ClinVar Genomic variation as it relates to human health

The c.557G>A (p.Arg186Gln) variant in the TNNI3 gene has been reported in multiple individuals with hypertrophic cardiomyopathy (PMID: 12707239, 15607392, 22301726, 23540544, 25524337, 25351510, 26169204, 27532257). This variant is not observed in gnomAD. This variant has been reported to co-segregate with HCM in multiple families with incomplete penetrance (PMID: 15607392, 23540544). This variant has also been reported in patients with HCM by other laboratories. The Arginine 186 is a moderately conserved residue, and multiple algorithms predicted the p.Arg186Gln change to be deleterious. Therefore, the c.557G>A (p.Arg186Gln) variant in the TNNI3 gene is classified as pathogenic.

The p.R186Q pathogenic mutation (also known as c.557G>A), located in coding exon 8 of the TNNI3 gene, results from a G to A substitution at nucleotide position 557. The arginine at codon 186 is replaced by glutamine, an amino acid with highly similar properties. This alteration has been reported in association with hypertrophic cardiomyopathy (HCM) in multiple individuals (Richard P, Circulation 2003 May; 107(17):2227-32; Millat G, Eur J Med Genet 2010; 53(5):261-7; Roberts WC, Am. J. Cardiol. 2013 Jun; 111(12):1818-22; Lopes LR, Heart 2015 Feb; 101(4):294-301). In addition, this alteration has been shown to segregate with disease across two families (Mogensen J, J. Am. Coll. Cardiol. 2004 Dec; 44(12):2315-25; Wang C, Mol. Genet. Genomics 2016 Feb; 291(1):79-92). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

The TNNI3 c.557G>A (p.Arg186Gln) missense variant has been identified in at least ten individuals with a phenotype consistent with hypertrophic cardiomyopathy (PMID: 12707239; 22301726; 20624503; 27532257; 23540544; 21239446; 25524337; 33906374; 35653365). This variant has been shown to segregate with disease across multiple families (PMID: 15607392; 26169204). The p.Arg186Gln variant is located in a known hotspot region and is not observed at a significant frequency in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. This variant has been classified as pathogenic by at least three submitters in ClinVar. Based on the available evidence, the c.557G>A (p.Arg186Gln) variant is classified as pathogenic for hypertrophic cardiomyopathy.

The p.Arg186Gln variant in TNNI3 has been identified in at least 14 individuals with HCM, segregated with disease in 14 affected relatives from 4 families (Rich ard 2004, Mogensen 2004, Millat 2010, Fokstuen 2011, Zhu Hu 2012, Roberts 2013, Wang 2015, Walsh 2016, LMM data). It was absent from large population studies. I n summary, this variant meets our criteria to be classified as pathogenic for HC M in an autosomal dominant manner based upon case observations, segregation stud ies and absence from controls. ACMG/AMP Criteria applied: PS4; PP1_Strong; PM2; BP4.

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000043395, PMID:12707239, PS1_S). A different missense change at the same codon has been reported to be associated with TNNI3 related disorder (ClinVar ID: VCV000546467, PMID:28567093, PM5_P). In silico tool predictions suggest damaging effect of the variant on gene or gene product (3CNET: 0.86, PP3_P). A missense variant is a common mechanism associated with Cardiomyopathy (PP2_P). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 186 of the TNNI3 protein (p.Arg186Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hypertrophic cardiomyopathy (PMID: 12707239, 15607392, 20624503, 21239446, 23540544, 25524337, 27532257). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 43395). 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. For these reasons, this variant has been classified as Pathogenic.

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 15607392, 22301726, 27532257, 21310275, 23540544, 19754353, 15524171, 20624503, 23782526, 26183555, 26199943, 28166811, 27681577, 16020591, 25524337, 12707239, 21239446, 26169204, 28567093, 31513939, 33673806, 33297573, 32746448, 35653365, 35626289, 36136372, 33906374, 36818426, Yuan2023[Article], 37730225, 25351510, Guo2023[article], 30150400, 35208637, 33567718, 36671572)

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Gain of function and loss of function are reported mechanisms of disease in this gene. The former is associated with familial restrictive cardiomyopathy 1 (MIM#115210) and hypertrophic cardiomyopathy 7 (MIM#613690), while the latter is associated with dilated cardiomyopathy 1FF (MIM#613286) (PMIDs: 19914256, 21533915). (I) 0108 - This gene is associated with both recessive and dominant disease. The recessive form of inheritance is the exception and has only been reported in a small number of families (PMIDs: 15070570, 23270746). (I) 0112 - The condition associated with this gene has incomplete penetrance (PMID: 15607392). (I) 0115 - Variants in this gene are known to have variable expressivity (PMID: 23270746). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to glutamine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v3) <0.001 for a dominant condition (1 heterozygote, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (4 heterozygotes, 0 homozygotes). (I) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants (DECIPHER). (SP) 0710 - Other missense variant comparable to the one identified in this case has inconclusive previous evidence for pathogenicity. p.(Arg186Trp) has been reported as likely pathogenic (ClinVar) and VUS (ClinVar, PMID: 35027292) in association with HCM and sudden death. p.(Arg186Gly) has been reported in a family with mixed morphologic features of HCM and left ventricular non-compaction (PMID: 28567093); however, we do not consider it comparable to inform pathogenicity because it has a major Grantham score. (I) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. It has been reported in multiple individuals with HCM (ClinVar, PMIDs: 33567718, 33297573, 27532257) and segregated with incomplete penetrance in two families (PMID: 15607392). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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 patient had HCM genetic testing with the GeneDx laboratory. The test included sequencing of 18 genes associated with HCM: MYH7, MYBPC3, TNNT2, TNNI3, TPM1, ACTC, MYL3, MYL2, LAMP2, PRKAG2, GLA, CAV3, MTTG, MTTI, MTTK, MTTQ, TTR, and TNNC1. Results reported on Nov 23rd 2010 showed that a variant associated with disease was identified: p.Arg186Gln (c.557G>A) in the TNNI3 gene. This variant has been reported in multiple cases of HCM. Richard et al (2003) found the p.Arg186Gln variant in one individual with HCM. No segregation data was reported. Mogensen et al (2004) observed the variant in two unrelated families with HCM. Segregation data was not reported separately for each family, however of 11 total genotype positive individuals in both families, 5 had HCM. No other variants have been reported at codon 186, however a variant has been reported with HCM at a nearby codon (p. Lys183Glu (Mogensen et al 2004)). Arginine is highly conserved across species and isoforms at position 186. This variant substitutes a polar, positively charged amino acid (Arg) with a polar, neutral amino acid (Gln). Richard et al (2003) did not identify the variant in 100 presumably healthy controls of unspecified ethnicity and Mogenson et al (2004) did not observe it in 75 presumably healthy individuals, for a total of 175 controls. Based on these data it is very likely that this variant causes cardiomyopathy.