rs387906397
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1PP5_Very_Strong
The NM_000256.3(MYBPC3):c.3330+2T>G variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000437 in 1,601,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Consequence
NM_000256.3 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MYBPC3 | ENST00000545968.6 | c.3330+2T>G | splice_donor_variant, intron_variant | Intron 30 of 34 | 5 | NM_000256.3 | ENSP00000442795.1 | |||
| MYBPC3 | ENST00000399249.6 | c.3330+2T>G | splice_donor_variant, intron_variant | Intron 29 of 33 | 5 | ENSP00000382193.2 |
Frequencies
GnomAD3 genomes 0.0000329 AC: 5AN: 152126Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1449852Hom.: 0 Cov.: 34 AF XY: 0.00000139 AC XY: 1AN XY: 719834
GnomAD4 genome 0.0000329 AC: 5AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74306
ClinVar
Submissions by phenotype
Hypertrophic cardiomyopathy 4 Pathogenic:6
This patient also harbours two VUS: a second missense variant in MYBPC3, and a missense variant in MYH7. -
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The MYBPC3 c.3330+2T>G variant, also reported as IVS31+2T>G, has been reported in the heterozygous state in many individuals with adult onset hypertrophic cardiomyopathy (HCM) and in the homozygous state in several individuals with severe neonatal onset HCM (Helms A et al., PMID: 25031304; Miller EM et al., PMID: 29212898; Morita H et al., PMID: 18403758, Xin B et al., PMID: 17937428; Zahka K et al., PMID: 18467358). One study showed that only 6 of 41 individuals heterozygous for this variant displayed features of HCM or left ventricular hypertrophy, implicating this variant may have a milder clinical presentation or reduced penetrance (De S et al., PMID: 21835286). This variant has been reported in the ClinVar database as a germline pathogenic variant by several submitters. This variant is only observed on one out of 31,314 alleles in the general population (gnomAD v.2.1.1), indicating it is not a common variant. This variant occurs within the canonical splice donor site, which is predicted to cause skipping of the exon, leading to an out of frame transcript. In support of this prediction, several functional studies show this variant causes skipping of exon 30 (also called exon 31 in some publications), leading to an out of frame transcript (Morita H et al., PMID: 18403758; Xin B et al., PMID: 17937428). Based on available information and the ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as pathogenic. -
The c.3330+2T>G variant in the MYBPC3 gene is predicted to disrupt a canonical splice site and thus alter the wildtype mRNA splicing. This variant was reported in multiple individuals affected with hypertrophic cardiomyopathy in homozygous or heterozygous state (PMID 17937428, 18258667, 18403758, 18467358, 25031304). Analysis of cDNA extract from multiple carriers showed skipping of exon 30 as a result of this c.3330+2T>G change. Therefore, this c.3330+2T>G variant in the MYBPC3 gene is classified as pathogenic. -
The MYBPC3 c.3330+2T>G variant results in the substitution of a thymine within the consensus splice donor site with a guanine, which may result in splicing defects. This variant has been reported in the literature in association with hypertrophic cardiomyopathy (HCM). At least 20 neonates from the Amish community affected with severe HCM were found to be homozygous for this variant, and were shown to have inherited the variant from parents who carried the variant in a heterozygous state (PMID: 17937428; PMID: 18467358). In addition, nine individuals from three families affected with HCM were heterozygous for the variant with incomplete penetrance (PMID: 7493025; PMID: 18403758). Heterozygous carriers of this variant were reported to be clinically indistinguishable from controls (PMID: 21835286). The variant was absent from 200 controls (PMID: 7493025), but is reported in the Genome Aggregation Database in five alleles at a frequency of 0.000074 in the European (non-Finnish) population (version 3.1.2). RNA isolated from patient cells showed that the splice donor variant resulted in skipping of exon 30, leading to premature truncation of the protein (PMID: 7493025; PMID: 17937428). Based on the available evidence, the c.3330+2T>G variant is classified as pathogenic for hypertrophic cardiomyopathy, but with variable expressivity and penetrance when present in a heterozygous state. -
not provided Pathogenic:4
Reported in the homozygous state in multiple Amish infants who presented with severe, neonatal HCM (Xin et al., 2007; Zahka et al., 2008); Not observed at a significant frequency in large population cohorts (gnomAD); Reported in ClinVar as a pathogenic/likely pathogenic variant (ClinVar Variant ID #8621; ClinVar); Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; Destroys the canonical splice donor site of intron 30 and was shown to lead to an aberrant splice transcript due to skipping of exon 30, a shift in the reading frame, and premature termination of translation in exon 31 (Xin et al., 2007); This variant is associated with the following publications: (PMID: 25335496, 10424815, 23840593, 31451126, 17937428, 25031304, 23054336, 20542340, 26440533, 27688314, 26914223, 27532257, 28615295, 24510615, 18403758, 18467358, 21835286, 29212898, 29121657, 22464770, 21492761, 18533079, 12707239, 7493025, 31447099, 34570182, 33906374) -
Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. MYBPC3 IVS30+2T>G Based on the data reviewed below, we consider it likely disease causing. We first reviewed this variant in July 2011, then reviewed again 1/25/2012, adding further details to case data and additional general population frequency data, both of which further support the variant's pathogenicity. It was reviewed again March 22nd, 2013, with additional general population frequency data available, again further supporting pathogenicity. This variant has been seen in multiple unrelated cases of HCM. Xin et al (2007) reported the variant in the homozygous state in multiple cases of severe neonatal HCM in the old order Amish. In initial reports on these families the authors noted that heterozygotes are likely at risk to develop cardiomyopathy, but unfortunately they did not report echo data on heterozygotes, though they did note that many reported cardiac symptoms such as chest pain, palpitations and fatigue. The authors recently published an update to these cases, noting that HCM was identified in multiple heterozygous individuals (Wang et al 2011). De et al (2011) reported on the carriers of this variant from that same community. They phenotyped 41 carries of IVS30+20T>G and found 6 had evidence of HCM. When compared to controls, the remaining 35 carriers had significantly higher ejection fractions and regional alterations in strain. We have seen this variant in one other family with HCM and in that family it was present in both our patient and his daughter who also has HCM. Zahka et al (2008) also studied Old Order Amish infants with severe HCM and found they were homozygous for this variant. A German group reported the variant in a methods paper on identification of HCM variants using array-based resequencing (Waldmuller et al 2008). Clinical data on the patient with the variant was not provided. Xin et al (2007) demonstrated that this variant led to skipping of exon 30 and creation of a frameshift and premature stop codon in exon 31. Theis et al (2008) studied myectomy samples from a carrier of this variant and also found an aberrant mRNA that led to a frameshift and premature stop codon. Immunohistochemistry revealed that the spatial organization of myosin binding protein C was severely disrupted. Many other variants in MYBPC3 that lead either to a truncated protein product or no protein at all have been implicated in hypertrophic cardiomyopathy. In total, the variant has not been seen in ~6750 published controls and publicly available general population samples. Specifically, Zahka et al (2008) report that they did not observe the variant in 50 presumably healthy European individuals. Theis et al (2008) report the variant was not observed in 200 presumably healthy individuals. Neither Xin et al (2007) or Waldmuller et al (2008) reported control data. The variant is not listed in either dbSNP or 1000 genomes (as of 1/25/2012). In addition, the variant is not currently listed in the NHLBI Exome Sequencing Project dataset, which includes variant calls on ~6500 Caucasian and African American individuals (as of March 13th, 2013). -
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Hypertrophic cardiomyopathy Pathogenic:3
This variant causes a T to G nucleotide substitution at the +2 position of intron 30 of the MYBPC3 gene. Functional RNA studies have shown that this variant causes out-of-frame skipping of exon 30, resulting in premature protein truncation (PMID: 17937428, 18403758, 25031304). This variant has been reported in many individuals affected with hypertrophic cardiomyopathy and has been observed frequently in Amish communities (PMID: 17937428, 18403758, 18467358, 21835286, 25031304). A clinical evaluation of 41 Amish adult carriers has shown that while 6 carriers had features of hypertrophic cardiomyopathy or left ventricular hypertrophy, remaining 35 carriers were asymptomatic, suggesting that this variant causes a mild disease in heterozygosity or shows reduced penetrance (PMID: 21835286). In more than ten homozygous children, this variant was associated with severe hypertrophic cardiomyopathy (PMID: 17937428, 18467358). This variant has been identified in 1/31314 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of MYBPC3 function is a known mechanism of disease. Based on available evidence, this variant is classified as Pathogenic. -
The c.3330+2T>G variant (also reported as IVS31+2T>G) in MYBPC3 has been identified in >10 homozygous Amish individuals with severe neonatal onset HCM, >10 heterozygous individuals with HCM, and segregated with disease in 1 affected relative (Morita 2008, Xin 2007, Zahka 2008, LMM data). One study found that 6 of 41 heterozygous individuals exhibited features of HCM or LVH, suggesting that it may be milder in isolation or have reduced penetrance (De 2011). This variant has been reported by other clinical laboratories in ClinVar (Variation ID 8621) and was also identified in 1/14944 European chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs387906397). c.3330+2T>G was demonstrated to cause abnormal splicing that resulted in the skipping of exon 30, which is predicted to lead to a frameshift beginning at codon 1064 and create a premature stop codon 38 amino acids downstream (Xin 2007, Morita 2008, Helms 2014). Heterozygous loss of function of the MYBPC3 gene is an established disease mechanism in HCM. In summary, this variant meets criteria to be classified as pathogenic for HCM, based on its recurrence in multiple affected individuals, extremely low frequency in the general population, functional evidence and predicted impact on the protein, although it may have reduced penetrance and variable expressivity in the heterozygous state. ACMG/AMP Criteria applied (Richards 2015): PS4, PM2, PVS1. -
This sequence change affects a donor splice site in intron 30 of the MYBPC3 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (rs387906397, gnomAD 0.007%). Disruption of this splice site has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 17937428, 18403758, 18467358, 21835286). ClinVar contains an entry for this variant (Variation ID: 8621). Studies have shown that disruption of this splice site results in skipping of exon 30, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 17937428, 25031304). For these reasons, this variant has been classified as Pathogenic. -
Left ventricular noncompaction 10 Pathogenic:1
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Hypertrophic cardiomyopathy 4;C3715165:Left ventricular noncompaction 10 Pathogenic:1
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Cardiomyopathy Pathogenic:1
This variant causes a T to G nucleotide substitution at the +2 position of intron 30 of the MYBPC3 gene. Functional RNA studies have shown that this variant causes out-of-frame skipping of exon 30, resulting in premature protein truncation (PMID: 17937428, 18403758, 25031304). This variant has been reported in many individuals affected with hypertrophic cardiomyopathy and has been observed frequently in Amish communities (PMID: 17937428, 18403758, 18467358, 21835286, 25031304). A clinical evaluation of 41 Amish adult carriers has shown that while 6 carriers had features of hypertrophic cardiomyopathy or left ventricular hypertrophy, remaining 35 carriers were asymptomatic, suggesting that this variant causes a mild disease in heterozygosity or shows reduced penetrance (PMID: 21835286). In more than ten homozygous children, this variant was associated with severe hypertrophic cardiomyopathy (PMID: 17937428, 18467358). This variant has been identified in 1/31314 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of MYBPC3 function is a known mechanism of disease. Based on available evidence, this variant is classified as Pathogenic. -
Primary familial hypertrophic cardiomyopathy Pathogenic:1
Variant summary: MYBPC3 c.3330+2T>G is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5' splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing (Xin_2007, Helms_2014). The variant was absent in 228534 control chromosomes. c.3330+2T>G has been reported in the literature in multiple individuals affected with Hypertrophic Cardiomyopathy (Xin_2007, Zahka_2008, Helms_2014). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function demonstrating a reduction in protein expression (Helms_2014). The following publications have been ascertained in the context of this evaluation (PMID: 17937428, 18467358, 25031304, 25335496). ClinVar contains an entry for this variant (Variation ID: 8621). Based on the evidence outlined above, the variant was classified as pathogenic. -
Cardiovascular phenotype Pathogenic:1
The c.3330+2T>G intronic pathogenic mutation results from a T to G substitution two nucleotides after coding exon 30 of the MYBPC3 gene. This alteration has been reported in a number of individuals in hypertrophic cardiomyopathy cohorts (Theis JL et al. Circ Heart Fail. 2009;2:325-33; Miller EM et al. J Genet Couns. 2013;22:258-67; Kapplinger JD et al. J Cardiovasc Transl Res. 2014;7:347-61; Walsh R et al. Genet. Med. 2017;19:192-203). This mutation has also been detected in the homozygous state in multiple Amish infants affected with severe neonate hypertrophic cardiomyopathy (Xin B, et al. Am. J. Med. Genet. A. 2007;143A(22):2662-7; Zahka K et al. Heart. 2008;94(10):1326-30). RNA studies in patient lymphocytes indicate that this particular alteration results in the skipping of exon 30, leading to a frame shift and premature protein truncation (Xin B et al. Am. J. Med. Genet. A. 2007;143A(22):2662-7). 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 and may result in the creation or strengthening of a novel splice donor site. In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
MYBPC3-related disorder Other:1
Variant interpreted as Pathogenic and reported on 03-19-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at