Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is known mechanism of disease in this gene. In addition, dominant-negative is also a suggested mechanism. (PMID: 25589632). (I) 0108 - This gene is associated with both recessive and dominant disease (OMIM). (I) 0112 - The condition associated with this gene has incomplete penetrance. Variants in this gene that result in a premature truncating codon (PTC) are known to have reduced penetrance in DCM (PMID: 25589632). (I) 0200 - Variant is predicted to result in a missense amino acid change from proline to leucine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.001 (3 heterozygotes, 0 homozygotes). (SP) 0502 - Missense variant with conflicting in silico predictions or uninformative conservation. (I) 0600 - Variant is located in the annotated C-terminal A-band and the exon has a PSI score of 100% (PMID: 25589632). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported as pathogenic and likely pathogenic in ClinVar and in over five unrelated individuals with hereditary myopathy with early respiratory failure in homozygous and heterozygous state, including de novo occurrence (PMID:23606733, PMID: 23486992, PMID: 25500009, PMID: 34670883, PMID: 34839411, PMID: 35741838, PMID: 33449170, PMID: 22526018, PMID: 28256728). Heterozygous individuals were reported to have a milder phenotype, subclinical disease or were unaffected, suggesting this variant exhibits variable expressivity and reduced penetrance (PMID:23606733, PMID: 23486992). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Functional studies suggest that this variant impacts protein folding (PMID: 24636144, PMID: 33449170). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

The frequency of this variant in the general population is consistent with pathogenicity. (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)) This variant has been identified in multiple unrelated individuals with hereditary myopathy with early respiratory failure (HMERF). Variable expressivity and reduced penetrance was also reported. Assessment of experimental evidence regarding the effect of this variant on protein function is inconclusive. Results were insufficient to demonstrate an effect on protein function related to disease. (PMID: 24636144, 33449170) This variant is also referred to as p.Pro22859Leu or p.Pro30091Leu in published literature.

PM1+PM2+PP1+PP2+PP3

This is a nonsynonymous variant in the TTN gene (OMIM: 188840). Pathogenic variants in this gene have been associated with autosomal dominant and autosomal recessive TTN-related disorders. Functional studies have shown that this variant alters TTN protein function (PMID: 24636144, 33449170) (PS3), and multiple computational algorithms predict a deleterious effect for this variant (REVEL score: 0.727) (PP3). This variant has a 0.0017% maximum allele frequency in non-founder control populations (https://gnomad.broadinstitute.org/) (PM2). It has been identified in the homozygous in at least 4 individuals reported in the published literature (PMID: 33449170, 23606733) (PM3), andhas also been reported in the heterozygous state in unrelated affected individuals with hereditary myofibrillar myopathy-9 with early respiratory failure(PMID: 22526018, 23486992, 38655354, 34839411). Inheritance from an unaffected or mildly affected parent has been reported, consistent with incomplete penetrance and variable expressivity (PMID: 33449170). Based on the current evidence, this variant is classified as likely pathogenic for autosomal dominant and autosomal recessive TTN-related disorders.

Identified in a patient with Lambert-Eaton Myasthenic Syndrome (LEMS) who also harbored a pathogenic variant in the CACNA1S gene (Cerino et al., 2022); Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies indicates this variant results in an insoluble protein due to improper folding (Hedburg et al., 2014); 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: 22526018, 25500009, 23486992, 23446887, 34839411, 24636144, 35741838, 32039858, 34670883)

Variant summary: TTN c.87491C>T (p.Pro29164Leu) results in a non-conservative amino acid change located in the A-band domain of the encoded protein sequence. Four of four in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 248136 control chromosomes (gnomAD). c.87491C>T has been reported in the literature in multiple individuals with characteristic features of hereditary myopathy with early respiratory failure (Palmio_2013, Yue_2014, Hedberg_2014, Cerino_2022). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function and this variant results in impaired protein solubility (Hedberg_2014). The following publications have been ascertained in the context of this evaluation (PMID: 35741838, 24231549, 23606733, 25500009). ClinVar contains an entry for this variant (Variation ID: 132137). Based on the evidence outlined above, the variant was classified as pathogenic.

The missense variant c.95195C>T p.Pro31732Leu in the TTN gene has been reported previously in heterozygous state in individuals affected with Hereditary myopathy with early respiratory failure. Experimental studies have shown that this missense change affects TTN function Algahtani et al., 2019; Hedberg et al., 2014. This variant is located in the A band of TTN. Variants in this region may be relevant for cardiac or neuromuscular disorders Roberts et al., 2015; Ceyhan-Birsoy et al., 2013. This variant is reported with the allele frequency 0.001% in the gnomAD Exomes. It is submitted to ClinVar as Pathogenic/ Likely pathogenic. The amino acid Pro at position 31732 is changed to a Leu changing protein sequence and it might alter its composition and physico-chemical properties. Computational evidence Polyphen, SIFT and MutationTaster predicts conflicting evidence on protein structure and function for this variant. The reference amino acid change at this position on the TTN is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic.

The p.P22667L variant (also known as c.68000C>T), located in coding exon 170 of the TTN gene, results from a C to T substitution at nucleotide position 68000. The proline at codon 22667 is replaced by leucine, an amino acid with similar properties. This variant (also referred to as p.P31732L and p.P30091L) has been detected in the homozygous and heterozygous states, including a de novo occurrence, in individuals with skeletal muscle and/or respiratory issues consistent with hereditary myopathy with early respiratory failure (HMERF). Homozygous individuals tended to be more severely affected, and not all heterozygous individuals were affected, suggesting this variant exhibits variable expressivity and reduced penetrance (Vasli N et al. Acta Neuropathol., 2012 Aug;124:273-83; Yue D et al. Neuromuscul. Disord., 2015 Feb;25:172-6; Palmio J et al. J Neurol Neurosurg Psychiatry, 2014 Mar;85:345-53; Pfeffer G et al. J. Neurol. Neurosurg. Psychiatry, 2014 Mar;85:331-8; Cerino M et al. Muscle Nerve, 2017 Nov;56:993-997; Savarese M et al. J Neuromuscul Dis, 2020;7:153-166; Rees M et al. Acta Neuropathol, 2021 Mar;141:431-453; Cerino M et al. Genes (Basel), 2022 Jun;13; Liang H et al. Heliyon. 2024 Apr;10(8):e29637). Functional studies suggest this variant may be destabilizing and impact protein folding (Hedberg C et al. Neuromuscul. Disord. 2014 May;24(5):373-9; Rees M et al. Acta Neuropathol, 2021 Mar;141:431-453). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is likely pathogenic for hereditary myopathy with early respiratory failure; however, the association of this alteration with cardiomyopathy is unknown.

Likely pathogenic/Pathogenic according to ACMG criteria. Variant from clinical tested patient.

This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 31732 of the TTN protein (p.Pro31732Leu). This variant is present in population databases (rs753334568, gnomAD 0.003%). This missense change has been observed in individual(s) with hereditary myopathy with early respiratory failure (HMERF) (PMID: 22526018, 23486992, 23606733, 25500009). In at least one individual the variant was observed to be de novo. This variant is also known as c.90272C>T (p.Pro30091Leu) and c.68576C>T (p.Pro22859Leu). ClinVar contains an entry for this variant (Variation ID: 132137). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this missense change affects TTN function (PMID: 24636144). This variant is located in the A band of TTN (PMID: 25589632). Variants in this region may be relevant for cardiac or neuromuscular disorders (PMID: 25589632, 23975875). For these reasons, this variant has been classified as Pathogenic.