12-110911176-C-G

Variant names:

• chr12-110911176-C-G
• rs199474813
• NM_000432.4:c.403-1G>C

Variant summary

Our verdict is Likely pathogenic. The variant received 9 ACMG points: 9P and 0B. PVS1 PP5

The NM_000432.4(MYL2):​c.403-1G>C variant causes a splice acceptor, intron change. The variant allele was found at a frequency of 0.0000311 in 1,606,146 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 Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.000040 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000030 (0 hom.)
• Consequence: MYL2 NM_000432.4 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:13 U:2 O:1
• Conservation: PhyloP100: 6.89
• Publications: 10 publications found

Genes affected

MYL2 (HGNC:7583): (myosin light chain 2) This gene encodes a major sarcomeric protein in mammalian striated muscle. The encoded protein plays a role in embryonic heart muscle structure and function, while phosphorylation of the encoded protein is involved in cardiac myosin cycling kinetics, torsion and function in adults. Mutations in this gene are associated with hypertrophic cardiomyopathy 10 and infant-onset myopathy. [provided by RefSeq, May 2022]

MYL2 Gene-Disease associations (from GenCC):

• hypertrophic cardiomyopathy

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• hypertrophic cardiomyopathy 10

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: ClinGen, G2P, PanelApp Australia, Labcorp Genetics (formerly Invitae)
• myopathy, myofibrillar, 12, infantile-onset, with cardiomyopathy

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics
• congenital fiber-type disproportion myopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• dilated cardiomyopathy

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• arrhythmogenic right ventricular cardiomyopathy

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Likely_pathogenic. The variant received 9 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease,
• PP5: Variant 12-110911176-C-G is Pathogenic according to our data. Variant chr12-110911176-C-G is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 31768.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYL2	NM_000432.4	c.403-1G>C		splice_acceptor_variant, intron_variant	Intron 6 of 6	ENST00000228841.15	NP_000423.2
MYL2	NM_001406745.1	c.361-1G>C		splice_acceptor_variant, intron_variant	Intron 5 of 5		NP_001393674.1
MYL2	NM_001406916.1	c.346-1G>C		splice_acceptor_variant, intron_variant	Intron 6 of 6		NP_001393845.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYL2	ENST00000228841.15	c.403-1G>C		splice_acceptor_variant, intron_variant	Intron 6 of 6	1	NM_000432.4	ENSP00000228841.8

Frequencies

GnomAD3 genomes AF: 0.0000400 AC: 6 AN: 149820 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000679

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000737

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000483 AC: 12 AN: 248224 AF XY: 0.0000521

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000163

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000810

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000302 AC: 44 AN: 1456326 Hom.: 0 Cov.: 31 AF XY: 0.0000304 AC XY: 22 AN XY: 724420

African (AFR) AF: 0.00 AC: 0 AN: 33330

American (AMR) AF: 0.00 AC: 0 AN: 44558

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25946

East Asian (EAS) AF: 0.0000762 AC: 3 AN: 39364

South Asian (SAS) AF: 0.0000116 AC: 1 AN: 86202

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5746

European-Non Finnish (NFE) AF: 0.0000361 AC: 40 AN: 1108500

Other (OTH) AF: 0.00 AC: 0 AN: 60062

GnomAD4 genome AF: 0.0000400 AC: 6 AN: 149820 Hom.: 0 Cov.: 31 AF XY: 0.0000274 AC XY: 2 AN XY: 72894

African (AFR) AF: 0.00 AC: 0 AN: 40586

American (AMR) AF: 0.0000679 AC: 1 AN: 14720

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3458

East Asian (EAS) AF: 0.00 AC: 0 AN: 5076

South Asian (SAS) AF: 0.00 AC: 0 AN: 4784

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10114

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.0000737 AC: 5 AN: 67800

Other (OTH) AF: 0.00 AC: 0 AN: 2066

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ExAC AF: 0.0000247 AC: 3

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:13 Uncertain:2 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:8 Other:1

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Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 26, 2012

Leiden Muscular Dystrophy (MYL2)

Significance: not provided

Review Status: no classification provided

Collection Method: curation

- -

Jul 22, 2021

AiLife Diagnostics, AiLife Diagnostics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

May 30, 2023

Clinical Genetics Laboratory, Skane University Hospital Lund

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Mar 04, 2021

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published functional studies demonstrated that the c.403-1G>C variant destroys the consensus splice acceptor site of intron 6, and that utilization of an upstream cryptic splice site results in replacement of the last 32 amino acid residues with 20 different amino acid residues and alters the C-terminal domain of MYL2 (Weterman et al., 2013); however additional studies are needed to validate the functional effect of this variant in vivo; Canonical splice site variant with an unclear effect on protein function; Reported in ClinVar as pathogenic (ClinVar Variant ID# 31768; Landrum et al., 2016); Observed in 11 Dutch infant patients, homozygous for c.403-1 G>C, who subsequently died from cardiomyopathy; predicted variants in this region of the MYL2 gene may only lead to disease when present in a homozygous state (Weterman et al., 2013); Observed in a 17 year-old Danish male individual with pronounced septal hypertrophy who inherited this variant from his affected father (Andersen et al., 2001); however, the proband's sister also harbored the variant and had no features of hypertrophy on ECG or echocardiogram (Andersen et al., 2001). Both the proband and his sister also harbored a missense variant in MYL2, located on the opposite MYL2 allele (in trans), and inherited from their unaffacted mother (Andersen et al., 2001).; This variant is associated with the following publications: (PMID: 24474197, 21415409, 23365102, 27378946, 29447731, 11748309, 30291343, 30847666, 31980526, 31620961, 31127036, 32665702) -

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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

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Clinical Genetics, Academic Medical Center

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

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Hypertrophic cardiomyopathy 10 Pathogenic:3

Nov 07, 2018

Illumina Laboratory Services, Illumina

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The MYL2 c.403-1G>C variant occurs in a canonical splice site (acceptor) and is therefore predicted to disrupt or distort the normal gene product. Across a selection of the available literature, the c.403-1G>C variant has been identified in a homozygous state in 11 probands from eight unrelated families, in a compound heterozygous state in two probands, and in a heterozygous state in one proband (Andersen et al. 2001; Weterman et al. 2013). All the homozygous probands died within six months of birth (Weterman et al. 2013). Parents for seven of the homozygous probands were found to be heterozygous for the c.403-1G>C variant but did not exhibit any clinical phenotype consistent with familial hypertrophic cardiomyopathy. Phenotypes of affected individuals included familial hypertrophic cardiomyopathy, pronounced proximal septal hypertrophy, and light chain myopathy (Andersen et al. 2001; Weterman et al. 2013). The c.403-1G>C variant was absent from 150 control subjects and is reported at a frequency of 0.000083 in the European (non-Finnish) population of the Genome Aggregation Database. Analysis of mRNA from proband muscle tissue identified activation of cryptic splice site that causes a frameshift which leads to the C-terminal region of the protein being altered (Weterman et al. 2013). In vitro analysis of c.403-1G>C in BL21 (DE3) cells found reduced binding to myosin heavy chain, decreased maximal contractile force, and induced conformational changes to the regulatory light chain protein when compared to wildtype (Zhou et al. 2016). Due to the potential impact of splice acceptor variants, the c.403-1G>C variant is classified as pathogenic for MYL2-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -

May 04, 2022

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

_x000D_ Criteria applied: PVS1_STR, PS4, PS3_SUP, PM2_SUP -

Nov 21, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 6 of the MYL2 gene. It does not directly change the encoded amino acid sequence of the MYL2 protein. RNA analysis indicates that this variant induces altered splicing and likely disrupts the C-terminus of the protein. This variant is present in population databases (rs199474813, gnomAD 0.01%). This variant has been observed in individual(s) with autosomal recessive MYL2-related conditions (PMID: 11748309, 23365102). It has also been observed to segregate with disease in related individuals. This variant has been reported in individual(s) with autosomal dominant hypertrophic cardiomyopathy (PMID: 11748309); however, the role of the variant in this condition is currently unclear. ClinVar contains an entry for this variant (Variation ID: 31768). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects MYL2 function (PMID: 27378946). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in activation of a cryptic splice site 23 nucleotides upstream of the original splice site and introduces a new termination codon (PMID: 23365102). However the mRNA is not expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

Myopathy, myofibrillar, 12, infantile-onset, with cardiomyopathy Pathogenic:2

Feb 21, 2022

MGZ Medical Genetics Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 05, 2021

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Cardiomyopathy Uncertain:1

Jan 15, 2024

Color Diagnostics, LLC DBA Color Health

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant causes a G to C nucleotide substitution at the -1 position of intron 6 of the MYL2 gene. This variant is also known as IVS6-1G>C in the literature. An RNA study has shown that this variant causes aberrant splicing due to the activation of cryptic acceptor site at c.403-24_403-23AG (PMID: 23365102, 27378946). As a result, the last 32 amino acids of the MYL2 protein are replaced with 19 new amino acids. The mutant protein has shown a decreased binding to myosin heavy chain compared to the wild type protein, resulting in reduced myosin-actin interaction and decreased maximal contractile force of cardiac muscles (PMID: 27378946). However, clinical relevance of this observation is not clear. This variant has primarily been reported in homozygous individuals, including infants from eight different families affected with an infantile cardioskeletal myopathy (PMID: 23365102), two siblings affected with a neonatal form of dilated cardiomyopathy (Posafalvi 2015, dissertation, University of Groningen), and in one child affected with ventricular noncompaction cardiomyopathy (PMID: 29447731). While these children showed severe phenotypes and died early in life, their heterozygous family members were not affected with cardiomyopathy, indicating that this variant is linked to an autosomal recessive phenotype. This variant has been reported in heterozygous state in a few individuals affected with hypertrophic cardiomyopathy (PMID: 11748309, 28939701, 30847666, 33495596) but has also been observed in unaffected adults (PMID: 11748309, 30291343, 31980526, 32665702). This variant has been identified in 12/248224 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, this variant is associated with autosomal recessive cardiomyopathy, but the available evidence is insufficient to determine the role of this variant in autosomal dominant cardiomyopathy conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance for autosomal dominant cardiomyopathy. -

Cardiovascular phenotype Uncertain:1

May 29, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.403-1G>C intronic variant results from a G to C substitution one nucleotide upstream from coding exon 7 of the MYL2 gene. This alteration has been identified in the homozygous state in multiple individuals from the Netherlands with infantile type I muscle fibre disease and cardiomyopathy, and haplotype analysis indicates that this variant is a Dutch founder mutation (Weterman MA et al. Brain, 2013 Jan;136:282-93). This alteration has also been reported in the homozygous state in a child with left ventricular noncompaction and in the heterozygous state in hypertrophic cardiomyopathy cohorts (Andersen PS et al. J. Med. Genet., 2001 Dec;38:E43; van Velzen HG et al. Am. J. Cardiol., 2016 09;118:881-887; van Waning JI et al. J. Am. Coll. Cardiol., 2018 Feb;71:711-722). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing. RNA studies have demonstrated that an alternate splice acceptor site located 23 nucleotides upstream of the native acceptor site is utilized in the presence of this alteration, resulting in the inclusion of 23 intronic nucleotides and a predicted frameshift (p.V135Hfs*20) that disrupts the C-terminal EF hand domain (Weterman MA et al. Brain, 2013 Jan;136:282-93). In vitro functional assays suggest that the resulting truncated protein alters MYL2 function, but the physiological relevance of this result is unclear (Zhou Z et al. Front Physiol, 2016 Jun;7:240). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. Although biallelic loss of function of MYL2 has been associated with autosomal recessive MYL2-related infantile onset myofibrillar myopathy with cardiomyopathy, haploinsufficiency of MYL2 has not been established as a mechanism of disease for autosomal dominant MYL2-related cardiomyopathy. Based on the supporting evidence, this variant is expected to be causative of autosomal recessive MYL2-related infantile onset myofibrillar myopathy with cardiomyopathy when present along with a second pathogenic variant on the other allele; however, its clinical significance for autosomal dominant MYL2-related cardiomyopathy is unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.46	D
BayesDel_noAF	Pathogenic	0.23
CADD	Pathogenic	34
DANN	Uncertain	0.99
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.84
FATHMM_MKL	Pathogenic	0.97	D
PhyloP100		6.9
GERP RS		5.0
Mutation Taster		=1/99	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.81		Position offset: 22
DS_AL_spliceai		0.99		Position offset: -1

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

Other links and lift over

dbSNP: rs199474813; hg19: chr12-111348980;