chr1-201365244-A-T

Variant names:

• chr1-201365244-A-T
• rs121964858
• NM_001276345.2:c.358T>A

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PM5 PP3_Moderate PP5_Very_Strong

The NM_001276345.2(TNNT2):​c.358T>A​(p.Phe120Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,614,038 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 Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F120L) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: TNNT2 NM_001276345.2 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:9
• Conservation: PhyloP100: 9.30

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]

ENSG00000286600 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 16 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, 11 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 chr1-201365242-A-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 177807.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.896
• PP5: Variant 1-201365244-A-T is Pathogenic according to our data. Variant chr1-201365244-A-T is described in ClinVar as [Pathogenic]. Clinvar id is 12412.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-201365244-A-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNNT2	NM_001276345.2	c.358T>A	p.Phe120Ile	missense_variant	Exon 10 of 17	ENST00000656932.1	NP_001263274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNNT2	ENST00000656932.1	c.358T>A	p.Phe120Ile	missense_variant	Exon 10 of 17		NM_001276345.2	ENSP00000499593.1

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152152 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: 0.000192

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461886 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 727246

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152152 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74344

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000192

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Dilated cardiomyopathy 1D Pathogenic:2

Apr 11, 2023

Genome-Nilou Lab

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 01, 2017

Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.328T>A (p.Phe110Ile) variant has not been observed in general population but reported with high prevalence and segregation pattern in multiple hypertrophic cardiomyopathy (HCM) patients (PMID: 7898523, 9714088). It is well conversed during evolution and predicted to be deleterious by multiple in silica prediction software. This variant has been showed to dramatically increase Ca2+ sensitivity of force development in cardiac muscle preparation (PMID: 10617660). It has been also observed in other clinical labs and reported as pathogenic. At the same amino acid position, Phe110Ile (c.330T>G), Phe110Val, Phe110L are reported as deleterious variants. Based on the above evidences, we interpret this variant as pathogenic. -

Cardiomyopathy Pathogenic:2

May 15, 2023

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: TNNT2 c.328T>A (p.Phe110Ile) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251494 control chromosomes. c.328T>A has been reported in the literature in multiple individuals affected with HCM, including families with segregation data (eg. Anan_1998, Lin_2000, etc). These data indicate that the variant is very likely to be associated with disease. Skinned papillary muscle fibers from transgenic mice expressing F110I and F110I-reconstituted human cardiac muscle preparations demonstrated increased Ca2 sensitivity of force and ATPase activity and impaired ATPase activation (Hernandez_2005, Szczesna_2000). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Feb 16, 2024

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces phenylalanine with isoleucine at codon 110 in the tropomyosin binding domain of the TNNT2 protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. A functional study has shown the mutant protein to exhibit increased Ca2+ sensitivity of force development and impaired ATPase activation in cardiac muscle preparation (PMID: 10617660). A transgenic mouse model for this variant has shown a phenotype consistent with decreased exercise tolerance and increased heart weight to body weight ratio (PMID: 16115869). This variant has been reported in over ten individuals affected with hypertrophic cardiomyopathy (PMID: 7898523, 9482583, 9714088, 22112859, 23494605, 29907873). It has been shown that this variant segregates with disease in multiple affected individuals across six families, and was associated with variable cardiac morphologies and a favorable prognosis (PMID: 9714088). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). A different variant affecting the same codon, p.Phe110Leu is considered to be disease-causing (ClinVar variation ID: 177807), suggesting that phenylalanine at this position is important for TNNT2 protein function. Based on the available evidence, this variant is classified as Pathogenic. -

Hypertrophic cardiomyopathy 2 Pathogenic:2

Aug 04, 1998

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Apr 11, 2023

Genome-Nilou Lab

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Pathogenic:1

Jan 30, 2013

Stanford Center for Inherited Cardiovascular Disease, Stanford University

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: 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 variant Phe110Ile (F110I; c.340T>A at the nucleotide level) The variant has been reported in at least 14 unrelated cases of HCM, and has segregated with disease in all affected family members tested (from 8 families). This includes strong segregation data from one Japanese family, and good segregation data from at least 3 others—plus extensive in vitro functional data and a Phe110Ile transgenic mouse model prone to arrhythmias. Cases: Watkins et al. (1995) first reported this variant in a proband with HCM, accompanied by weak segregation data: The variant was also present in the only other affected member of the family. Koga et al. (1996) detected it in 2 different Japanese 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. Anan et al. (1998) identified 6 different Japanese HCM families with the Phe110Ile variant. In 4 families, segregation analysis was possible. The variant segregated with disease in the following number of family members in each family: 3 (max separation: 2nd degree); 3 (max separation: 1st degree); 4 (max separation: 2nd degree); 3 (max separation: 2nd degree). Lin et al. (2000) reported Phe110Ile variants in a large Japanese HCM family, associated with significant biventricular hypertrophy and a high incidence of sudden death. Phe110Ile segregated with disease in all 6 affected individuals, 2 of whom were severely-affected homozygotes. The most distantly-related affected carriers of the variant were 3rd degree relatives (cousins). One family member died suddenly at age 18 while running and could not be genotyped. Konno et al. (2003, 2005) reported Phe110Ile in 2 Japanese individuals (it is not clear if they are related). Otsuka et al. (2011) found the variant in two unrelated Japanese probands, and in a third unrelated Japanese proband who also carried a TNNT2 Pro80Ser variant inherited from the other parent. Transgenic mice expressing Phe110Ile did not develop significant cardiac hypertrophy or fibrosis, but the variant impaired acute exercise tolerance; muscle fibers containing the variant had increased calcium sensitivity of force and an increased “energy cost” (ratio of ATPase/force) compared to wildtype (Hernandez 2005). Baudenbacher et al. (2008) showed the variant created arrhythmia (VT) susceptibility in transgenic mice. Other changes at codon 110 have also been associated with disease: Phe110Leu (we classify as likely disease causing) and Phe110Val (we classify as 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. This includes Ala104Val (HCM) and Arg113Trp (DCM) (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 is available for the Phe110Ile variant specifically: Yanaga et al. (1999) showed the variant to potentiate the maximum level of ATPase activity in cardiac myofibrils. Nakaura et al. (1999) showed it to increase maximum contractile activity of skinned cardiac muscle fibers. Szczesna et al. (2000) showed it increased calcium sensitivity of force development in skinned cardiac muscle preparations, and troponin complexes containing the variant had impaired activation of myosin-ATPase. Takahashi-Yanaga et al. (2001) showed Phe110Ile to impair multiple calcium-regulating functions o -

Cardiomyopathy, familial restrictive, 3 Pathogenic:1

Apr 11, 2023

Genome-Nilou Lab

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hypertrophic cardiomyopathy Pathogenic:1

Apr 25, 2024

All of Us Research Program, National Institutes of Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces phenylalanine with isoleucine at codon 110 in the tropomyosin binding domain of the TNNT2 protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. A functional study has shown the mutant protein to exhibit increased Ca2+ sensitivity of force development and impaired ATPase activation in cardiac muscle preparation (PMID: 10617660). A transgenic mouse model for this variant has shown a phenotype consistent with decreased exercise tolerance and increased heart weight to body weight ratio (PMID: 16115869). This variant has been reported in over ten individuals affected with hypertrophic cardiomyopathy (PMID: 7898523, 9482583, 9714088, 22112859, 23494605, 29907873). It has been shown that this variant segregates with disease in multiple affected individuals across six families, and was associated with variable cardiac morphologies and a favorable prognosis (PMID: 9714088). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). A different variant affecting the same codon, p.Phe110Leu is considered to be disease-causing (ClinVar variation ID: 177807), suggesting that phenylalanine at this position is important for TNNT2 protein function. Based on the available evidence, this variant is classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
CardioboostCm	Pathogenic	0.97
BayesDel_addAF	Pathogenic	0.51	D
BayesDel_noAF	Pathogenic	0.49
CADD	Pathogenic	30
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.96	.;.;.;D;.;.;.;.;D;.
Eigen	Pathogenic	0.90
Eigen_PC	Pathogenic	0.82
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	0.98	.;D;D;D;D;D;.;D;.;.
M_CAP	Pathogenic	0.53	D
MetaRNN	Pathogenic	0.90	D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	3.1	.;.;.;M;.;.;.;.;.;.
PrimateAI	Uncertain	0.78	T
PROVEAN	Pathogenic	-5.7	D;D;.;.;.;.;.;D;D;D
REVEL	Pathogenic	0.91
Sift	Pathogenic	0.0	D;D;.;.;.;.;.;D;D;D
Sift4G	Benign	0.075	T;T;T;T;T;T;T;T;.;D
Polyphen		1.0	.;.;.;D;.;.;.;.;D;.
Vest4		0.83
MutPred		0.41		.;.;.;Gain of methylation at K125 (P = 0.117);.;.;.;.;.;Gain of methylation at K125 (P = 0.117);
MVP		0.98
MPC		1.7
ClinPred		1.0	D
GERP RS		5.0
Varity_R		0.85
gMVP		0.99

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: rs121964858; hg19: chr1-201334372;