier reported to be affected. This enables activation of the PP1_strong criteria for observing >=7 meioses (Kelly et al., 2018). This variant is also carried by 30 of 1198 unrelated probands with HCM tested at the nearby Careggi University Hospital as opposed to 0 of 356 non-HCM probands tested in the same lab (p=6.22E-4), enabling activation of the PS4_strong criteria (Mazzarotto & Girolami et al., 2018; Kelly et al., 2018). Computational evidence is also to be considered supportive of pathogenicity, as multiple in silico pathogenicity predictors classify this variant as damaging / deleterious, enabling activation of the PP3 criteria supporting pathogenicity. In conclusion, the activation of 2 strong, 2 moderate and 1 supporting criteria in favour of pathogenicity enables classification of the MYH7:Arg869His variant as pathogenic for HCM.

The variant NM_000257.4:c.2606G>A (chr14:23424842) in MYH7 was detected in 7 heterozygotes out of 58K WGS Icelanders (MAF= 0,006%). Following imputation in a set of 166K Icelanders (7 imputed heterozygotes) we observed a suggestive association with cardiomyopathy (OR=62,1 , P-value=0,03) using 1974 cases and 365360 controls. This variant has been reported in ClinVar previously as likely pathogenic, pathogenic, and as a variant of uncertain significance. Based on ACMG criteria (PS4, PM2_Supporting, PP1_Moderate, PP5) this variant classifies as likely pathogenic.

The MYH7 c.2606G>A variant is predicted to result in the amino acid substitution p.Arg869His. This variant has been reported in multiple individuals with hypertrophic cardiomyopathy (see for example, Table S1, Bos et al. 2014. PubMed ID: 24793961; Table 2, Adalsteinsdottir et al. 2014. PubMed ID: 25078086; Table S5, Viswanathan et al. 2017. PubMed ID: 29121657). Moreover, this variant has been observed to be enriched in the disease cohort in a case-control study for hypertrophic cardiomyopathy (Table S1, Homburger et al. 2016. PubMed ID: 27247418). This variant is reported in six out of ~250,000 alleles in gnomAD. Alternate nucleotide substitutions affecting the same amino acid (p.Arg869Gly, p.Arg869Cys, p.Arg869Pro, and p.Arg869Leu) have been reported in multiple individuals with hypertrophic cardiomyopathy (Table 1, Richard et al. 2000. PubMed ID: 10900182; Table 1, Nakashima et al. 2020. PubMed ID: 32830170; Table S1, Chung et al. 2021. PubMed ID: 33658040; Table S1, Walsh et al. 2017. PubMed ID: 27532257). In summary, the c.2606G>A (p.Arg869His) variant is interpreted as likely pathogenic.