rs727504242

chr19-55154082-G-Achr19-55154082-G-C

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1 PP3_Moderate PP5_Very_Strong

The NM_000363.5(TNNI3):c.497C>T(p.Ser166Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,612,566 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S166P) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000048 (0 hom.)
• Consequence: TNNI3 NM_000363.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:17
• Conservation: PhyloP100: 3.53

Genes affected

TNNI3 (HGNC:11947): (troponin I3, cardiac type) Troponin I (TnI), along with troponin T (TnT) and troponin C (TnC), is one of 3 subunits that form the troponin complex of the thin filaments of striated muscle. TnI is the inhibitory subunit; blocking actin-myosin interactions and thereby mediating striated muscle relaxation. The TnI subfamily contains three genes: TnI-skeletal-fast-twitch, TnI-skeletal-slow-twitch, and TnI-cardiac. This gene encodes the TnI-cardiac protein and is exclusively expressed in cardiac muscle tissues. Mutations in this gene cause familial hypertrophic cardiomyopathy type 7 (CMH7) and familial restrictive cardiomyopathy (RCM). Troponin I is useful in making a diagnosis of heart failure, and of ischemic heart disease. An elevated level of troponin is also now used as indicator of acute myocardial injury in patients hospitalized with moderate/severe Coronavirus Disease 2019 (COVID-19). Such elevation has also been associated with higher risk of mortality in cardiovascular disease patients hospitalized due to COVID-19. [provided by RefSeq, Aug 2020]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PM1: In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 13 uncertain in NM_000363.5
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.901
• PP5: Variant 19-55154082-G-A is Pathogenic according to our data. Variant chr19-55154082-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 177630.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-55154082-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNNI3	NM_000363.5	c.497C>T	p.Ser166Phe	missense_variant	7/8	ENST00000344887.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNNI3	ENST00000344887.10	c.497C>T	p.Ser166Phe	missense_variant	7/8	1	NM_000363.5	P1

Frequencies

GnomAD3 genomes AF: 0.00000659 AC: 1 AN: 151740 Hom.: 0 Cov.: 31

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

GnomAD3 exomes AF: 0.00000803 AC: 2 AN: 249054 Hom.: 0 AF XY: 0.00000739 AC XY: 1 AN XY: 135230

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000177

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000479 AC: 7 AN: 1460826 Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4 AN XY: 726742

Gnomad4 AFR exome AF: 0.0000299

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: 0.00000540

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000659 AC: 1 AN: 151740 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 74090

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000113

ExAC AF: 0.00000827 AC: 1

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:17

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:9

Likely pathogenic, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Apr 11, 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. The variant has been seen in at least 9 unrelated published cases of HCM (see details below). The testing lab also states in their report that they have seen this particular variant in multiple unrelated individuals tested for HCM. Unfortunately, there is no segregation data presented in any of these studies. 2 of these 9 patients identified with this p.S166F variant also harbored another variant in a sarcomeric gene (including one novel missense variant in MYH7, and one nonsense variant in MYBPC3). Erdmann J et al. 2003 screened for mutations in 6 sarcomeric genes (MYBPC3, MYH7, TNNT2, TPM1, TNNI3, and TNNC1) in 108 patients with clinical diagnosis of HCM. This particular p.S166F variant was identified in 1 individual with HCM, though notably this individual also carried a novel missense variant in MYH7. p.S166F in TNNI3 was absent from 50 German controls. No segregation data is presented. While the authors note the highly conserved residue 166 and change in charge, they conclude that there is no proof that both missense variants (if any) are disease causing. Van Driest S et al. 2003 identified p.S166F in 3 unrelated patients with HCM. There was no family history or segregation data available. This variant was absent from 200 healthy controls from Coriell (100 African Americans and 100 European Americans). The same group subsequently screened this same cohort for mutations in MYBPC3, and identified an individual with HCM with both p.S166F in TNNI3 as well as a nonsense variant in MYBPC3. Given that this was the same cohort as their 2003 paper, the total unrelated HCM patients with the S166F variant from the Van Driest group appears to be 3, though notably with one occurring in the presence of another (likely pathogenic) variant. Mogensen J et al. 2004 identified p.S166F in 1 proband with HCM in a UK cohort and this proband’s clinically unaffected sister (though no ages or details are provided). Absent from 75 Caucasian controls. No segregation data presented. Additionally, the authors only screened this cohort of HCM patients for mutations in TNNI3.Finally, Van den Wijngaard A et al. 2011 identified this variant in 4 unrelated patients with HCM in the Netherlands, though no segregation data available and weak methodology in that sounds like they only screened TNNI3 in this large cohort of cardiomyopathy patients. In silico analysis with PolyPhen-2 predicts the variant to be possibly damaging, and Mutation Taster considers this variant disease-causing. Ser166Phe results in a non-conservative amino acid substitution of a neutral, polar Serine with a non-polar Phenylalanine. The Serine at codon 166 is completely conserved across species, as are neighboring amino acids. This variant occurs in exon 7 of 8 coding exons. Other variants have been reported in association with disease at nearby codons (Lys164Thr, Leu167Pro). One paper found that the majority of TNNI3 mutations as of 2011 were identified in exons 7 and 8, encoding domains interacting with cardiac actin (ACTC1) and cardiac troponin C (TNNC1).Disease-causing variants in MYBPC3 and MYH7 are most common in HCM, accounting for 20%-45% and 15%-20% of the disease, respectively. Cardiac troponin T type 2 (TNNT2) and troponin I type 3 (TNNI3) each account for ~5%. Variation in other sarcomere genes is less frequent. In total the variant has not been seen in approximately 6,350 published controls and individuals from publicly available population datasets (this includes 350 published controls from the literature, and individuals from publicly available population datasets). There is no variation at codon 166 listed in the NHLBI Exome Sequencing Project dataset, which curre -
Likely pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Sep 09, 2021	PM1, PM2_supporting, PS3_supporting, PS4_moderate -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Jul 20, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Jun 17, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Dec 19, 2022	Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrated that p.(S166F) significantly increased the calcium sensitivity and slowed the rate of calcium dissociation from the Troponin complex, and may influence TnC-TnI interactions (Liu et al., 2012); 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: 11121119, 24510615, 31737537, 22361390, 22675533, 15607392, 15519027, 12860912, 12974739, 21839045, 26526134, 19914256, 26914223, 27532257, 30847666, 31447099, 33662488, 36411388, 35626289, 35470684, 21533915) -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

Hypertrophic cardiomyopathy Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Dec 11, 2023	This missense variant replaces serine with phenylalanine at codon 166 in the C-terminal mobile domain of the TNNI3 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). One in-vitro functional study showed that this variant led to an increase in calcium sensitivity as well as a decrease in the rate of calcium dissociation from the troponin complex (PMID: 22675533). This variant has been reported in individuals affected with hypertrophic cardiomyopathy (PMID: 12860912, 12974739, 15519027, 15607392 , 21533915, 21839045, 15519027, 27532257, 30847666, 31737537, 33662488). One of these individuals also carried a pathogenic variant in the MYBPC3 gene (PMID: 15519027, 21839045). This variant has also been reported in an individual affected with atrioventricular block (PMID: 35470684) and in a case of sudden infant death (PMID: 22361390). This variant has been identified in 2/249054 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	May 25, 2020	The p.Ser166Phe variant in TNNI3 has been reported at least 10 individuals with HCM and 1 infant with sudden infant death (Van Driest 2003, Mogensen 2004, van den Wigngaard 2011, Brion 2012, LMM data). One of these individuals also carried a pathogenic variant in MYBPC3 and had an early age of disease onset (Van Driest 2004). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID: 177630) and has been identified in 0.002% (2/113184) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org/). In vitro functional studies support an impact on protein function (Liu 2012). Additionally, computational prediction tools and conservation analyses are consistent with pathogenicity. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant HCM. ACMG/AMP Criteria applied:PM2, PS4_Moderate, PP3, PS3_Supporting. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 08, 2024	This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 166 of the TNNI3 protein (p.Ser166Phe). This variant is present in population databases (rs727504242, gnomAD 0.002%). This missense change has been observed in individuals with autosomal dominant hypertrophic cardiomyopathy (PMID: 21533915). ClinVar contains an entry for this variant (Variation ID: 177630). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects TNNI3 function (PMID: 22675533). For these reasons, this variant has been classified as Pathogenic. -

Cardiomyopathy Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Jun 06, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Aug 08, 2023	This missense variant replaces serine with phenylalanine at codon 166 in the C-terminal mobile domain of the TNNI3 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). One in-vitro functional study showed that this variant led to an increase in calcium sensitivity as well as a decrease in the rate of calcium dissociation from the troponin complex (PMID: 22675533). This variant has been reported in individuals affected with hypertrophic cardiomyopathy (PMID: 12860912, 12974739, 15519027, 15607392 , 21533915, 21839045, 15519027, 27532257, 30847666, 31737537, 33662488, 35626289). One of these individuals also carried a pathogenic variant in the MYBPC3 gene (PMID: 15519027, 21839045). This variant has also been reported in an individual affected with atrioventricular block (PMID: 35470684), in a case of sudden infant death (PMID: 22361390), and in an individual affected with juvenile ischemic stroke (PMID: 36411388). This variant has been identified in 2/249054 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Hypertrophic cardiomyopathy 7 Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	Jan 18, 2018	The c.497C>T (p.Ser166Phe) variant has been reported in several patients with hypertrophic cardiomyopathy (HCM) [PMID 21533915, 12974739, 26914223]. One of the reported patient also carried a variant in MYH7 (p.Cys905Phe) [PMID 12974739]. The variant was detected in 4/1,040 patients in the Netherland and is consider a founder mutation in this population [PMID 21533915]. Functional assays showed that this change alters the calcium binding properties of the Tn complex [PMID 22675533]. This variant was observed in only one individual at the heterozygous state in the ExAC population database (http://exac.broadinstitute.org/variant/19-55665450-G-A).Serine at position 166 of the TNNI3 protein is conserved in mammals and while not clinically validated, computer-based algorithms (SIFT and Polyphen-2) predict this p.Ser166Phe change to be deleterious. This variant is thus classified as likely pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Dec 30, 2021	- -

Cardiovascular phenotype Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 17, 2022

The p.S166F variant (also known as c.497C>T), located in coding exon 7 of the TNNI3 gene, results from a C to T substitution at nucleotide position 497. The serine at codon 166 is replaced by phenylalanine, an amino acid with highly dissimilar properties. This alteration has been reported in hypertrophic cardiomyopathy (HCM) cohorts and has been described as a Finnish founder mutation (Erdmann J, Clin. Genet. 2003 Oct; 64(4):339-49; Van Driest SL, J. Am. Coll. Cardiol. 2004 Nov; 44(9):1903-10; Mogensen J, J. Am. Coll. Cardiol. 2004 Dec; 44(12):2315-25; van den Wijngaard A, Neth Heart J 2011 Aug; 19(7-8):344-51; Maron BJ, Heart Rhythm 2012 Jan;9(1):57-63). This alteration was also reported once in a sudden infant death syndrome (SIDS) cohort (Brion M, Forensic Sci. Int. 2012 Jun; 219(1-3):278-81). In some of the reported cases, the p.S166F alteration was seen in individuals who also had variants in other cardiac-related genes (Erdmann J, Clin. Genet. 2003 Oct; 64(4):339-49; Van Driest SL, J. Am. Coll. Cardiol. 2004 Nov; 44(9):1903-10; Maron BJ, Heart Rhythm 2012 Jan;9(1):57-63). In addition, this alteration has been shown to have an impact on protein function ( Liu B, PLoS ONE 2012 Jun; 7(6):e38259). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.43
CardioboostCm	Benign	0.090
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Uncertain	-0.020
Cadd	Pathogenic	27
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.94	D;D
Eigen	Uncertain	0.22
Eigen_PC	Benign	0.18
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Benign	0.84	T;T
M_CAP	Pathogenic	0.36	D
MetaRNN	Pathogenic	0.90	D;D
MetaSVM	Uncertain	0.60	D
MutationAssessor	Uncertain	2.4	M;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.59	T
PROVEAN	Uncertain	-4.2	D;.
REVEL	Pathogenic	0.70
Sift	Uncertain	0.0020	D;.
Sift4G	Benign	0.072	T;T
Polyphen		0.76	P;.
Vest4		0.81
MutPred		0.82		Loss of disorder (P = 0.0185);.;
MVP		0.93
MPC		1.6
ClinPred		0.96	D
GERP RS		3.7
Varity_R		0.71

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: rs727504242; hg19: chr19-55665450;