rs876657663

Variant names:

• chr2-178759039-AAACGTGT-A
• rs876657663
• NM_001267550.2:c.10241_10247delACACGTT

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_001267550.2(TTN):​c.10241_10247delACACGTT​(p.Tyr3414LeufsTer7) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. Y3414Y) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TTN NM_001267550.2 frameshift
• Clinical Significance: Likely pathogenic criteria provided, multiple submitters, no conflicts P:2
• Conservation: PhyloP100: 9.29
• Publications: 1 publications found

Genes affected

TTN (HGNC:12403): (titin) This gene encodes a large abundant protein of striated muscle. The product of this gene is divided into two regions, a N-terminal I-band and a C-terminal A-band. The I-band, which is the elastic part of the molecule, contains two regions of tandem immunoglobulin domains on either side of a PEVK region that is rich in proline, glutamate, valine and lysine. The A-band, which is thought to act as a protein-ruler, contains a mixture of immunoglobulin and fibronectin repeats, and possesses kinase activity. An N-terminal Z-disc region and a C-terminal M-line region bind to the Z-line and M-line of the sarcomere, respectively, so that a single titin molecule spans half the length of a sarcomere. Titin also contains binding sites for muscle associated proteins so it serves as an adhesion template for the assembly of contractile machinery in muscle cells. It has also been identified as a structural protein for chromosomes. Alternative splicing of this gene results in multiple transcript variants. Considerable variability exists in the I-band, the M-line and the Z-disc regions of titin. Variability in the I-band region contributes to the differences in elasticity of different titin isoforms and, therefore, to the differences in elasticity of different muscle types. Mutations in this gene are associated with familial hypertrophic cardiomyopathy 9, and autoantibodies to titin are produced in patients with the autoimmune disease scleroderma. [provided by RefSeq, Feb 2012]

TTN-AS1 (HGNC:44124): (TTN antisense RNA 1) This gene encodes a non-coding RNA transcribed from the opposite strand to the titin gene. [provided by RefSeq, Aug 2016]

ACMG classification

Our verdict: Pathogenic. The variant received 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 2-178759039-AAACGTGT-A is Pathogenic according to our data. Variant chr2-178759039-AAACGTGT-A is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 228298.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTN	NM_001267550.2	c.10241_10247delACACGTT	p.Tyr3414LeufsTer7	frameshift_variant	Exon 44 of 363	ENST00000589042.5	NP_001254479.2
TTN	NM_133379.5	c.10241_10247delACACGTT	p.Tyr3414LeufsTer7	frameshift_variant	Exon 44 of 46	ENST00000360870.10	NP_596870.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTN	ENST00000589042.5	c.10241_10247delACACGTT	p.Tyr3414LeufsTer7	frameshift_variant	Exon 44 of 363	5	NM_001267550.2	ENSP00000467141.1
TTN	ENST00000360870.10	c.10241_10247delACACGTT	p.Tyr3414LeufsTer7	frameshift_variant	Exon 44 of 46	5	NM_133379.5	ENSP00000354117.4

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:1

Aug 25, 2024

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Located in a region of TTN within the I-band in which the majority of loss of function variants are significantly associated with autosomal dominant titinopathies (PMID: 27625338, 27869827); Reported in association with DCM, although patient-specific details were not provided (PMID: 37652022); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27625338, 27869827, 37652022) -

Primary dilated cardiomyopathy Pathogenic:1

Apr 26, 2017

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Tyr3414fs variant in TTN has not been previously reported in individuals w ith cardiomyopathy or in large population studies, though the ability of these s tudies to accurately detect deletions may be limited. This variant is predicted to cause a frameshift, which alters the protein?s amino acid sequence beginning at position 3414 and leads to a premature termination codon 7 amino acids downst ream. This alteration is then predicted to lead to a truncated or absent protein . Frameshift and other truncating variants in TTN are strongly associated with D CM if they are located in the exons encoding for the A-band (Herman 2012, Pugh 2 014) or are located in an exon that is highly expressed in the heart (Roberts 20 15). The p.Tyr3414fs variant is located in the I-band in the highly expressed ex on 44. In summary, although additional studies are required to fully establish i ts clinical significance, the p.Tyr3414fs variant is likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		9.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs876657663; hg19: chr2-179623766;