1-201365291-C-T

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>A(p.Arg104His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 14/22 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R104C) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: TNNT2 NM_001276345.2 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:8
• 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 hotspot region, there are 9 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 10 uncertain 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 ClinVar as [Likely_pathogenic]. Clinvar id is 165549.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.95
• PP5: Variant 1-201365291-C-T is Pathogenic according to our data. Variant chr1-201365291-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 43628.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-201365291-C-T is described in Lovd as [Pathogenic]. Variant chr1-201365291-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNNT2	NM_001276345.2	c.311G>A	p.Arg104His	missense_variant	10/17	ENST00000656932.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNNT2	ENST00000656932.1	c.311G>A	p.Arg104His	missense_variant	10/17		NM_001276345.2	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461760 Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2 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: 0.0000166

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:8

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypertrophic cardiomyopathy Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jan 08, 2024	This missense variant replaces arginine with histidine 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). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in over 15 individuals affected with hypertrophic cardiomyopathy (PMID: 19659763, 20031602, 20624503, 25351510, 26507537, 27532257, 28566242, 31308319, 32746448, 35026164, 35581268, 36357925, 26507537, 28566242). It has been shown that this variant segregates with disease in 3 affected individuals across 2 families (PMID: 26507537, 28566242). In one family, this variant has been reported to occur de novo in an individual affected with hypertrophic cardiomyopathy and with no family history (PMID: 36357925). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Different variants affecting the same codon, p.Arg94Cys and p.Arg94Leu, are considered to be disease-causing (ClinVar variation ID: 165549 and 43629), suggesting that arginine at this position is important for TNNT2 protein function. Based on the available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 19, 2017	The p.Arg94His variant in TNNT2 has been reported in at least 6 individuals with HCM, including 3 de novo occurrences (Ho 2009, Millat 2010, Ripoll-Vera 2016, W alsh 2016, LMM data, ClinVar Variation ID 43628). The variant also segregated wi th disease in 2 affected members of 1 family (Ripoll-Vera 2016), and was absent from large population studies. Arginine (Arg) at position 94 is highly conserved in mammals and across evolutionarily distant species and the change to histidin e (His) was predicted to be pathogenic using a computational tool clinically val idated by our laboratory. This tool's pathogenic prediction is estimated to be c orrect 94% of the time (Jordan 2011). In addition, 2 other likely disease-causin g variants at this position (p.Arg94Cys and p.Arg94Leu) have been reported in mu ltiple individuals with HCM (Varnava 1999, Walsh 2016). In summary, the p.Arg94H is variant meets criteria to be classified as pathogenic for HCM in an autosomal dominant manner. -

Dilated cardiomyopathy 1D Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Jul 21, 2023

Not observed at significant frequency in large population cohorts (gnomAD); 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: 25351510, 25524337, 20624503, 23283745, 11606294, 29398688, 10978365, 27532257, 26507537, 31308319, 31737537, 35653365, 33025817, 32746448, 33906374, 34076677, 35514357, 28566242, 20031602) -

Cardiomyopathy, familial restrictive, 3 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Hypertrophic cardiomyopathy 2 Pathogenic:1

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

Jun 13, 2022

The p.R94H pathogenic mutation (also known as c.281G>A), located in coding exon 8 of the TNNT2 gene, results from a G to A substitution at nucleotide position 281. The arginine at codon 94 is replaced by histidine, an amino acid with highly similar properties. This variant was reported in multiple individuals diagnosed with hypertrophic cardiomyopathy (HCM), and co-segregation was observed in three affected relatives from two families (Ho CY et al. Circ Cardiovasc Genet. 2009;2:314-21; Ripoll-Vera T et al. Rev Esp Cardiol (Engl Ed) 2016;69:149-58; Jiménez-Jáimez J et al. Rev Esp Cardiol (Engl Ed), 2017 Oct;70:808-816). This alteration was also detected in one individual diagnosed with HCM in childhood, in whom this variant was noted to occur de novo and in the presence of an alteration in the MYH7 gene (Millat G et al. Eur J Med Genet 2010; 53:261-7). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. Based on internal structural analysis, this variant is in a functionally important region (motif) and near other pathogenic variants (Palm T et al. Biophys. J., 2001 Nov;81:2827-37; Gangadharan B et al. Proc. Natl. Acad. Sci. U.S.A., 2017 10;114:11115-11120). In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

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

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Nov 21, 2023

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 94 of the TNNT2 protein (p.Arg94His). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of hypertrophic cardiomyopathy (PMID: 2003160, 20624503; Invitae). ClinVar contains an entry for this variant (Variation ID: 43628). 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: 11606294). 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: 10525521, 10978365, 11606294). 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	0.92
CardioboostCm	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.55	D
BayesDel_noAF	Pathogenic	0.56
Cadd	Pathogenic	34
Dann	Pathogenic	1.0
Eigen	Pathogenic	0.91
Eigen_PC	Pathogenic	0.83
FATHMM_MKL	Pathogenic	0.98	D
M_CAP	Pathogenic	0.65	D
MetaRNN	Pathogenic	0.95	D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D
PrimateAI	Pathogenic	0.83	D
PROVEAN	Pathogenic	-4.7	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		0.84
MutPred		0.78		.;.;.;Gain of glycosylation at K103 (P = 0.1628);.;.;.;.;.;Gain of glycosylation at K103 (P = 0.1628);.;.;
MVP		0.99
MPC		1.6
ClinPred		1.0	D
GERP RS		5.0
Varity_R		0.81
gMVP		0.93

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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; COSMIC: COSV52663672; COSMIC: COSV52663672;