chr1-201365291-C-A

Position:

• chr1-201365291-C-A

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_001276345.2(TNNT2):​c.311G>T​(p.Arg104Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/22 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R104C) has been classified as Pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: TNNT2 NM_001276345.2 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:10
• Conservation: PhyloP100: 7.89

Genes affected

TNNT2 (HGNC:11949): (troponin T2, cardiac type) This gene encodes the cardiac isoform of troponin T. The encoded protein is the tropomyosin-binding subunit of the troponin complex, which is located on the thin filament of striated muscles and regulates muscle contraction in response to alterations in intracellular calcium ion concentration. Mutations in this gene have been associated with familial hypertrophic cardiomyopathy as well as with dilated cardiomyopathy. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a chain Troponin T, cardiac muscle (size 296) in uniprot entity TNNT2_HUMAN there are 88 pathogenic changes around while only 9 benign (91%) in NM_001276345.2
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr1-201365292-G-A is described in Lovd as [Pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.946
• PP5: Variant 1-201365291-C-A is Pathogenic according to our data. Variant chr1-201365291-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 43629.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-201365291-C-A is described in Lovd as [Pathogenic]. Variant chr1-201365291-C-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNNT2	NM_001276345.2	c.311G>T	p.Arg104Leu	missense_variant	10/17	ENST00000656932.1	NP_001263274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNNT2	ENST00000656932.1	c.311G>T	p.Arg104Leu	missense_variant	10/17		NM_001276345.2	ENSP00000499593	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461760 Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1 AN XY: 727196

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:10

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 20, 2022	Published functional studies demonstrated altered calcium regulation of muscle contraction (Lu et al., 2003; Harada et al., 2004); 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: 14654368, 10525521, 28073646, 22144547, 27532257, 11606294, 14722098, 18258667, 23074333, 25611685, 32659924, 30165862, 20513729) -
Likely pathogenic, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Sep 03, 2014	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 variant Arg94Leu (R94L; c.281G>T at the nucleotide level) The variant has been reported in at least 3 unrelated cases of HCM with moderate segregation data in one family and functional data available. Varnava et al. (1999, 2001) identified this variant in an HCM family with a history of four SCD under age 45. It segregated with the disease in 3 affected family members tested, which included two siblings and their cousin. In addition, a child of one of the siblings who had an abnormal ECG but normal echo at age 6 also had the variant. Melacini et al. (2010) detected the variant in an Italian HCM transplant patient. Pasquale et al. (2011) detected it in an HCM patient followed in the UK. Another change at this same codon, Arg94Cys, has been associated with HCM (we consider that variant to be of uncertain significance, probably 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 Val85Leu, Asp86Ala, Arg92Trp, Arg92Gln, Arg92Leu, Lys97Asn and Ala104Val (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 the Arg94Leu variant impairs binding of troponin T to tropomyosin and makes the protein less effective at promoting the binding of tropomyosin to actin. Lu et al. (2003) found it increased the calcium sensitivity of force generation, but had no effect on the protein’s affinity for tropomyosin. Harada & Potter (2004) showed the variant to alter the contractile properties of skinned cardiac fibers, including the response of cardiac contraction to changes in pH. This is a nonconservative amino acid change from a basic, positively-charged Arginine to a nonpolar Leucine. The Arginine at codon 94 is completely conserved across 39 vertebrate species examined. In silico analysis with PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/) predicts the variant to be “probably damaging”. Pasquale et al. (2011) report that the SIFT prediction for the variant is “not tolerated”. In total the variant has not been seen in ~6190 published controls and publicly available population datasets. There is no variation at codon 94 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 no variation at this codon listed in dbSNP or 1000 genomes (as of 1/15/2012). The variant was not observed in published controls: Varnava et al. (1999) did not find the variant in 100 normal controls. Varnava et al. (2001) did not detect it in at least 90 control individuals. Melacini et al. (2010) did not find it in 400 (Italian?) controls. Pasquale et al. (2011) did not find it in 200 Caucasian controls. -

Hypertrophic cardiomyopathy Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 19, 2018	proposed classification - variant undergoing re-assessment, contact laboratory -
Likely pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Nov 28, 2023	This missense variant replaces arginine with leucine at codon 94 in the tropomyosin binding domain 1 of the TNNT2 protein. Computational prediction suggests that this variant may have a deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Experimental functional studies using rabbit skinned muscle fibers have shown that this variant causes an increase in calcium sensitivity (PMID: 14654368, 14722098). In-vitro functional characterization studies have shown that this variant causes instability in the tropomyosin overlap complex (PMID: 11606294). This variant has been reported in multiple individuals affected with hypertrophic cardiomyopathy (PMID: 10525521, 20513729, 22144547, 27532257, 28073646, 32659924, 33495597). It has been shown that this variant segregates with disease in two affected individuals in one family (PMID: 28073646). This variant has also been reported in an individual affected with restrictive cardiomyopathy (PMID: 30165862). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Different variants affecting the same codon, p.Arg94His and p.Arg94Cys, are considered to be disease-causing (ClinVar variation ID: 43628 and 165549), suggesting that arginine at this position is important for TNNT2 protein function. Based on the available evidence, this variant is classified as Likely Pathogenic. -

Dilated cardiomyopathy 1D Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Dilated cardiomyopathy 1D;C1861864:Hypertrophic cardiomyopathy 2 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine

Dec 31, 2019

The c.281G>T variant results in an amino acid change from an arginine to a leucine at codon 94 of the TNNT2 protein (p.Arg94Leu). The variant has been reported in an individual with familial hypertrophic cardiomyopathy (HCM) and segregates in the family (PMID: 10525521). It has also been reported in multiple unrelated individuals affected with HCM (PMID: 27532257). Functional studies support an effect of this variant on calcium-dependent force generation (PMID: 14654368). Different missense variants at this location (p.Arg94Cys, p.Arg94His) have been reported in association with HCM (PMID: 22112859, 23711808, 2003160, 20624503). This variant is not present in population databases (gnomAD). Therefore, this variant in the TNNT2 gene is classified as likely pathogenic. -

Cardiomyopathy, familial restrictive, 3 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 22, 2024

The p.R94L pathogenic mutation (also known as c.281G>T), located in coding exon 8 of the TNNT2 gene, results from a G to T substitution at nucleotide position 281. The arginine at codon 94 is replaced by leucine, an amino acid with dissimilar properties. This alteration has been reported in several hypertrophic cardiomyopathy (HCM) cohorts and has been shown to segregate with disease in a family (Varnava A et al. Heart. 1999;82:621-4; Melacini P et al. Eur Heart J. 2010 Sep;31(17):2111-23; Pasquale F et al. Circ Cardiovasc Genet. 2012 Feb;5(1):10-7). Functional in vitro analyses involving skinned cardiac fibers have suggested that this alteration affects TNNT2 protein function (Lu QW et al. J Mol Cell Cardiol. 2003;35:1421-7). In addition, an alteration involving the same amino acid, p.R94H (c.281G>A), has been reported in individuals with HCM (Millat G et al. Eur J Med Genet. 2010;53:261-7). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Hypertrophic cardiomyopathy 2 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Dilated cardiomyopathy 1D;C1861864:Hypertrophic cardiomyopathy 2;C2676271:Cardiomyopathy, familial restrictive, 3 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Oct 17, 2023

This sequence change replaces arginine, which is basic and polar, with leucine, which is neutral and non-polar, at codon 94 of the TNNT2 protein (p.Arg94Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hypertrophic cardiomyopathy (PMID: 10525521, 27532257). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 43629). 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. Experimental studies have shown that this missense change affects TNNT2 function (PMID: 14654368, 14722098). This variant disrupts the p.Arg94 amino acid residue in TNNT2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 10978365). 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.97
CardioboostCm	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.56	D
BayesDel_noAF	Pathogenic	0.56
CADD	Pathogenic	33
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.97	.;.;.;D;.;.;.;.;D;.;.;D
Eigen	Pathogenic	0.91
Eigen_PC	Pathogenic	0.83
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	0.99	.;D;D;D;D;D;.;D;.;.;D;.
M_CAP	Pathogenic	0.70	D
MetaRNN	Pathogenic	0.95	D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.1	.;.;.;M;.;.;.;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D
PrimateAI	Pathogenic	0.84	D
PROVEAN	Pathogenic	-6.5	D;D;.;.;.;.;.;D;D;D;D;D
REVEL	Pathogenic	0.98
Sift	Pathogenic	0.0	D;D;.;.;.;.;.;D;D;D;D;D
Sift4G	Pathogenic	0.0010	D;D;D;D;D;D;D;D;.;D;D;.
Polyphen		1.0	.;.;.;D;.;.;.;.;D;.;.;.
Vest4		0.95
MutPred		0.74		.;.;.;Loss of methylation at K103 (P = 0.0781);.;.;.;.;.;Loss of methylation at K103 (P = 0.0781);.;.;
MVP		0.95
MPC		1.6
ClinPred		1.0	D
GERP RS		5.0
Varity_R		0.91
gMVP		0.97

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs397516457; hg19: chr1-201334419;