Submissions for variant NM_001276345.2(TNNT2):c.304C>T (p.Arg102Trp)

gnomAD frequency: 0.00001  dbSNP: rs397516456

Total submissions: 17

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000768491	SCV000060228	pathogenic	Hypertrophic cardiomyopathy	2015-04-01	criteria provided, single submitter	clinical testing	The p.Arg92Trp variant in TNNT2 has been reported in the literature and by our l aboratory in >20 individuals with HCM and segregated with disease in >15 affecte d relatives from >5 families (Koga 1996, Ackerman 2002, Moolman 1997, Moolman-Sm ook 1999, Fujino 2001, Varnava 2001, Van Driest 2003, Marsiglia 2010, Yang 2011, Fujita 2013; LMM unpublished data). This variant has been identified in 1/66730 of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac. broadinstitute.org; dbSNP rs397516456). Please note that for diseases with clini cal variability or reduced penetrance, pathogenic variants may be present at a l ow frequency in the general population. In vitro functional studies and mouse mo dels provide evidence that the p.Arg92Trp variant impacts protein function (Palm 2001, Harada 2004, Ertz-berger 2005, Manning 2012). In summary, this variant me ets our criteria to be classified as pathogenic for HCM in an autosomal dominant manner (http://www.partners.org/personalizedmedicine/LMM) based upon segregatio n studies and functional evidence.
GeneDx	RCV000159280	SCV000209226	pathogenic	not provided	2022-10-28	criteria provided, single submitter	clinical testing	Not observed at significant frequency in large population cohorts (gnomAD); Functional studies indicate R92W disrupts tropomyosin binding and increases calcium sensitivity of the cardiac thin filament (Palm et al., 2001, Harada et al., 2004; Revera et al., 2008, Manning et al., 2012a, Manning et al., 2012b); 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: 11606294, 22579624, 21310275, 18029407, 19880069, 26955724, 22334656, 10521296, 12860912, 27590665, 28166811, 27532257, 26507537, 30025578, 28202948, 29563334, 16326803, 31513939, 29572196, 33025817, 14722098, 31006259, 33996946, 30847666, 31737537, 33673806, 11346248, 35626289, 35208637, 9060892, 8951566)
Blueprint Genetics	RCV000208103	SCV000264252	pathogenic	Primary familial hypertrophic cardiomyopathy	2015-11-05	criteria provided, single submitter	clinical testing
Invitae	RCV000474512	SCV000541909	pathogenic	Hypertrophic cardiomyopathy 2; Dilated cardiomyopathy 1D; Cardiomyopathy, familial restrictive, 3	2024-01-30	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 92 of the TNNT2 protein (p.Arg92Trp). This variant is present in population databases (rs397516456, gnomAD 0.0009%). This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 8951566, 9060892, 26507537). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 43627). 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: 14722098, 22334656). This variant disrupts the p.Arg92 amino acid residue in TNNT2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 7898523, 8205619, 9201030, 10085122, 10617660, 14722098, 18403758). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics	RCV000620701	SCV000739951	pathogenic	Cardiovascular phenotype	2022-05-02	criteria provided, single submitter	clinical testing	The p.R92W pathogenic mutation (also known as c.274C>T), located in coding exon 8 of the TNNT2 gene, results from a C to T substitution at nucleotide position 274. The arginine at codon 92 is replaced by tryptophan, an amino acid with dissimilar properties. This alteration has been reported in multiple patients with hypertrophic cardiomyopathy (HCM) and has shown strong segregation with the disease (Moolman JC et al, J. Am. Coll. Cardiol. 1997 Mar; 29(3):549-55; Moolman-Smook JC et al, Am. J. Hum. Genet. 1999 Nov; 65(5):1308-20; Varnava AM et al, Circulation 2001 Sep; 104(12):1380-4; Ackerman MJ et al, J. Am. Coll. Cardiol. 2002 Jun; 39(12):2042-8; Fujino N et al, Clin Cardiol 2001 May; 24(5):397-402; Van Driest SL et al, Circulation 2003 Jul; 108(4):445-51). In addition, in vitro studies suggest this alteration might interfere with tropomycin binding (Palm T et al, Biophys. J. 2001 Nov; 81(5):2827-37; Harada K et al, J. Biol. Chem. 2004 Apr; 279(15):14488-95). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Center for Human Genetics, University of Leuven	RCV000768491	SCV000886796	pathogenic	Hypertrophic cardiomyopathy	2018-10-31	criteria provided, single submitter	clinical testing
3billion	RCV001807762	SCV002058465	pathogenic	Hypertrophic cardiomyopathy 2	2022-01-03	criteria provided, single submitter	clinical testing	Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000043627, PS1_S). The variant was co-segregated with Cardiomyopathy, hypertrophic, 2 in multiple affected family members with additional meioses meeting strong evidence levels (PMID: 9060892, 8951566, 26507537) (PP1_S). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 14722098, 22334656, PS3_S). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.835, 3CNET: 0.997, PP3_P). A missense variant is a common mechanism associated with Cardiomyopathy (PP2_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000007, PM2_M). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000012409, PM5_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
Fulgent Genetics, Fulgent Genetics	RCV000474512	SCV002815780	pathogenic	Hypertrophic cardiomyopathy 2; Dilated cardiomyopathy 1D; Cardiomyopathy, familial restrictive, 3	2021-11-09	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV003450681	SCV004181494	pathogenic	Dilated cardiomyopathy 1D	2023-04-11	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV003450682	SCV004181496	pathogenic	Cardiomyopathy, familial restrictive, 3	2023-04-11	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001807762	SCV004181497	pathogenic	Hypertrophic cardiomyopathy 2	2023-04-11	criteria provided, single submitter	clinical testing
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV003486557	SCV004239775	pathogenic	Cardiomyopathy	2023-03-01	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV003486557	SCV004359945	pathogenic	Cardiomyopathy	2022-12-08	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with tryptophan at codon 92 in the tropomyosin binding domain 1 of the TNNT2 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). Functional studies using in vitro modeling have shown that this variant may result in impaired tropomyosin binding (PMID: 11606294, 14722098). Additionally, functional studies using mouse models have demonstrated systolic dysfunction and decreased ventricular mass (PMID: 16326803). This variant has been reported in over 15 individuals affected with hypertrophic cardiomyopathy (PMID: 9060892, 10521296, 11346248, 11560853, 12084606, 12860912, 20414521, 22321274, 23494605, 28615295, 29572196, 9060892, 11346248 23494605, 29572196). It has been shown that this variant segregates with disease in multiple affected family members across multiple families (PMID: 9060892, 11346248 23494605, 29572196). A different variant occurring at the same codon, p.Arg92Gln, is a well documented pathogenic mutation (Clinvar variation ID: 12409), indicating that arginine at this position is important for TNNT2 protein function. This variant has been identified in 2/282802 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.
Stanford Center for Inherited Cardiovascular Disease, Stanford University	RCV000159280	SCV000280515	pathogenic	not provided	2014-07-02	no assertion criteria provided	clinical testing	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. TNNT2 Arg92Trp (R92W; at the nucleotide level) This variant has been reported in at least 16 unrelated cases of HCM with good segregation data in 2 families and weak segregation data in two more. Strong functional data is available both in vitro and in a transgenic mouse model. Koga et al. (1996) found Arg92Trp in two Japanese HCM families. The variant was “present in all affected family members” (a total of 5 people), but specific segregation data for each family is not provided. Moolman et al. (1997) detected this variant in 2 South African families of mixed ancestry with HCM. Segregation data was available for one of these families, with five affected family members carrying the variant. Moolman-Smook et al. (1999) detected it in 4 additional HCM probands of mixed ancestry from South Africa. Varnava et al. (2001) detected it in 2 unrelated cases. Fujino et al. (2001)/Shimizu et al. (2003) identified it in 2 Japanese families. In one family, Arg92Trp segregated with disease in 6 affected family members (5 siblings and one of their children). In the other, two affected siblings carried the variant. Ackerman et al. (2002) detected it in one HCM patient at the Mayo Clinic; it segregated with disease in the patient and her mother. Waldmuller et al. (2002) used this variant in developing a microarray screen for recurring HCM variants. Van Driest et al (2003) detected it in another HCM case at the Mayo Clinic. Van Driest et al. (2004) reported a double-heterozygote carrying Arg92Trp plus a Val256Ile variant in MYBPC3. Konno et al. (2005) detected it in 8 Japanese individuals from HCM families (it is not clear if they are related, or how many have LVH).***note that the cases reported in Van Driest et al (2003, 2004) and Ackerman et al (2002) may overlap. Some authors have suggested that p.Arg92Trp in TNNT2 is associated with a higher risk of sudden death with mild or even absent hypertrophy (Moolman et al 1997, 1999). Two other mutations at the same codon have also been reported in families with HCM: p.Arg92Leu and p.Arg92Gln (we categorize both as very likely disease causing). Variation at nearby loci of TNNT2 (within 10 amino acids to either side) has been associated with disease, supporting the functional importance of this region of the protein. These HCM variants include Glu83Lys, Val85Leu, Asp86Ala, Arg94Leu, Arg94Cys, and Lys97Asn (Willott et al. 2010; Harvard Sarcomere Protein Gene Mutation Database). The region between residues ~80-180 of TNNT2 has been described as essential for anchoring the troponin-tropomyosin complex to the thin filament (Hinkle et al. 1999, Palm et al. 2001). In vitro functional data from Palm et al. (2001) suggests that a change at codon 92—whether Arg92Trp, Arg92Gln or Arg92Leu—impairs binding of troponin T to tropomyosin, and makes the protein less effective at promoting the binding of tropomyosin to actin. Harada & Potter (2004) showed the Arg92Trp variant to alter the contractile properties of skinned cardiac fibers, including the response of cardiac contraction to changes in pH. He et al. (2007) showed that transgenic mice bearing the Arg92Trp or Arg92Leu variant had a greater “energy cost” for cardiac muscle contraction than wild-type mice. The magnitude of these changes was mutation-specific: Arg92Trp hearts showed more severe energetic abnormalities and greater contractile dysfunction than Arg92Leu hearts. Guinto et al. (2009) showed diastolic dysfunction in transgenic mice carrying the variant, and altered calcium kinetics in isolated transgenic myocytes. This is a nonconservative amino acid change from a basic, positively-charged Arginine to a nonpolar Tryptophan. The Arginine at codon 92 is highly conserved across 39 vertebrate species examined (it is a Lysine in medaka) and surrounding residues are also highly conserved. In silico analysis with PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/) predicts the variant to be “probably damaging”. In total the variant has not been seen in ~5990 published controls and publicly available population datsets. There is no variation at codon 92 listed in the NHLBI Exome Sequencing Project dataset, which currently includes variant calls on ~3500 Caucasian and ~1800 African American individuals (as of 1/15/2012). There is also no variation at this codon listed in dbSNP or 1000 genomes (as of 1/15/2012). The variant was not observed in published controls: Koga et al. (1996) did not detect the variant in more than 100 Japanese controls. Moolman et al. (1997) reported that the variant was absent from 100 control individuals. Moolman-Smook et al. (1999) did not find it in 100 controls (unclear if these were the same controls as in 1997). Fujino et al. (2001) did not detect it in 100 controls. Varnava et al. (2001) did not detect it in at least 90 control individuals. Van Driest et al. (2003) did not detect it in 100 Caucasian and 100 African American controls.
Clinical Genetics, Academic Medical Center	RCV000159280	SCV001917468	pathogenic	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000159280	SCV001930094	pathogenic	not provided		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000159280	SCV001954196	pathogenic	not provided		no assertion criteria provided	clinical testing