ClinVar Genomic variation as it relates to human health

Reported as g.293378delA in the heterozygous state in individuals from two Spanish families with tibial muscular dystrophy (TMD) (Hackman et al., 2008); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Frameshift variant predicted to result in protein truncation as the last 29 amino acids are replaced with 8 different amino acids, and other loss-of-function variants have been reported downstream in the Human Gene Mutation Database (Stenson et al., 2014); This variant is associated with the following publications: (PMID: 20301498, 23975875, 18948003, 26627873, 26516846, 27854229, 24395473, 30238059, 31589614, 32528171, 32403337, 32039858)

The heterozygous p.Lys35963AsnfsTer9 variant in TTN was identified by our study in the compound heterozygous state with a pathogenic variant in one individual with limb-girdle muscular dystrophy (LGMD). The presence of this variant in combination with a pathogenic variant and in an individual with LGMD increases the likelihood that the p.Lys35963AsnfsTer9 variant is pathogenic. This variant has been identified in 0.001083% (3/277072) of chromosomes in the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs281864929). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at position 35963 and leads to a premature termination codon 9 amino acids downstream. This termination codon occurs within the last exon and is more likely to escape nonsense mediated decay (NMD) and result in a truncated protein. However, the truncated protein region in the last exon includes the A-band (PMID: 26777568). This variant has also been reported in ClinVar (Variation ID: 38439). Loss of function of the TTN gene is an established disease mechanism in autosomal recessive LGMD. In summary, the p.Lys35963AsnfsTer9 variant is pathogenic based off of our findings, multiple reports in ClinVar, and the literature. ACMG/AMP Criteria applied: PM2, PVS1_Strong, PM3, PM1 (Richards 2015).

The variant results in a shift of the reading frame, and is therefore predicted to result in the loss of a functional protein. Found in at least one patient with expected phenotype for this gene, and found in general population data at a frequency that is consistent with pathogenicity.

Variant summary: TTN c.100185delA (p.Lys33395AsnfsX9) results in a premature termination codon within the last exon (M-band region, PSI 100%), predicted to cause a truncation of the encoded protein. The variant allele was found at a frequency of 4e-06 in 249174 control chromosomes (gnomAD). c.100185delA has been reported in the literature in multiple individuals affected with Autosomal Recessive Titinopathy and some individuals with a cardiac-related phenotype (e.g. Ceyhan-Birsoy_2013, Evila_2017, Gonzalez-Quereda_2020, Yoneda_2021, Barbosa-Gouveia_2022). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 35628876, 23975875, 27796757, 32403337, 34495297). Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change creates a premature translational stop signal (p.Lys35963Asnfs*9) in the TTN gene. While this is not anticipated to result in nonsense mediated decay, it is expected to create a truncated TTN protein. This variant is present in population databases (rs281864930, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with autosomal recessive centronuclear myopathy, autosomal recessive tibial muscular dystrophy and/or dilated cardiomyopathy and atrial fibrillation (PMID: 23975875, 24395473, 26516846, 26627873, 34495297). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as p.K33395NfsX9. ClinVar contains an entry for this variant (Variation ID: 38439). This variant is located in the M band of TTN (PMID: 25589632). Truncating variants in this region have been previously reported in individuals affected with autosomal recessive myopathy and muscular dystrophy (PMID: 18948003, 23975875, 24395473). Truncating variants in this region have also been identified in individuals affected with autosomal dominant dilated cardiomyopathy and/or cardio-related conditions (PMID: 27869827, 32964742). For these reasons, this variant has been classified as Pathogenic.

The c.80694delA pathogenic mutation, located in coding exon 190 of the TTN gene, results from a deletion of one nucleotide at nucleotide position 80694, causing a translational frameshift with a predicted alternate stop codon (p.K26898Nfs*9). This exon is located in the M-band region of the N2-B isoform of the titin protein and is constitutively expressed in TTN transcripts (percent spliced in or PSI 100%). This mutation (also referred to as K33395Nfs*9 (c.100185delA), p.K35963Nfs*9 (c.107889delA), p.K33394Nfs*9 (c.100185delA) in the literature) has been reported in the homozygous and compound heterozygous state with other truncating variants in TTN in association with skeletal muscle disease phenotypes including distal myopathy, centronuclear myopathy, and tibial muscular dystrophy (Hackman P et al. Neuromuscul. Disord., 2008 Dec;18:922-8; Ceyhan-Birsoy O et al. Neurology, 2013 Oct;81:1205-14; Evilä A et al. Ann. Neurol., 2014 Feb;75:230-40; Evilä A et al. Neuromuscul. Disord., 2016 Jan;26:7-15; Välipakka S et al. Neurol Genet, 2017 Dec;3:e204). This variant has also been detected in sudden death and dilated cardiomyopathy cohorts; however, details were not provided (Campuzano O et al. Int J Mol Sci, 2015 Oct;16:25773-87). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. While truncating variants in TTN are present in 1-3% of the general population, truncating variants in the M-band have been reported in association with autosomal recessive titinopathies, primarily presenting with skeletal myopathy phenotypes (Ceyhan-Birsoy O et al. Neurology. 2013 Oct 1;81(14):1205-14; De Cid R et al. Neurology. 2015;85(24):2126-35). In addition, regardless of their position, TTN truncating variants encoded in constitutive exons (PSI >90%) have been found to be significantly associated with dilated cardiomyopathy (DCM), though truncating variants in the A-band are the most common cause of DCM (Herman DS et al. N. Engl. J. Med., 2012 Feb;366:619-28; Roberts AM et al. Sci Transl Med, 2015 Jan;7:270ra6; Schafer S et al. Nat. Genet., 2017 01;49:46-53). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation in association with autosomal recessive titinopathy; however, the clinical significance of this alteration with respect to cardiomyopathy remains unclear.

The TTN c.107889delA variant is predicted to result in a frameshift and premature protein termination (p.Lys35963Asnfs*9). This variant has been reported in individuals with tibial muscular dystrophy, centronuclear myopathy, dilated cardiomyopathy and sudden cardiac death (Hackman et al. 2008. PubMed ID: 18948003; Ceyhan-Birsoy et al. 2013. PubMed ID: 23975875; Evilä et al. 2014. PubMed ID: 24395473; Evilä et al. 2015. PubMed ID: 26627873; Campuzano et al. 2015. PubMed ID: 26516846). The c.107889delA variant is located in the M-band region of the TTN protein and other premature stop variants in this exon have previously been reported to be pathogenic for recessive and dominant TTN-related disorders (Human Gene Mutation Database). RNAseq studies from heart tissue indicate this exon is commonly included in TTN mRNA transcripts (PSI of 100%); however, this analysis in muscle tissue was not performed (Roberts A.M. et al. 2015. PMID: 25589632; https://cardiodb.org/titin/titin_transcripts.php). TTN truncating variants are reported in 1-2% of presumably healthy individuals and occur more frequently in exons with low PSI values, indicating this variant is more likely to be disease causing (Roberts A.M. et al. 2015. PMID: 25589632; Herman D.S. et al. 2012. PMID: 22335739). Many cases of recessive TTN-related myopathies in which the individual is compound heterozygous for two loss of function variants in TTN have also been reported (See Ceyhan-Birsoy O. et al. 2013. PMID: 23975875; Chauveau C et al. 2014. PMID: 24105469; Evilä A et al. 2016. PMID: 27796757; Ge et al. 2019. PubMed ID: 31053406). This variant is reported in 0.0016% of alleles in individuals of European (Non-Finnish) descent in gnomAD. In summary, the c.107889delA variant is categorized as pathogenic for TTN-related disorders.

Converted during submission to Pathogenic.

Variant interpretted as pathogenic and reported on 01/12/2018 by GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.