2-178598609-G-T

Variant names:

• chr2-178598609-G-T
• rs878854318
• NM_001267550.2:c.57008C>A

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_001267550.2(TTN):​c.57008C>A​(p.Ser19003*) variant causes a stop gained change. The variant was absent in control chromosomes in GnomAD project. 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)
• Consequence: TTN NM_001267550.2 stop_gained
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 6.70
• 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 12 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 2-178598609-G-T is Pathogenic according to our data. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178598609-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 238805.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTN	NM_001267550.2	c.57008C>A	p.Ser19003*	stop_gained	Exon 292 of 363	ENST00000589042.5	NP_001254479.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTN	ENST00000589042.5	c.57008C>A	p.Ser19003*	stop_gained	Exon 292 of 363	5	NM_001267550.2	ENSP00000467141.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

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

Oct 22, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is found in the A-band of this gene. While this particular variant has not been reported in the literature, truncating variants in the A-band of TTN are likely pathogenic (PMID: 25589632). This sequence change creates a premature translational stop signal at codon 19003 (p.Ser19003*). It is expected to result in a truncated protein product. For these reasons, this variant has been classified as Likely Pathogenic. This variant is not present in population databases (ExAC no frequency). ClinVar contains an entry for this variant (Variation ID: 238805). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.62	D
BayesDel_noAF	Pathogenic	0.66
CADD	Pathogenic	61
DANN	Uncertain	0.98
Eigen	Pathogenic	1.3
Eigen_PC	Pathogenic	1.2
FATHMM_MKL	Pathogenic	1.0	D
PhyloP100		6.7
Vest4		0.96
GERP RS		5.9
Mutation Taster		=0/200	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: rs878854318; hg19: chr2-179463336;