12-110919133-C-T

Position:

• chr12-110919133-C-T

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1 PP3 PP5_Very_Strong

The NM_000432.4(MYL2):​c.64G>A​(p.Glu22Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,932 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000021 (0 hom.)
• Consequence: MYL2 NM_000432.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:22 O:1
• Conservation: PhyloP100: 7.53

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 Pathogenic. Variant got 11 ACMG points.

• PM1: In a chain Myosin regulatory light chain 2, ventricular/cardiac muscle isoform (size 164) in uniprot entity MLRV_HUMAN there are 33 pathogenic changes around while only 3 benign (92%) in NM_000432.4
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.803
• PP5: Variant 12-110919133-C-T is Pathogenic according to our data. Variant chr12-110919133-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 14065.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110919133-C-T is described in Lovd as [Pathogenic]. Variant chr12-110919133-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYL2	NM_000432.4	c.64G>A	p.Glu22Lys	missense_variant	2/7	ENST00000228841.15	NP_000423.2
MYL2	NM_001406745.1	c.64G>A	p.Glu22Lys	missense_variant	2/6		NP_001393674.1
MYL2	NM_001406916.1	c.7G>A	p.Glu3Lys	missense_variant	2/7		NP_001393845.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYL2	ENST00000228841.15	c.64G>A	p.Glu22Lys	missense_variant	2/7	1	NM_000432.4	ENSP00000228841.8
MYL2	ENST00000548438.1	c.64G>A	p.Glu22Lys	missense_variant	2/6	3		ENSP00000447154.1
MYL2	ENST00000663220.1	c.7G>A	p.Glu3Lys	missense_variant	2/7			ENSP00000499568.1
MYL2	ENST00000546404.1	c.64G>A	p.Glu22Lys	missense_variant	2/2	2		ENSP00000499645.1

Frequencies

GnomAD3 genomes AF: 0.0000197 AC: 3 AN: 152100 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

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: 0.0000294

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000199 AC: 5 AN: 251472 Hom.: 0 AF XY: 0.0000221 AC XY: 3 AN XY: 135908

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000578

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000176

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.0000212 AC: 31 AN: 1461714 Hom.: 0 Cov.: 30 AF XY: 0.0000220 AC XY: 16 AN XY: 727142

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000447

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000243

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome AF: 0.0000197 AC: 3 AN: 152218 Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2 AN XY: 74422

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000655

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000282 Hom.: 0

ExAC AF: 0.00000824 AC: 1

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:22 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:7

Pathogenic, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Dec 13, 2022	PS4, PP3, PM2_SUP, PS3 -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 04, 2022	Haplotype analysis suggests this variant is a founder mutation in the Dutch population (Claes et al., 2016); Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate that E22K alters MYL2 function (Szczesna et al., 2001; Szczesna-Cordary et al., 2004; Roopnarine et al., 2003; Szczesna-Cordary et al., 2007, Farman et al., 2014; Zhang et al., 2021); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 14594949, 16751284, 9724616, 31513939, 17606808, 12668451, 25324513, 8673105, 12404107, 21310275, 27532257, 28166811, 28138913, 27435932, 28606303, 26497160, 28790153, 16076902, 30605904, 21896538, 10948063, 30847666, 33673806, 32665702, 32880476, 33087929, 33662488, 11102452, 33548158) -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Sep 01, 2022	MYL2: PP1:Strong, PM1, PM2, PS4:Moderate -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Jan 03, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Blueprint Genetics	Oct 18, 2017	- -

Hypertrophic cardiomyopathy 10 Pathogenic:6 Other:1

not provided, no classification provided	curation	Leiden Muscular Dystrophy (MYL2)	Mar 26, 2012	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Nov 01, 2002	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 20, 2024	This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 22 of the MYL2 protein (p.Glu22Lys). This variant is present in population databases (rs104894368, gnomAD 0.006%). This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 8673105, 12404107, 26497160, 27532257). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 14065). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects MYL2 function (PMID: 12668451, 14594949, 16076902, 17606808, 25324513, 26497160). For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Center for Medical Genetics Ghent, University of Ghent	Jul 15, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	Sep 21, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	Jul 28, 2017	- -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Hypertrophic cardiomyopathy Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jul 10, 2024	This missense variant replaces glutamic acid with lysine at codon 22 of the MYL2 protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. A transgenic mouse model has shown that this variant causes a phenotype consistent with hypertrophic cardiomyopathy, including decline in rigor tension and enhanced actin-activated myosin ATPase activity (PMID: 33548158). Additional functional studies have shown that this variant affects protein function by altering calcium sensitivity of force and ATPase activity in vitro and in transgenic mice (PMID: 12668451, 14594949, 16076902, 17606808, 25324513). This variant has been reported in over 40 individuals affected with hypertrophic cardiomyopathy from over 20 families (PMID: 8673105, 12404107, 26497160, 27532257, 33495596, 33495597, 33673806; ClinVar SCV000203862.4). This variant has shown reduced penetrance and late-onset disease with moderate symptoms in some individuals. A study of 38 carriers from 14 Dutch families has suggested that this variant together with the presence of an additional risk factor, such as hypertension, contributes to the development of hypertrophic cardiomyopathy (PMID: 26497160). This variant has been identified in 5/251472 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Molecular Genetics, Royal Melbourne Hospital	Jul 07, 2023	This sequence change in MYL2 is predicted to replace glutamic acid with lysine at codon 22, p.(Glu22Lys). The glutamic acid residue is highly conserved (100 vertebrates, UCSC). There is a small physicochemical difference between glutamic acid and lysine. The highest population minor allele frequency in the population database gnomAD v2.1 is 0.006% (2/34,590 alleles) in the Latino/Admixed American population. The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls (odds ratio = 8.4, 95 % CI:1.64 to 43.5; VariantFX Cardiac Allele Frequencies, DECIPHER vs gnomAD v2.1 Latino/Admixed American population). The variant has been reported to segregate with cardiomyopathy across multiple affected families and is associated with incomplete penetrance and later onset of hypertrophic cardiomyopathy (PMID: 26497160). In vitro functional assays and transgenic mouse models showed a significant change in the calcium-binding properties for this variant indicating it impacts protein function (PMID: 11102452, 16076902, 17606808, 14594949, 12668451). Computational evidence predicts a deleterious effect for the missense substitution (REVEL = 0.714). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.6.1, this variant is classified as LIKELY PATHOGENIC. Following criteria are met: PP1_Strong, PP3, PS3_Moderate, PS4_Moderate -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Sep 24, 2019	The p.Glu22Lys variant in MYL2 has been reported in >25 individuals with HCM and segregated in >20 affected relatives (Álvarez-Acosta 2014, Claes 2015, Poetter 1996, Kabaeva 2002, Walsh 2017, LMM data). This variant reportedly did not segregate with disease in several affected relatives, though at least 4 of these individuals were reported to have additional risk factors or carried additional variants in cardiomyopathy related genes (Alvarez-Acosta 2014, Claes 2015). This variant has also been identified in 5/251472 chromosomes by gnomAD (http://gnomad.broadinstitute.org) and had been reported in ClinVar (Variation ID #14065). Multiple in vitro and transgenic animal studies have shown that the p.Glu22Lys variant impacts protein function (Levine 1998, Roopnarine 2003, Szczesna 2001, Szczsna-Cordary 2004, Szczsna-Cordary 2007). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant HCM. ACMG/AMP Criteria applied: PS4, PP1_Strong, PS3_Moderate, PM2. -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Human Genetics, University of Leuven	Oct 31, 2018	- -

Cardiomyopathy Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Mar 21, 2023	This missense variant replaces glutamic acid with lysine at codon 22 of the MYL2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that this variant affects protein function by altering calcium sensitivity of force and ATPase activity in vitro and in transgenic mice (PMID: 12668451, 14594949, 16076902, 17606808, 25324513). This variant has been reported in over 40 individuals affected with hypertrophic cardiomyopathy from over 20 families (PMID: 8673105, 12404107, 26497160, 27532257; ClinVar SCV000203862.4). This variant has shown reduced penetrance and late-onset disease with moderate symptoms in some individuals. A study of 38 carriers from 14 Dutch families has suggested that this variant together with the presence of an additional risk factor, such as hypertension, contributes to the development of hypertrophic cardiomyopathy (PMID: 26497160). This variant has been identified in 5/251472 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Mar 28, 2022	- -

MYL2-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Apr 25, 2023

The MYL2 c.64G>A variant is predicted to result in the amino acid substitution p.Glu22Lys. This variant was reported in multiple individuals with hypertrophic cardiomyopathy (see for example, Poetter et al. 1996. PubMed ID: 8673105; Robyns et al. 2020. PubMed ID: 31513939; Walsh et al. 2017. PubMed ID: 27532257). Multiple functional studies suggest this variant alters protein function (see for example, Zhang et al. 2021. PubMed ID: 33548158; Szczesna-Cordary et al. 2007. PubMed ID: 17606808). This variant is reported in 0.0058% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/12-111356937-C-T). This variant is interpreted as pathogenic. -

Cardiovascular phenotype Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 25, 2023

The p.E22K variant (also known as c.64G>A), located in coding exon 2 of the MYL2 gene, results from a G to A substitution at nucleotide position 64. The glutamic acid at codon 22 is replaced by lysine, an amino acid with similar properties. This alteration has been previously detected in numerous hypertrophic cardiomyopathy (HCM) cohorts and has been shown to segregate with HCM in several families (Poetter K et al. Nat. Genet., 1996 May;13:63-9; Kabaeva ZT et al. Eur. J. Hum. Genet., 2002 Nov;10:741-8; Lopes LR et al. Heart, 2015 Feb;101:294-301; Alejandra Restrepo-Cordoba M et al. J Cardiovasc Transl Res, 2017 Feb;10:35-46; Walsh R et al. Genet. Med., 2017 02;19:192-203). This variant is a founder mutation with shared haplotype in the Netherlands; however, the presence of this allele in unaffected relatives and the existence of additional risk factors in many of the affected carriers suggests this allele exhibits reduced penetrance and may not cause disease on its own (Claes GR et al. Eur. Heart J., 2016 06;37:1815-22). Multiple in vitro functional studies suggest this alteration may impact protein function, but adult transgenic mice expressing E22K do not exhibit detectable cardiac hypertrophy (Sanbe A et al. Circ. Res., 2000 Aug;87:296-302; Roopnarine O. Biophys. J., 2003 Apr;84:2440-9; Szczesna-Cordary D et al. J. Cell. Sci., 2005 Aug;118:3675-83; Farman GP et al. J. Appl. Physiol., 2014 Dec;117:1471-7). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic; however, it may represent a risk factor or a milder allele that presents with incomplete penetrance. -

Death in early adulthood Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Forensic Genetics Laboratory, Harris County Institute of Forensic Sciences

Mar 27, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.89
CardioboostCm	Uncertain	0.84
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Pathogenic	0.14
CADD	Pathogenic	33
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.67	D;.
Eigen	Uncertain	0.49
Eigen_PC	Uncertain	0.50
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Pathogenic	0.97	D;D
M_CAP	Pathogenic	0.45	D
MetaRNN	Pathogenic	0.80	D;D
MetaSVM	Uncertain	-0.047	T
MutationAssessor	Benign	1.5	L;.
PrimateAI	Uncertain	0.77	T
PROVEAN	Uncertain	-3.3	D;D
REVEL	Pathogenic	0.71
Sift	Uncertain	0.0020	D;D
Sift4G	Uncertain	0.044	D;D
Polyphen		0.98	D;.
Vest4		0.89
MutPred		0.54		Gain of methylation at E22 (P = 0.0052);Gain of methylation at E22 (P = 0.0052);
MVP		0.90
MPC		0.79
ClinPred		0.91	D
GERP RS		4.4
Varity_R		0.92
gMVP		0.85

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

Publications

LitVar

Other links and lift over

dbSNP: rs104894368; hg19: chr12-111356937; COSMIC: COSV57405974; COSMIC: COSV57405974;