Submissions for variant NM_001276345.2(TNNT2):c.887G>A (p.Arg296His)

gnomAD frequency: 0.00005  dbSNP: rs141121678

Total submissions: 16

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000036626	SCV000060281	uncertain significance	not specified	2018-07-16	criteria provided, single submitter	clinical testing	Variant classified as Uncertain Significance - Favor Benign. The p.Arg286His var iant in TNNT2 has been reported in >13 individuals with HCM and segregated with disease in at least 1 affected relative (Van Driest 2003, Van Driest 2004, Ande rsen 2009, Zhao 2016, Ripoll-Vera 2016, Viswanathan 2017). This variant has been identified in 0.09% (16/18472) of East Asian chromosomes by the Genome Aggregat ion Database (gnomAD, http://gnomad.broadinstitute.org/) and is reported in Clin Var (Variation ID: 43677). Computational prediction tools and conservation analy sis suggest that the p.Arg286His variant may impact the protein, though this inf ormation is not predictive enough to determine pathogenicity. In summary, while the clinical significance of the p.Arg286His variant is uncertain, its frequency suggests that it is more likely to be benign. ACMG/AMP Criteria applied: PS4, P P3, BS1.
GeneDx	RCV000223838	SCV000209271	uncertain significance	not provided	2023-10-02	criteria provided, single submitter	clinical testing	Although instances of segregation with disease have been reported, this variant has also been observed in several unaffected family members (Chiou et al., 2014; Ripoll-Vera et al., 2016; GeneDx data); Published functional studies are contradictory as to whether this variant significantly affects protein function (Pettinato et al., 2020; Pua et al., 2020); 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: 24111713, 18761664, 23785128, 25524337, 12707239, 25351510, 7898523, 23711808, 23299917, 25637381, 15519027, 12860912, 22321274, 26507537, 20031601, 28138913, 27532257, 28771489, 15958377, 29121657, 30165862, 33025817, 28356264, 25086479, Kassem2017[CaseReport], 32815737, 35216312, AlloubaM2022[Preprint], 34127679, 27082122, 19035361, 37107598)
Ambry Genetics	RCV000245252	SCV000319027	uncertain significance	Cardiovascular phenotype	2024-03-12	criteria provided, single submitter	clinical testing	The p.R286H variant (also known as c.857G>A), located in coding exon 15 of the TNNT2 gene, results from a G to A substitution at nucleotide position 857. The arginine at codon 286 is replaced by histidine, an amino acid with highly similar properties. This variant has been detected in numerous individuals with hypertrophic cardiomyopathy (HCM); however, it has also been reported in control cohorts, and some HCM cases had additional cardiac variants detected (Van Driest SL et al., Circulation 2003 Jul; 108(4):445-51; Andersen PS et al., Hum. Mutat. 2009 Mar; 30(3):363-70; Berge KE et al., Clin. Genet. 2014 Oct; 86(4):355-60; Chiou KR et al., J Cardiol 2015 Mar; 65(3):250-6; Lopes LR et al., Heart 2015 Feb; 101(4):294-301; Ripoll-Vera T et al., Rev Esp Cardiol (Engl Ed) 2016 Feb; 69(2):149-58; Pua CJ et al. Circ Genom Precis Med, 2020 10;13:424-434). Limited studies in iPSC-CMs suggest this variant may have some functional impact (Pua CJ et al. Circ Genom Precis Med, 2020 10;13:424-434). Based on data from gnomAD, the frequency for this variant is above the maximum credible frequency for a disease-causing variant in this gene based on internally established thresholds (Karczewski et al. Nature. 2020 May;581(7809):434-443; Whiffin et al. Genet Med. 2017 10;19:1151-1158). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this alteration remains unclear.
Invitae	RCV000459071	SCV000541916	uncertain significance	Hypertrophic cardiomyopathy 2; Dilated cardiomyopathy 1D; Cardiomyopathy, familial restrictive, 3	2024-01-26	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 286 of the TNNT2 protein (p.Arg286His). This variant is present in population databases (rs141121678, gnomAD 0.09%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 12860912, 23711808, 25086479, 26507537, 27082122, 28356264). ClinVar contains an entry for this variant (Variation ID: 43677). 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 TNNT2 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects TNNT2 function (PMID: 32815737). 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.
Blueprint Genetics	RCV000223838	SCV000927474	uncertain significance	not provided	2017-11-22	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV001187862	SCV001354764	uncertain significance	Cardiomyopathy	2022-12-26	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with histidine at codon 286 of the TNNT2 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). Functional studies using induced pluripotent stem cells provide some evidence that this variant may impact TNNT2 function (PMID: 32815737). This variant has been reported in multiple individuals and families affected with hypertrophic cardiomyopathy (PMID: 12860912, 19035361, 23711808, 24111713, 25086479, 25351510, 26507537, 27082122, 27532257, 28356264, 28771489, 32815737). Compound heterozygous individuals showed a more severe phenotype than heterozygous individuals (PMID: 25086479). Family studies are inconclusive as to whether this variant segregates with hypertrophic cardiomyopathy or not (PMID: 19035361, 25086479, 26507537). This variant has been identified in healthy control cohorts, and is estimated to have a low penetrance (PMID: 32815737). This variant has been identified in 19/273936 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, this is a variant with unknown functional impact that has been reported in multiple individuals affected with hypertrophic cardiomyopathy. However, this variant also occurs at an appreciable frequency in the general population and it is inconclusive whether this variant segregates with disease in affected families. Additional studies are necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV001187862	SCV002042864	uncertain significance	Cardiomyopathy	2023-05-26	criteria provided, single submitter	clinical testing
Fulgent Genetics, Fulgent Genetics	RCV000459071	SCV002780746	uncertain significance	Hypertrophic cardiomyopathy 2; Dilated cardiomyopathy 1D; Cardiomyopathy, familial restrictive, 3	2021-10-17	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV003450727	SCV004180472	uncertain significance	Dilated cardiomyopathy 1D	2023-04-11	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV003450728	SCV004180473	uncertain significance	Cardiomyopathy, familial restrictive, 3	2023-04-11	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV003450726	SCV004180474	uncertain significance	Hypertrophic cardiomyopathy 2	2023-04-11	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV001187862	SCV004817898	uncertain significance	Cardiomyopathy	2023-10-30	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with histidine at codon 286 of the TNNT2 protein. Computational prediction tools indicate that this variant's impact on protein structure and function is inconclusive. Functional studies using induced pluripotent stem cells provide some evidence that this variant may impact TNNT2 function (PMID: 32815737). This variant has been reported in multiple individuals and families affected with hypertrophic cardiomyopathy (PMID: 12860912, 19035361, 23711808, 24111713, 25086479, 25351510, 26507537, 27082122, 27532257, 28356264, 28771489, 32815737, 33495596, 33495597, 37107598). Some of these individuals also carried pathogenic variants in other genes associated with hypertrophic cardiomyopathy (PMID: 25086479 , 37107598). Compound heterozygous individuals showed a more severe phenotype than heterozygous individuals (PMID: 25086479). Family studies are inconclusive as to whether this variant segregates with hypertrophic cardiomyopathy or not (PMID: 19035361, 25086479, 26507537). This variant has been identified in healthy control cohorts, and is estimated to have a low penetrance (PMID: 32815737). This variant has been identified in 19/273936 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, this is a variant with unknown functional impact that has been reported in multiple individuals affected with hypertrophic cardiomyopathy. However, this variant also occurs at an appreciable frequency in the general population and it is inconclusive whether this variant segregates with disease in affected families. Additional studies are necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
CSER _CC_NCGL, University of Washington	RCV000148899	SCV000190645	likely pathogenic	Primary familial hypertrophic cardiomyopathy	2014-06-01	no assertion criteria provided	research
Stanford Center for Inherited Cardiovascular Disease, Stanford University	RCV000223838	SCV000280534	uncertain significance	not provided	2016-01-28	no assertion criteria provided	provider interpretation	p.Arg286His (c.857 G>A) in TNNT2 (NM_001001430.1) We re-reviewed this variant on September 2nd, 2014 and again on January 21st, 2015. This variant is difficulty to parse without current understanding of the genome and the genetic basis of HCM. It is more common in Asian individuals unselected for HCM than we would expect for a pathogenic HCM variant. However, there are many cases, suggesting it may be enriched in cases. Notably, there are many non-Asian cases. Given these data, it seems likely that the variant is contributing to HCM in the patient and these other cases. It maybe a modifier or susceptibility factor However, it may not be the primary driver. Until we can better understand the role of variants like this we will consider it a variant of uncertain significance. This variant has been reported in at least 13 unrelated probands with HCM, in addition to this patient. Unfortunately several of this cases are unpublished. Also most of those cases don't have ancestry data available and the majority that do are Asian, like the patient. There is no segregation data on this variant. We have seen this variant one other Asian family with HCM in our center. Van Driest et al (2003) first reported this variant in two unrelated probands with HCM in their American cohort (ancestry not reported). The same group later reported an individual with HCM who had this variant and a variant in MYBPC3, p.Ala833Thr (Van Driest et al 2004). Unfortunately it is unclear if that case is the same as one of the previously reported cases. Andersen et al (2008 (2009 on pubmed)) reported the variant in two unrelated probands with HCM in their Dutch cohort. Ancestry was not reported. Ripoll-Vera et al (2015) reported a total of 5 families with HCM with this variant in their Spanish cohort. This was out of 180 families with hereditary cardiomyopathies, most of them having HCM (total number with HCM not specified). Probands underwent sequencing of MYBPC3, MYH7, TNNT2, TNNI3, and TPM1, One family with this variant also carried Arg326Gln in MYBPC3, which is in ClinVar with an assertion of likely benign or benign by 7 different groups (all concordant). In addition to the proband, three unaffected relatives in three different families carried p.Arg286His. It appears that no affected relatives had genetic testing. They noted a founder effect for one other variant observed in their cohort but did not report whether they assessed possible founder effect for p.Arg286His. Ancestry is not reported, however the cases were ascertained at a hospital in the Balearic Islands, Spain. This report is presumably redundant with their abstract from the 2011 European Society of Cardiology meeting and a thesis available online by Tomas Ripoll Vera). Yang et al (2011) observed the variant in 1 of 100 individuals with HCM in their Chinese cohort (article is in Chinese but an English abstract was reviewed). This is very likely the same case reported in an abstract from the 2011 Annual Congress of the European Cardiac Arrhythmia Society by what appears to be the same group (Wenling et al). The arginine at codon 286 is conserved across species. This is a conservative amino acid change with a polar Arginine replaced with a polar Histidine. In silico analysis with Polyphen predicts the variant to be probably damaging. Another variant at the same codon has been reported in association with HCM (p.Arg286Cys; Richard et al 2003, Miliou et al 2005; no segregation data). Two variants at codon 278 have also been reported in HCM cases (p.Arg278Pro, p.Arg278Cys). The variant was reported online in 7 of 44405 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 January 20th, 2015). Specifically, the variant was observed in 7 of 3196 East Asian individuals (MAF 0.0009387). It was also seen in one European. 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. The variant was not observed in the following laboratory and published control samples:at least 400 ethnically diverse presumably healthy individuals, about 100 of these are of East Asian descent (Familion); Van Driest et al (2003) did not identify the variant in 100 Caucasian and 100 African American presumably healthy controls; Andersen et al (2003) did not observe the variant in 100 Dutch controls; Yang et al (2011) did not observe it in 200 controls, who were presumably Chinese since the study was done in China.
Clinical Genetics, Academic Medical Center	RCV000223838	SCV001917415	uncertain significance	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000223838	SCV001927786	uncertain significance	not provided		no assertion criteria provided	clinical testing