rs397516482

Variant names:

• chr1-201361286-T-A
• rs397516482
• NM_001276345.2:c.803A>T

Variant summary

Our verdict is Uncertain significance. The variant received 5 ACMG points: 5P and 0B. PM2 PP3_Moderate PP5

The NM_001276345.2(TNNT2):​c.803A>T​(p.Lys268Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
• Consequence: TNNT2 NM_001276345.2 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:6 U:3
• Conservation: PhyloP100: 7.85
• Publications: 6 publications found

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]

TNNT2 Gene-Disease associations (from GenCC):

• dilated cardiomyopathy

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• dilated cardiomyopathy 1D

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• hypertrophic cardiomyopathy

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• hypertrophic cardiomyopathy 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• hypertrophic cardiomyopathy 3

  Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
• cardiomyopathy, familial restrictive, 3

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• familial isolated dilated cardiomyopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• familial isolated restrictive cardiomyopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• left ventricular noncompaction

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• cardiomyopathy

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
• arrhythmogenic right ventricular cardiomyopathy

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ENSG00000286600 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.911
• PP5: Variant 1-201361286-T-A is Pathogenic according to our data. Variant chr1-201361286-T-A is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 43670.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNNT2	NM_001276345.2	c.803A>T	p.Lys268Ile	missense_variant	Exon 15 of 17	ENST00000656932.1	NP_001263274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNNT2	ENST00000656932.1	c.803A>T	p.Lys268Ile	missense_variant	Exon 15 of 17		NM_001276345.2	ENSP00000499593.1

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152150 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 31

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152150 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74336

African (AFR) AF: 0.00 AC: 0 AN: 41416

American (AMR) AF: 0.00 AC: 0 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5198

South Asian (SAS) AF: 0.00 AC: 0 AN: 4834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 68010

Other (OTH) AF: 0.00 AC: 0 AN: 2092

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000113

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:6 Uncertain:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Cardiomyopathy Pathogenic:2

May 17, 2023

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

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 13, 2024

Color Diagnostics, LLC DBA Color Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces lysine with isoleucine at codon 258 of the TNNT2 protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. A functional study using human induced pluripotent stem cells has shown that this variant may impact TNNT2 protein function in manner consistent with hypertrophic cardiomyopathy (PMID: 33025817). This variant has been reported in over 15 individuals affected with hypertrophic cardiomyopathy (PMID: 25611685, 26656175, 27483260, 27532257, 28640247, 29875424, 33495596, 33495597, 33673806; communication with an external laboratory; ClinVar SCV000060273.6, SCV000767829.7, SCV000209262.13). One of these individuals also carried a pathogenic variant in a different gene associated with cardiomyopathy (SCV000209262.13). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Hypertrophic cardiomyopathy Pathogenic:1 Uncertain:1

Mar 29, 2023

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Lys258Ile variant in TNNT2 has been reported in 8 individuals with hypertrophic cardiomyopathy (HCM; Bottillo 2016 PMID: 26656175, Rubattu 2016 PMID: 27483260, Walsh 2017 PMID: 27532257, Hathaway 2021 PMID: 33673806, LMM Data, Invitae Personal Communication 2023). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 43670) and has been identified in 0.0015% (1/68010) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). In vitro functional studies provide some evidence that this variant may impact protein function (Pettinato 2020 PMID: 33025817); however, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PS4_Moderate, PM2_Supporting, PP3. -

Jul 29, 2024

All of Us Research Program, National Institutes of Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces lysine with isoleucine at codon 258 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). A functional study using human induced pluripotent stem cells has shown that this variant may impact TNNT2 protein function in manner consistent with hypertrophic cardiomyopathy (PMID: 33025817); the clinical relevance of this observation is not known. This variant has been reported in over 15 individuals affected with hypertrophic cardiomyopathy (PMID: 25611685, 26656175, 27483260, 27532257, 28640247, 29875424, 33495596, 33495597, 33673806; communication with an external laboratory; ClinVar SCV000060273.6, SCV000767829.7, SCV000209262.13). One of these individuals also carried a pathogenic variant in a different gene associated with cardiomyopathy (SCV000209262.13). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Primary familial hypertrophic cardiomyopathy Pathogenic:1

Jun 26, 2017

Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiovascular phenotype Pathogenic:1

Feb 21, 2025

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.K258I variant (also known as c.773A>T), located in coding exon 13 of the TNNT2 gene, results from an A to T substitution at nucleotide position 773. The lysine at codon 258 is replaced by isoleucine, an amino acid with dissimilar properties. This variant (also referred to as p.K252I and p.K265I) was reported in individual(s) with features consistent with hypertrophic cardiomyopathy (Bottillo I et al. Gene, 2016 Feb;577:227-35; Rubattu S et al. Int J Mol Sci. 2016;17(8):1239; Walsh R et al. Genet. Med., 2017 02;19:192-203; Ko C et al. Genet Med. 2018 Jan;20(1):69-75Mazzarotto F et al. Genet Med. 2019 Feb;21(2):284-292; Hathaway J et al. BMC Cardiovasc Disord. 2021 Mar;21(1):126; external communication; Ambry internal data). One functional study indicated this variant may impact protein function (Pettinato AM et al. Circulation. 2020 Dec;142(23):2262-2275). 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 majority of available evidence to date, this variant is likely to be pathogenic. -

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

Dec 19, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces lysine, which is basic and polar, with isoleucine, which is neutral and non-polar, at codon 258 of the TNNT2 protein (p.Lys258Ile). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hypertrophic cardiomyopathy (PMID: 26656175, 27483260, 27532257; internal data). This variant is also known as c.A775T, p.Lys252Ile, c.794C>T and p.Lys265Ile. ClinVar contains an entry for this variant (Variation ID: 43670). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on TNNT2 protein function. For these reasons, this variant has been classified as Pathogenic. -

not specified Uncertain:1

Jan 30, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: TNNT2 c.773A>T (p.Lys258Ile) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 6.6e-06 in 152150 control chromosomes in gnomAD database (v4.0.0). c.773A>T has been reported in the literature in individuals affected with Cardiomyopathy (e.g. Botillo_2016, Walsh_2016, Hathaway_2021, Ho_2018, Ko_2018) with limited clinical details. These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported.The following publications have been ascertained in the context of this evaluation (PMID: 26656175, 33673806, 30297972, 28640247, 27483260, 27532257). ClinVar contains an entry for this variant (Variation ID: 43670). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -

not provided Uncertain:1

Aug 09, 2017

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The K258I variant in the TNNT2 gene has been published as a variant of uncertain significance in an individual with early onset HCM and a family history of disease, however no clinical details or segregation data was provided (reported as c.794 A>T, K265I, using alternate nomenclature) (Rubattu et al., 2016). It was also reported in an individual diagnosed with HCM who harbored five additional cardiogenetic variants (reported as c.755 A>T, K252I, using alternate nomenclature) (Bottillo et al., 2016). Additionally, K258I was reported as a variant of uncertain significance in two individuals in a HCM cohort, although no clinical or segregation data was provided and it is unknown if there were other co-occurring variants (Walsh et al., 2017).This variant was not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server), indicating it is not a common benign variant. The K258I variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties and this substitution occurs at a position that is conserved across species. Finally, in silico analysis predicts this variant is probably damaging to the protein structure/function. However, this variant lacks observation in a significant number of affected individuals, segregation data, and functional evidence, which would further clarify its pathogenicity. Therefore, based on the currently available information, it is unclear whether the K258I variant in the TNNT2 gene is pathogenic or rare benign. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
CardioboostCm	Uncertain	0.80
BayesDel_addAF	Pathogenic	0.36	D
BayesDel_noAF	Pathogenic	0.27
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.95	.;.;.;.;D;.;.;.;.;.;D
Eigen	Uncertain	0.65
Eigen_PC	Uncertain	0.55
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.98	.;D;D;D;D;D;D;.;.;D;.
M_CAP	Pathogenic	0.85	D
MetaRNN	Pathogenic	0.91	D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.88	D
MutationAssessor	Pathogenic	3.2	.;.;.;.;M;.;.;.;.;.;.
PhyloP100		7.8
PrimateAI	Uncertain	0.70	T
PROVEAN	Pathogenic	-6.9	D;D;.;.;.;.;.;.;D;D;D
REVEL	Pathogenic	0.90
Sift	Uncertain	0.0060	D;D;.;.;.;.;.;.;D;D;D
Sift4G	Pathogenic	0.0010	D;D;D;D;D;D;D;D;D;D;.
Polyphen		0.99	.;.;.;.;D;.;.;.;.;.;.
Vest4		0.72
MutPred		0.46		.;.;.;.;Loss of disorder (P = 0.0045);.;.;.;.;.;.;
MVP		0.97
MPC		1.4
ClinPred		1.0	D
GERP RS		3.7
Varity_R		0.93
gMVP		0.90
Mutation Taster		=16/84	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs397516482; hg19: chr1-201330414;