NM_001267550.2:c.104515C>T

Variant names:

• chr2-178532100-G-A
• rs1553488049
• NM_001267550.2:c.104515C>T

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.104515C>T​(p.Arg34839*) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000274 in 1,461,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: TTN NM_001267550.2 stop_gained
• Clinical Significance: Likely pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 4.36
• Publications: 0 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 2-178532100-G-A is Pathogenic according to our data. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178532100-G-A is described in CliVar as Likely_pathogenic. Clinvar id is 535030.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.104515C>T	p.Arg34839*	stop_gained	Exon 358 of 363	ENST00000589042.5	NP_001254479.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTN	ENST00000589042.5	c.104515C>T	p.Arg34839*	stop_gained	Exon 358 of 363	5	NM_001267550.2	ENSP00000467141.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1461654 Hom.: 0 Cov.: 40 AF XY: 0.00000550 AC XY: 4 AN XY: 727114

African (AFR) AF: 0.00 AC: 0 AN: 33476

American (AMR) AF: 0.00 AC: 0 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39692

South Asian (SAS) AF: 0.00 AC: 0 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53382

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000360 AC: 4 AN: 1111846

Other (OTH) AF: 0.00 AC: 0 AN: 60374

GnomAD4 genome Cov.: 32

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Apr 19, 2024

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Located in the M-line region of TTN in which the majority of loss of function variants have been associated with autosomal recessive titinopathies (PMID: 17444505); Observed in an infant with hypertrophic cardiomyopathy and sudden death in conjunction with variants in the ELAC2 and MYPN genes (Venegas EdPG et al. (2018) Repertorio de Medicina y Cirugiia. 27 (1):39-43); This variant is associated with the following publications: (PMID: 17444505, Venegas2018, 36264615, 36977548) -

Mar 18, 2021

Revvity Omics, Revvity

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Autosomal recessive limb-girdle muscular dystrophy type 2J;C1858763:Dilated cardiomyopathy 1G Pathogenic:1

Dec 30, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Arg34839*) 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 not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with dilated cardiomyopathy (PMID: 36264615, 36977548; internal data). ClinVar contains an entry for this variant (Variation ID: 535030). 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 dominant or 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, internal data). 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. -

Cardiomyopathy Pathogenic:1

Aug 18, 2022

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiovascular phenotype Pathogenic:1

Dec 02, 2024

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.R25774* variant (also known as c.77320C>T), located in coding exon 185 of the TTN gene, results from a C to T substitution at nucleotide position 77320. This changes the amino acid from an arginine to a stop codon within coding exon 185. 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 variant (referred to as NM_001267550.1:c.104515C>T, p.R34839*) was reported in individual(s) with features consistent with dilated cardiomyopathy (Bourfiss M et al. Circ Genom Precis Med. 2022 Dec;15(6):e003704; Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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 majority of available evidence to date, this variant is likely to be pathogenic in association with autosomal recessive titinopathy; however, the clinical significance of this alteration with respect to cardiomyopathy remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.53	D
BayesDel_noAF	Pathogenic	0.52
CADD	Pathogenic	79
DANN	Benign	0.96
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.90
FATHMM_MKL	Uncertain	0.93	D
PhyloP100		4.4
Vest4		0.72
GERP RS		4.6
Mutation Taster		=3/197	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1553488049; hg19: chr2-179396827; COSMIC: COSV60194588; COSMIC: COSV60194588;