Submissions for variant NM_001267550.2(TTN):c.67348+1G>A

gnomAD frequency: 0.00001  dbSNP: rs758279518

Total submissions: 8

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000414246	SCV000331945	likely pathogenic	not provided	2015-07-01	criteria provided, single submitter	clinical testing
GeneDx	RCV000414246	SCV000491396	likely pathogenic	not provided	2016-01-13	criteria provided, single submitter	clinical testing	Although the c.62425+1 G>A variant has not been reported as a pathogenic variant or as a benign variant to our knowledge, it destroys the canonical splice donor site in intron 268 and is predicted to cause abnormal gene splicing. This variant is predicted to lead to either an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. Other truncating TTN variants have been reported in approximately 3% of control alleles (Herman et al., 2012). However, the c.62425+1 G>A variant is located in the A-band region of titin, where the majority of truncating pathogenic variants associated with DCM have been reported (Herman et al., 2012). Multiple other downstream splice site variants in the TTN gene have been reported in HGMD in association with DCM (Stenson et al., 2014), including another variant affecting the same donor site (c.62425+5 G>A). Furthermore, the c.62425+1 G>A variant was not observed in approximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. In summary, c.62425+1 G>A in the TTN gene is interpreted as a pathogenic variant.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000821995	SCV000962772	likely pathogenic	Dilated cardiomyopathy 1G; Autosomal recessive limb-girdle muscular dystrophy type 2J	2024-11-24	criteria provided, single submitter	clinical testing	This sequence change affects a donor splice site in intron 318 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 (rs758279518, gnomAD 0.005%). Disruption of this splice site has been observed in individual(s) with clinical features of autosomal recessive TTN-related conditions (PMID: 29691892, 34782754). ClinVar contains an entry for this variant (Variation ID: 281260). 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 A band of TTN (PMID: 25589632). Truncating variants in this region are significantly overrepresented in patients affected with dilated cardiomyopathy (PMID: 25589632). Truncating variants in this region have also been reported in individuals affected with autosomal recessive centronuclear myopathy (PMID: 23975875). 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.
Clinical Genetics Laboratory, Region Ostergotland	RCV001175311	SCV001250897	likely pathogenic	Dilated cardiomyopathy 1A	2019-10-10	criteria provided, single submitter	clinical testing	This variant is located in the A band of TTN (PMID: 25589632). Truncating variants in this region are significantly overrepresented in patients affected with dilated cardiomyopathy (PMID: 25589632). We have confirmed that this variant affects splicing and leads to frame shift. RNA was extracted from heart tissue from a patient with dilated cardiomyopathy, who carried this variant. Sanger sequencing of this RNA showed that the variant resulted in a 50bp deletion, c.59595-c.59644, leading to frame shift.
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	RCV001358693	SCV001554505	uncertain significance	Early-onset myopathy with fatal cardiomyopathy		criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002374451	SCV002625516	likely pathogenic	Cardiovascular phenotype	2024-08-12	criteria provided, single submitter	clinical testing	The c.40153+1G>A intronic variant results from a G to A substitution one nucleotide after coding exon 145 of the TTN gene. This exon is located in the A-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 NM_001267550:c.67348+1G>A) has been detected in the homozygous state in a proband with early onset dilated cardiomyopathy and sudden death, and co-occurred in trans with a second TTN variant in a neonatal case with features of neuromuscular disease (Oates EC et al. Ann Neurol, 2018 Jun;83:1105-1124; Denommé-Pichon AS et al. Eur J Hum Genet, 2022 May;30:567-576). 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. 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 A-band are the most common cause of dilated cardiomyopathy (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). TTN truncating variants encoded in constitutive exons (PSI >90%) have been found to be significantly associated with DCM regardless of their position in titin (Schafer S et al. Nat. Genet., 2017 01;49:46-53). Based on the majority of available evidence to date, this variant is likely to be pathogenic.
New York Genome Center	RCV003227735	SCV003925343	likely pathogenic	Dilated cardiomyopathy 1G; Hypertrophic cardiomyopathy 9	2022-04-06	criteria provided, single submitter	clinical testing	The c.67348+1G>A variant has previously been reported homozygous in an individual with dilated cardiomyopathy in childhood [PMID: 29691892] and compound heterozygous in an individual with early-onset myopathy, as a Variant of Uncertain Significance [PMID: 34782754]. It has been deposited in ClinVar [ClinVar ID:281260] as Variant of Uncertain Significance in an individual with early-onset myopathy with fatal cardiomyopathy (1 submission, associated with PMID: 34782754) and Likely Pathogenic (4 submissions) in individuals with dilated cardiomyopathy or limb-girdle muscular dystrophy, type 2J. The c.67348+1G>A variant is observed in 2 alleles (0.0008% MAF with 0 homozygotes) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8), suggesting it is not a common benign variant in the populations represented in those databases. The c.67348+1G>A variant is located in the canonical splice donor site after exon 318 of this 363-exon gene, and is presumed to affect mRNA splicing which might result in exon skipping (in-phase exon) or full/partial intron retention, while an entry in ClinVar suggests functional studies have been performed for this variant and shown to result in a 50bp deletion, c.59595-c.59644, leading to frame shift. This data was not available to our lab for independent verification. This variant is located in the A band of TTN, where most truncating variants associated with dilated cardiomyopathy are located[PMID:26777568, 27869827, 28045975]. Truncating variants in this region have also been reported in individuals affected with autosomal recessive centronuclear myopathy [PMID: 23975875]. Based on available evidence this c.67348+1G>A variant identified in TTN is classified as Likely Pathogenic.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV004786649	SCV005400327	likely pathogenic	Dilated cardiomyopathy 1G	2023-12-21	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Likely 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 termination codon (PTC) are known to have reduced penetrance in DCM (PMID: 25589632). (I) 0211 - Canonical splice site variant without proven consequence on splicing (no functional available). A ClinVar entry from a clinical laboratory reports that sanger sequencing of RNA from an individual with this variant that showed a 50bp deletion leading to a frameshift, however this data was not available to independently review. (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 (v2: 2 heterozygotes, 0 homozygotes). (SP) 0505 - Abnormal splicing is predicted by in silico tools and affected nucleotide is highly conserved. (SP) 0600 - Variant is located in the annotated C-terminal A-band and the exon has a PSI score of 100 (PMID: 25589632). (I) 0710 - Another splice site comparable to the one identified in this case has inconclusive previous evidence for pathogenicity. The variant c.67348+5G>A has been classified as a VUS in ClinVar, and has been observed as homozygous in an individual with DCM in the literature (PMID: 22335739). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as likely pathogenic by multiple laboratories in ClinVar including one laboratory that observed the variant as heterozygous in an individual with DCM. This variant has also been observed as homozygous in an individual with DCM, and as compound heterozygous in a individual with Salih myopathy where the variant was classified as a VUS (PMIDs: 34782754, 29691892). (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1206 - This variant has been shown to be paternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign