rs587780488

Positions:

• chr2-178642237-C-G
• chr2-178642237-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP2 PP5

The NM_001267550.2(TTN):​c.40558G>C​(p.Val13520Leu) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000133 in 1,427,914 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.000013 (0 hom.)
• Consequence: TTN NM_001267550.2 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5 U:4 O:1
• Conservation: PhyloP100: 5.19

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

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), TTN. . Gene score misZ -1.1021 (greater than the threshold 3.09). Trascript score misZ 6.9794 (greater than threshold 3.09). GenCC has associacion of gene with dilated cardiomyopathy, tibial muscular dystrophy, early-onset myopathy with fatal cardiomyopathy, autosomal recessive centronuclear myopathy, hypertrophic cardiomyopathy, hypertrophic cardiomyopathy 9, TTN-related myopathy, dilated cardiomyopathy 1G, arrhythmogenic right ventricular cardiomyopathy, myopathy, myofibrillar, 9, with early respiratory failure, familial isolated dilated cardiomyopathy, childhood-onset progressive contractures-limb-girdle weakness-muscle dystrophy syndrome, autosomal recessive limb-girdle muscular dystrophy type 2J.
• PP5: Variant 2-178642237-C-G is Pathogenic according to our data. Variant chr2-178642237-C-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 130666.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=2, Pathogenic=1, Uncertain_significance=4, not_provided=1}. Variant chr2-178642237-C-G is described in Lovd as [Pathogenic]. Variant chr2-178642237-C-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTN	NM_001267550.2	c.40558G>C	p.Val13520Leu	missense_variant, splice_region_variant	219/363	ENST00000589042.5	NP_001254479.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTN	ENST00000589042.5	c.40558G>C	p.Val13520Leu	missense_variant, splice_region_variant	219/363	5	NM_001267550.2	ENSP00000467141	P1
TTN-AS1	ENST00000659121.1	n.502+44556C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.0000133 AC: 19 AN: 1427914 Hom.: 0 Cov.: 30 AF XY: 0.0000198 AC XY: 14 AN XY: 707114

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000174

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000756

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5 Uncertain:4 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:2 Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Jan 26, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Athena Diagnostics	Mar 10, 2020	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2024	TTN: PM3:Strong, PM2, PP3, PS3:Supporting -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Dec 24, 2015	The c.35635G>C (V11879L, aka c.32854 G>C or V10952L) variant in the TTN gene has been published previouslyin one individual with dilated cardiomyopathy (DCM) (Herman et al., 2012). This variant has also been reported inassociation with autosomal recessive centronuclear myopathy (CNM) (Ceyhan-Birsoy et al., 2013; Brownstein et al.,2014). The c.32854 G>C variant has been identified at GeneDx in one family with autosomal recessive CNM whoalso harbor a TTN canonical splice site variant in trans. The c.35635G>C variant was not associated with anincreased risk of DCM in family members who only harbored this variant. This variant is located in the I-band regionof titin and a splicing assay demonstrated that the c.35635 G>C variant results in skipping of exon 168 leading toeither a truncated protein product or complete absence of protein from this allele due to nonsense mediated mRNAdecay (Ceyhan-Birsoy et al., 2013). Other splice site variants have been reported in the Human Gene MutationDatabase in association with autosomal recessive CNM and autosomal dominant DCM (Stenson et al., 2014).Furthermore, the NHLBI Exome Sequencing Project reports c.32854 G>C was not observed in approximately 5,900individuals of European and African American backgrounds, indicating it is not a common benign variant in thesepopulations. However, other truncating TTN variants have been reported in approximately 3% of control alleles(Herman et al., 2012). The contribution of the c.35635 G>C variant to the pathogenesis of autosomal dominant DCMis unclear. Therefore, this variant is likely pathogenic. -
Uncertain significance, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Feb 03, 2014	- -

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

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 03, 2023

This sequence change replaces valine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 13520 of the TTN protein (p.Val13520Leu). RNA analysis indicates that this missense change induces altered splicing and likely results in a shortened protein product. This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with autosomal recessive centronuclear myopathy or limb-girdle muscular dystrophy and/or dilated cardiomyopathy (PMID: 22335739, 23975875, 30681174). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as c.35635G>C or c.32854G>C. ClinVar contains an entry for this variant (Variation ID: 130666). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change results in skipping of exon 219, but is expected to preserve the integrity of the reading-frame (PMID: 23975875). 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). For these reasons, this variant has been classified as Pathogenic. -

Dilated cardiomyopathy 1G Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

Genomics England Pilot Project, Genomics England

-

- -

TTN-related myopathy Pathogenic:1

Likely pathogenic, criteria provided, single submitter

curation

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Nov 21, 2024

The heterozygous p.Val13520Leu variant in TTN was identified by our study in 1 individual with TTN-related myopathy, in the compound heterozygous state along with a likely pathogenic variant (Variation ID: 2500881). Trio exome analysis revealed that this variant was in trans with the likely pathogenic variant. The p.Val13520Leu variant has been reported in at least 3 individuals with TTN-related myopathy (PMID: 23975875, 22335739), and has been identified in 0.002% (19/1161372) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs587780488). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. Of the 3 affected individuals, 2 were compound heterozygotes that carried a reported pathogenic/likely pathogenic variant in trans, which increases the likelihood that the p.Val13520Leu variant is pathogenic (Variation ID: 2500881, 223313; PMID: 22335739, Seqr). This variant has been reported in ClinVar (Variation ID: 130666) and has been interpreted as pathogenic/likely pathogenic by Labcorp Genetics, GeneDx, CeGaT Center for Human Genetics Tuebingen, and Genomics England Pilot Project, and as a variant of uncertain significance by Cardiovascular Biomedical Research Unit (Royal Brompton & Harefield NHS Foundation Trust), Athena diagnostics, Genetic Services Laboratory (University of Chicago), and AiLife Diagnostics. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. This variant is located in the first base of the exon, which is part of the 3’ splice region. Computational tools do suggest an impact to splicing. However, this information is not predictive enough to determine/rule out pathogenicity. Loss of function of the TTN gene is an established disease mechanism in autosomal recessive TTN-related myopathy. Minigene assay shows evidence of exon skipping of exon 168. This variant is in an in-frame exon and is more likely to escape nonsense mediated decay (NMD) and result in a truncated protein. The number of missense variants reported in TTN in the general population is lower than expected, suggesting there is little benign variation in this gene and slightly increasing the possibility that a missense variant in this gene may not be tolerated. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic for TTN-related myopathy. ACMG/AMP Criteria applied: PM3_strong, PVS1_moderate, PP2, PM2_supporting (Richards 2015). -

Primary dilated cardiomyopathy Uncertain:1

Uncertain significance, criteria provided, single submitter

research

Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust

Oct 08, 2014

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. -

Cardiomyopathy Other:1

not provided, no classification provided

phenotyping only

GenomeConnect, ClinGen

-

Variant classified as pathogenic on 12/26/2012 by GeneDx. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.67
BayesDel_addAF	Benign	-0.040	T
BayesDel_noAF	Benign	-0.30
CADD	Pathogenic	29
DANN	Uncertain	0.98
DEOGEN2	Benign	0.037	.;.;.;.;.;.;.;T
Eigen	Uncertain	0.68
Eigen_PC	Pathogenic	0.69
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.87	D;D;D;.;D;D;D;D
M_CAP	Pathogenic	0.54	D
MetaRNN	Benign	0.38	T;T;T;T;T;T;T;T
MetaSVM	Uncertain	-0.13	T
MutationAssessor	Uncertain	2.2	.;.;.;M;.;.;M;.
MutationTaster	Benign	0.83	D;D;D;D;D;D
PrimateAI	Uncertain	0.71	T
PROVEAN	Benign	-1.7	N;N;.;.;N;N;.;N
REVEL	Benign	0.16
Sift	Benign	0.036	D;T;.;.;T;T;.;T
Polyphen		0.99	.;.;.;D;.;.;D;.
Vest4		0.29
MutPred		0.21		.;.;.;Loss of MoRF binding (P = 0.1006);.;.;Loss of MoRF binding (P = 0.1006);.;
MVP		0.56
MPC		0.45
ClinPred		0.69	D
GERP RS		5.5

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.98
SpliceAI score (max)		0.76		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.27		Position offset: -29
DS_DL_spliceai		0.76		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs587780488; hg19: chr2-179506964;