Submissions for variant NM_001267550.2(TTN):c.40558+1G>A

gnomAD frequency: 0.00004  dbSNP: rs368219776

Total submissions: 13

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust	RCV000209704	SCV000189731	uncertain significance	Primary dilated cardiomyopathy	2014-10-08	criteria provided, single submitter	research	This TTN truncating variant (TTNtv) was identified in one individual in this cohort and is located in an exon that is highly expressed in the heart. In the seven cohorts assessed, TTNtv were found in 14% of ambulant DCM, 22% end-stage or familial DCM, and 2% controls. Heterozygous nonsense, frameshift and canonical splice-disrupting variants found in constitutive and other highly utilised exons are highly likely to be pathogenic when identified in individuals with phenotypically confirmed DCM. TTNtv found incidentally in healthy individuals (excluding familial assessment of DCM relatives) are thought to have low penetrance, particularly when identified in exons that are not constitutively expressed in the heart.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000221188	SCV000272642	uncertain significance	not specified	2019-01-18	criteria provided, single submitter	clinical testing	The c.32854+1G>A variant in TTN has been reported in 1 individual with DCM, and segregated with disease in 1 affected relative (Herman 2012). This variant has also been identified in 4/15632 European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs368219776). The c.32854+1G>A variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and is predicted to cause altered splicing leading to an abnormal or absent protein. Splice and other truncating variants in TTN are strongly associated with DCM, particularly if they are located in the exons encoding for the A-band region of the protein (Herman 2012, Pugh 2014). Variants in the I-band, where the c.32854+1G>A variant is located, occur at a greater frequency in controls than in individuals with DCM (Pugh 2014). This decreases the likelihood, but does not rule out that this variant has a role in disease. In summary, while there is some suspicion for a pathogenic role, the clinical significance of the c.32854+1G>A variant is uncertain.
Eurofins Ntd Llc (ga)	RCV000725594	SCV000338006	uncertain significance	not provided	2018-06-11	criteria provided, single submitter	clinical testing
Invitae	RCV000456920	SCV000542903	likely pathogenic	Dilated cardiomyopathy 1G; Autosomal recessive limb-girdle muscular dystrophy type 2J	2023-12-27	criteria provided, single submitter	clinical testing	This sequence change affects a donor splice site in intron 219 of the TTN gene. It is expected to disrupt RNA splicing and likely results in a truncated or disrupted TTN protein. This variant is present in population databases (rs368219776, gnomAD 0.01%). This variant has not been observed in the literature in individuals with autosomal recessive TTN-related conditions. This variant has been reported in individual(s) with dilated cardiomyopathy (PMID: 22335739, 28333919, 30535219; Invitae); however, the role of the variant in this condition is currently unclear. ClinVar contains an entry for this variant (Variation ID: 223256). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant is located in the I band of TTN (PMID: 25589632). Truncating variants in this region have been reported in individuals affected with autosomal recessive centronuclear myopathy (PMID: 23975875). 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). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV000770044	SCV000901470	uncertain significance	Cardiomyopathy	2017-04-18	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000778575	SCV000914879	uncertain significance	TTN-Related Disorders	2019-01-12	criteria provided, single submitter	clinical testing	The TTN c.32854+1G>A variant (also referred to as c. 40558+1G>A or c. 35635+1G>A) occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. This variant has been reported in two studies and is found in two individuals with dilated cardiomyopathy; it is not clear if they are related (Herman et al. 2012). This variant was also present in a presumable healthy individual (Roberts et al. 2015) and it is reported at a frequency of 0.0002559 in the European (non-Finnish) population of the Exome Aggregation Consortium. Based on the evidence, the c.32854+1G>A variant is classified as a variant of unknown significance but suspicious for pathogenicity for TTN-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Illumina Laboratory Services, Illumina	RCV001132686	SCV001292354	benign	Myopathy, myofibrillar, 9, with early respiratory failure	2019-01-12	criteria provided, single submitter	clinical testing	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Illumina Laboratory Services, Illumina	RCV001132687	SCV001292355	benign	Tibial muscular dystrophy	2019-01-12	criteria provided, single submitter	clinical testing	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
CeGaT Center for Human Genetics Tuebingen	RCV000725594	SCV001747285	uncertain significance	not provided	2021-07-01	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002381720	SCV002690366	uncertain significance	Cardiovascular phenotype	2020-09-08	criteria provided, single submitter	clinical testing	The c.13363+1G>A intronic variant results from a G to A substitution one nucleotide after coding exon 46 of the TTN gene. Coding exon 46 is located in the I-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 variant (also referred to as c.35635+1G>A and c.40558+1G>A) has been reported in dilated cardiomyopathy cohorts, but also in population-based cohorts (Herman DS et al. N Engl J Med. 2012 Feb;366(7):619-28; Roberts AM et al. Sci Transl Med. 2015 Jan;7(270):270ra6). This variant was detected in a sudden death victim reported to have dilated cardiomyopathy who also had variants in other cardiac-related genes, and this alteration did not segregate with disease in the family (Bagnall RD et al. Genet Med. 2017 Oct;19(10):1127-1133). This variant has also been detected in an early-onset atrial fibrillation cohort (Choi SH et al. JAMA. 2018 12;320(22):2354-2364). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing and often result in a transcript encoding a truncated protein. Truncating variants in the A-band of titin are the most common cause of dilated cardiomyopathy (DCM), and, regardless of their position, truncating variants encoded in constitutive exons (PSI >90%) have been found to be significantly associated with DCM (Herman DS et al. N. Engl. J. Med. 2012;366:619-28; Roberts AM et al. Sci Transl Med. 2015;7:270ra6; Schafer S et al. Nat. Genet. 2017;49:46-53). However, TTN truncating variants have also been reported in 1-3% of the general population (Herman DS et al. N. Engl. J. Med. 2012;366:619-28). Since the exact splicing impact of this alteration is unknown and supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Revvity Omics, Revvity	RCV000725594	SCV003825434	uncertain significance	not provided	2023-03-10	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000221188	SCV003934117	uncertain significance	not specified	2023-05-11	criteria provided, single submitter	clinical testing	Variant summary: TTN c.32854+1G>A is located in a canonical splice-site, and therefore could affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. The sequence of this splice site deviates from the consensus, therefore computational tools were not able to predict the impact of the variant on normal splicing, although one predicts the variant abolishes the 5' donor site. However, these predictions have yet to be confirmed by functional studies. The variant is located in the I-band region, neighboring a symmetric exon that is highly expressed in the heart (Roberts_2015). The variant allele was found at a frequency of 5.5e-05 in 234996 control chromosomes, predominantly at a frequency of 0.00013 within the Non-Finnish European subpopulation in the gnomAD database. This frequency is not higher than the estimated maximum expected for a pathogenic variant in TTN causing Dilated Cardiomyopathy (0.00039), allowing no conclusion about variant significance. The variant, c.32854+1G>A (aka c.40558+1G>A), has been reported in the literature in heterozygous state in at least three individuals affected with Dilated Cardiomyopathy (e.g. Herman_2012, Bagnall_2017), however in one of these cases other potentially causal co-occurring variants were also present. In addition, the variant was also reported in 3 / 13,131 asymptomatic individuals aged 70 years and older without a history of atherothrombotic cardiovascular disease events in the ASPREE study (Lacaze_2021). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 22335739, 25589632, 28333919, 30535219, 33226272, 34135346, 35177841). Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014, mostly without evidence for independent evaluation, and all laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.
Division of Human Genetics, Children's Hospital of Philadelphia	RCV000477783	SCV000536714	uncertain significance	Dilated cardiomyopathy 1G; Autosomal recessive limb-girdle muscular dystrophy type 2J; Tibial muscular dystrophy; Myopathy, myofibrillar, 9, with early respiratory failure; Early-onset myopathy with fatal cardiomyopathy; Hypertrophic cardiomyopathy 9	2015-11-13	no assertion criteria provided	research