12-110911176-C-G

Position:

• chr12-110911176-C-G

Variant summary

Our verdict is Likely pathogenic. Variant got 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:1 O:1
• Conservation: PhyloP100: 6.89

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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 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 id is 31768.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, not_provided=1, Pathogenic=3, Likely_pathogenic=4}. Variant chr12-110911176-C-G is described in Lovd as [Likely_pathogenic]. Variant chr12-110911176-C-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYL2	NM_000432.4	c.403-1G>C		splice_acceptor_variant, intron_variant		ENST00000228841.15	NP_000423.2
MYL2	NM_001406745.1	c.361-1G>C		splice_acceptor_variant, intron_variant			NP_001393674.1
MYL2	NM_001406916.1	c.346-1G>C		splice_acceptor_variant, intron_variant			NP_001393845.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYL2	ENST00000228841.15	c.403-1G>C		splice_acceptor_variant, intron_variant		1	NM_000432.4	ENSP00000228841.8
MYL2	ENST00000548438.1	c.361-1G>C		splice_acceptor_variant, intron_variant		3		ENSP00000447154.1
MYL2	ENST00000663220.1	c.346-1G>C		splice_acceptor_variant, intron_variant				ENSP00000499568.1

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

GnomAD3 exomes AF: 0.0000483 AC: 12 AN: 248224 Hom.: 0 AF XY: 0.0000521 AC XY: 7 AN XY: 134348

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 SAS exome AF: 0.00

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000762

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000361

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000679

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000737

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000378

ExAC AF: 0.0000247 AC: 3

ClinVar

Significance: Conflicting classifications of pathogenicity

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

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:8 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	May 30, 2023	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 04, 2021	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) -
not provided, no classification provided	curation	Leiden Muscular Dystrophy (MYL2)	Mar 26, 2012	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Jul 22, 2021	- -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Hypertrophic cardiomyopathy 10 Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 04, 2023	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 protein 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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Nov 07, 2018	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	May 04, 2022	_x000D_ Criteria applied: PVS1_STR, PS4, PS3_SUP, PM2_SUP -

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

Pathogenic, no assertion criteria provided	literature only	OMIM	Aug 05, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Feb 21, 2022	- -

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

May 29, 2024

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
GERP RS		5.0

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

Publications

LitVar

Other links and lift over

dbSNP: rs199474813; hg19: chr12-111348980;