ClinVar Genomic variation as it relates to human health

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

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".

The p.Ala797Thr variant in MYH7 has been identified in >30 individuals with HCM and segregated with disease in >10 affected relatives from several families (Moolman 1995 PMID: 7581410, Moolman-Shook 1999 PMID: 10521296, Moolman-Smook 2000 PMID: 11186938, Van Driest 2004 PMID: 15358028, Laredo 2006 PMID: 17125710, Kassem 2013 PMID: 23233322, Bos 2014 PMID: 24793961, LMM data). This variant has been reported by other clinical laboratories in ClinVar (Variation ID 42901) and has been identified in 0.005% (2/41412) African/African American chromosomes by gnomAD (http://gnomad.broadinstitute.org; v.3.1.2). Please note that for diseases with clinical variability and reduced penetrance, pathogenic variants may be present at a low frequency in the general population. Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. Of note, this variant lies in the head region of the protein. Missense variants in this region have been reported and statistically indicated to be more likely to cause disease (Walsh 2017 PMID: 27532257). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant HCM. ACMG/AMP Criteria applied: PS4, PP1_Strong, PM1, PM2_Supporting.

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.

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.

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

In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 7581410, 19287818, 24093860, 28615295, 28420666, 31589614, 33673806, 33297573, 26582918, 30755392, 29260236, 25937619, 26743238, 16858239, 23299917, 25031304, 23233322, 15358028, 10521296, 17125710, 18029407, 25637381, 28166811, 27737317, 26969327, 24793961, 27247418, 27831900, 27532257, 28138913, 28971120, 28606303, 21310275, 28790153, 29687901, 28408708, 25351510, 24111713, 23782526, 23283745, 22857948, 20031618, 19880069, 11186938, 31006259, 32420109, 32233023, 30291343, 31447099, 32894683, 33087929, 35208637, 35653365, 35288587, 34542152, 29300372)

Missense variation is an established mechanism of disease for MYH7-related disorders (PMID: 7731997, 12975413). The c.2389G>A (p.Ala797Thr) variant affects a weakly conserved amino acid and in silico tools used to predict the effect of this variant on protein function yield discordant results. This variant has been previously reported as a heterozygous change in patients with hypertrophic cardiomyopathy (PMID: 27532257, 7581410, 33673806, 11447480, 24793961, 35653365, 17125710, 33297573, 35288587). In addition, this variant has been previously reported as a heterozygous change in onepatient with Wolff-Parkinson-White syndrome (PMID: 32233023). The c.2389G>A (p.Ala797Thr) variant is located in a mutational hotspot for pathogenic variations associated with hypertrophic cardiomyopathy (PMID: 27532257). The c.2389G>A (p.Ala797Thr) variant is presentin the heterozygous state in the gnomAD population database at a frequency of 0.002% (6/251468) and is absent in the homozygous state, thus is presumed to be rare. Based on the available evidence, c.2389G>A (p.Ala797Thr) is classified as Pathogenic.

The MYH7 c.2389G>A variant is predicted to result in the amino acid substitution p.Ala797Thr. This variant has been reported in several individuals with autosomal dominant hypertrophic cardiomyopathy (see for example, Bos et al. 2014. PubMed ID: 24793961, Supplemental Table 1; Walsh et al. 2017. PubMed ID: 27532257, Table S1A). It occurs in a region that is enriched for disease-associated missense variants (Human Gene Mutation Database). This variant is reported in 0.012% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/14-23894525-C-T), and it is classified as likely pathogenic and pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/42901/). We interpret this variant to be pathogenic.

This missense variant replaces alanine with threonine at codon 797 in the myosin head/motor 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). To our knowledge, functional studies have not been reported for this variant. 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, 33673806) 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). Based on the available evidence, this variant is classified as Pathogenic.

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). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MYH7 protein function. 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.

The MYH7 c.2389G>A; p.Ala797Thr variant (rs3218716; ClinVar Variation ID: 42901), also known as A797T, is a known founder variant in Black South African population (Moolman-Smook 2002). This variant has been shown to co-segregated with disease in multiple individuals and has been identified in multiple unrelated individuals (selected references: Moolman-Smook 2002, Mattos 2016, Walsh 2017). This variant is associated with mild-moderate hypertrophic cardiomyopathy and displays incomplete penetrance (Moolman-Smook 2000). Based on available information, this variant is considered to be pathogenic. References: Mattos BP et al. Prevalence and Phenotypic Expression of Mutations in the MYH7, MYBPC3 and TNNT2 Genes in Families with Hypertrophic Cardiomyopathy in the South of Brazil: A Cross-Sectional Study. Arq Bras Cardiol. 2016 Sep;107(3):257-265. PMID: 27737317. Moolman-Smook J et al. Expression of HCM causing mutations: lessons learnt from genotype-phenotype studies of the South African founder MYH7 A797T mutation. J Med Genet. 2000 Dec;37(12):951-6. PMID: 11186938. Walsh R et al. Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. Genet Med. 2017 Feb;19(2):192-203. PMID: 27532257.

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0105 - The mechanism of disease for this gene is not clearly established; however, missense variants have been proposed to act in a dominant negative manner (PMID: 24714796). (I) 0108 - This gene is associated with both recessive and dominant disease. Disease associated with this gene usually has autosomal dominant inheritance; however, a recessive inheritance pattern has been observed in severe cases (OMIM). (I) 0112 - The condition associated with this gene has incomplete penetrance (PMID: 29300372). (I) 0200 - Variant is predicted to result in a missense amino acid change from alanine to threonine. (I) 0252 - This variant is homozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (6 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (1 heterozygote, 0 homozygotes). (I) 0503 - Missense variant consistently predicted to be tolerated by multiple in silico tools or not conserved in placental mammals with a minor amino acid change. (SB) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants. This variant is found within the head region, which is enriched with pathogenic missense variants (PMID: 29300372). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant is a common pathogenic variant reported in individuals with hypertrophic cardiomyopathy and has shown a founder effect in the South African population (ClinVar, PMIDs: 28408708, 28615295). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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 observe the variant in 200 control individuals. GeneDx input 2011/12?: No, you’re not “that counselor” ? I think it’s good that we can share this info – it’s not getting any easier, that’s for sure. We literally just discussed this one last week. We had discussed changing our interpretation to a VUS, but again, the reported literature won out over the low frequency in dbSNP/1000 Genomes (I think some of that is the same HapMap data, if I’m remembering right). After a review of everyone we’ve seen it in, A797T was present in two sets of affected (HCM) relatives in two families as an isolated mutation (ages of dx ranging from teens to 60s). A third family also had two affected relatives with A797T, but they also had an MYBPC3 nonsense mutation and we can’t make much of that. The remaining cases provided no clinical info on family members, so we don’t have any other segregation/non-segregation data. This one could end up following 998, but Sherri felt strongly that we cannot over-rule the literature with the low frequency population data. That said, we’re keeping an eye on this one. I just came across a similar situation for a LQTS mutation that had reported just once, but with such extensive functional studies and co-segregation with a specific phenotype in a 3 generation pedigree – and then I saw it was reported in 2/180 alleles from indiv. of Hispanic ancestry in 1000 Genomes. Seems too high to be a real mutation, but I contacted the researcher who first reported it and he only had more conclusive information to share (as I probably should have guessed). So we’re continuing to work on how to interpret these accurately, and with the acknowledgement we don’t know the whole story… I wish I had something more helpful to add, but I’ll have to wait and see if we end up getting more conclusive evidence that would affect how we’re reporting A797T. ~Amy

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