rs45501500

chr1-201363390-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1 PM2 PP5

The NM_001276345.2(TNNT2):c.506G>A(p.Arg169Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,876 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R169G) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: TNNT2 NM_001276345.2 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:6
• Conservation: PhyloP100: 4.46

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 Uncertain_significance. Variant got 5 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 9 uncertain in NM_001276345.2
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-201363390-C-T is Pathogenic according to our data. Variant chr1-201363390-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 43647.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=5, Likely_pathogenic=1, Pathogenic=1}. Variant chr1-201363390-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.506G>A	p.Arg169Gln	missense_variant	12/17	ENST00000656932.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNNT2	ENST00000656932.1	c.506G>A	p.Arg169Gln	missense_variant	12/17		NM_001276345.2	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461876 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 727240

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: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:6

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not specified Uncertain:2

Uncertain significance, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Mar 14, 2012	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.Arg159Gln (c.476G>A) in TNNT2 gene. This variant has been reported in two unrelated cases of DCM . One proband was a Caucasian female who was diagnosed with DCM at 20 years of age, 1 week postpartum (Hershberger et al 2008, Hershberger et al 2009, Morales et al 2010). The other was a case of infantile DCM diagnosed at 4 months of age with transplant at 12 years of age (Hershberger et al 2009, Rampersaud et al 2010). There is no co-segregation data on the variant. This is a semi-conservative amino acid substitution with a positively charged Arginine replaced with a neutral Glutamine. Conservation analysis indicates that Arginine is conserved at this position only through mammals but is class conserved throughout evolution. In silico analysis yields conflicting results with SIFT predicting the amino acid change to be tolerated while PolyPhen predicts the substitution to the probably damaging to final protein. Missense variants in nearby codons (p.Arg151Cys, p.Ala157Ser and p.Glu163Lys) have been reported in association with cardiomyopathy. Hershberger et al (2009) reported that p.Arg159Gln affects Ca2+ sensitivity of the myofilaments; this is an integral part of force/contraction generation in the cardiomyocyte. The above authors report the absence of the variant in 253 presumably healthy control individuals. From this control group 188 were Caucasian, 24 African American, 22 Asian and 19 were of Hispanic ancestry. The variant is not currently listed in the NHLBI Exome Sequencing Project dataset, which includes variant calls on ~5,000 Caucasian and African American individuals (as of December 2011). The variant is also listed in dbSNP (rs45501500), which notes that 246 individuals of varying ethnicity drawn from population DNA samples from Coriell were all wildtype. -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	May 27, 2016	Variant classified as Uncertain Significance - Favor Pathogenic. The p.Arg159Gln variant in TNNT2 has been identified in 1 Caucasian individual with peripartum DCM, 1 Caucasian individual with LVNC, and 1 Black individual with DCM. It segre gated with disease in 1 affected relative (Hershberger 2008, Morales 2010, LMM u npublished data). Studies have shown that the p.Arg159Gln variant may affect pro per myocyte function (Hershberger 2009); however, this in vitro assay may not ac curately represent biological function. This variant has not been identified by large population studies and was predicted to be pathogenic using a computationa l tool clinically validated by our laboratory. This tool's pathogenic prediction is estimated to be correct 94% of the time (Jordan 2011). In summary, while the re is some suspicion for a pathogenic role, the clinical significance of the p.A rg159Gln variant is uncertain. -

not provided Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jun 23, 2021	Reported in association with cardiomyopathy (Hershberger et al., 2008; Rampersaud et al., 2011; Walsh et al., 2017; Mazzarotto et al., 2020); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Reported to decrease calcium sensitivity of the myofilaments, which could lead to altered contractility dynamics of the heart (Hershberger et al., 2009); however, it is not known whether these findings are biological or clinically relevant in vivo; Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 20458009, 19412328, 27532257, 21483645, 31983221, 26582918, 27535533, 20031601) -
Uncertain significance, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Jun 01, 2020	- -

Dilated cardiomyopathy 1D Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

May 06, 2021

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Likely pathogenic. Following criteria are met: 0105 - The mechanism of disease for this gene is not clearly established. Functional studies have suggested loss-of-function, gain-of-function and dominant-negative mechanisms based on calcium sensitivity, contractibility and mouse models (PMID: 18612386, 32098556, 33025817). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity. p.(Arg92Gln) has been described in families which has both dilated cardiomyopathy (DCM) and hypertrophic cardimyopathy (PMID: 26507537). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to glutamine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated troponin domain (NCBI). (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0808 - Previous reports of pathogenicity for this variant are conflicting. This variant has been reported in at least three unrelated individuals with DCM (ClinVar, PMID: 20458009, 19412328, 20031601, 27532257, 31983221), and has been described as both likely pathogenic and as a VUS (ClinVar, LOVD). Additionally, it has been observed in another individual with DCM and classified using ACMG guidelines as pathogenic. However, this publication is yet to be peer reviewed (Lesurf R, et al. (2020)). (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Functional studies using porcine cardiac fibres demonstrated that this variant results in reduced calcium sensitivity (PMID: 20031601). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

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

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Dec 11, 2023

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 159 of the TNNT2 protein (p.Arg159Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with dilated cardiomyopathy (PMID: 20031601, 27532257, 31983221, 33500567, 35653365, 36166435; Invitae). This variant is also known as p.Arg169Gln. ClinVar contains an entry for this variant (Variation ID: 43647). 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: 20031601). For these reasons, this variant has been classified as Pathogenic. -

Cardiomyopathy Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Aug 15, 2019

- -

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 21, 2021

The c.476G>A (p.R159Q) alteration is located in exon 11 (coding exon 10) of the TNNT2 gene. This alteration results from a G to A substitution at nucleotide position 476, causing the arginine (R) at amino acid position 159 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.29
CardioboostCm	Pathogenic	0.97
BayesDel_addAF	Uncertain	0.16	D
BayesDel_noAF	Uncertain	-0.010
Cadd	Pathogenic	30
Dann	Pathogenic	1.0
Eigen	Uncertain	0.54
Eigen_PC	Uncertain	0.51
FATHMM_MKL	Benign	0.69	D
M_CAP	Pathogenic	0.80	D
MetaRNN	Uncertain	0.72	D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationTaster	Benign	0.94	D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.62	T
PROVEAN	Benign	-2.0	N;N;.;D;.;.;.;.;N;N;N;N
REVEL	Uncertain	0.49
Sift	Uncertain	0.0020	D;D;.;D;.;.;.;.;D;D;D;D
Sift4G	Uncertain	0.020	D;D;D;D;D;T;D;T;D;D;.;D
Polyphen		0.98, 0.99	.;.;.;.;D;.;.;.;.;.;D;.
Vest4		0.65
MutPred		0.44		.;.;.;.;Loss of MoRF binding (P = 0.0476);.;.;.;.;.;.;Loss of MoRF binding (P = 0.0476);
MVP		0.97
MPC		1.2
ClinPred		0.90	D
GERP RS		4.9
Varity_R		0.088
gMVP		0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs45501500; hg19: chr1-201332518;