rs143139258

Positions:

• chr12-110913097-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 7P and 4B. PM1 PP3_Strong PP5 BS2

The NM_000432.4(MYL2):​c.401A>C​(p.Glu134Ala) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000418 in 1,613,870 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. 14/24 in silico tools predict a damaging outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E134D) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00027 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00043 (1 hom.)
• Consequence: MYL2 NM_000432.4 missense, splice_region
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:6 U:9 O:1
• Conservation: PhyloP100: 7.64

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 Uncertain_significance. Variant got 3 ACMG points.

• PM1: In a domain EF-hand 3 (size 35) in uniprot entity MLRV_HUMAN there are 17 pathogenic changes around while only 1 benign (94%) in NM_000432.4
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.
• PP5: Variant 12-110913097-T-G is Pathogenic according to our data. Variant chr12-110913097-T-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 43475.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=3, Uncertain_significance=9, not_provided=1, Pathogenic=1}. Variant chr12-110913097-T-G is described in Lovd as [Pathogenic].
• BS2: High AC in GnomAd4 at 41 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYL2	NM_000432.4	c.401A>C	p.Glu134Ala	missense_variant, splice_region_variant	6/7	ENST00000228841.15
MYL2	NM_001406745.1	c.359A>C	p.Glu120Ala	missense_variant, splice_region_variant	5/6
MYL2	NM_001406916.1	c.344A>C	p.Glu115Ala	missense_variant, splice_region_variant	6/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYL2	ENST00000228841.15	c.401A>C	p.Glu134Ala	missense_variant, splice_region_variant	6/7	1	NM_000432.4	P1
MYL2	ENST00000548438.1	c.359A>C	p.Glu120Ala	missense_variant, splice_region_variant	5/6	3
MYL2	ENST00000663220.1	c.344A>C	p.Glu115Ala	missense_variant, splice_region_variant	6/7
MYL2	ENST00000549029.1			downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.000270 AC: 41 AN: 152002 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000262

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: 0.000471

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000199 AC: 50 AN: 251490 Hom.: 0 AF XY: 0.000228 AC XY: 31 AN XY: 135920

Gnomad AFR exome AF: 0.000123

Gnomad AMR exome AF: 0.000231

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: 0.000352

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000434 AC: 634 AN: 1461868 Hom.: 1 Cov.: 33 AF XY: 0.000435 AC XY: 316 AN XY: 727234

Gnomad4 AFR exome AF: 0.0000597

Gnomad4 AMR exome AF: 0.000246

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: 0.000537

Gnomad4 OTH exome AF: 0.000397

GnomAD4 genome AF: 0.000270 AC: 41 AN: 152002 Hom.: 0 Cov.: 33 AF XY: 0.000229 AC XY: 17 AN XY: 74226

Gnomad4 AFR AF: 0.000121

Gnomad4 AMR AF: 0.000262

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000471

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000440 Hom.: 0

Bravo AF: 0.000295

TwinsUK AF: 0.000270 AC: 1

ALSPAC AF: 0.000259 AC: 1

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000581 AC: 5

ExAC AF: 0.000157 AC: 19

EpiCase AF: 0.000327

EpiControl AF: 0.000356

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:6 Uncertain:9 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:1 Uncertain:2 Other:1

not provided, no classification provided	literature only	Leiden Muscular Dystrophy (MYL2)	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 20, 2016	Variant summary: c.401A>C affects a conserved nucleotide, resulting in amino acid change from Glu to Ala. 5/5 in-silico tools predict this variant to be damaging. This variant was found in 19/121996 control chromosomes at a frequency of 0.0001557, predominantly observed in Latino and non-Finnish European subpopulations with MAF of 0.0003455 and 0.0002248 respectively in ExAC. The frequencies exceed the maximal expected frequency of a pathogenic allele (0.000075). This variant has been reported in multiple HCM pts and functional study showed that the actin binding in contraction is compromised by the E134A mutation (Burghardt_2013). An internal LCA sample carried this variant with co-occurrence of a pathogenic MYBPC3 variant (c.1504C>T, p.R502W). Via Clinivar, two clinical labs list variant with classification of likely pathogenic, one classified it as pathogenic, and another lab classified variant as VUS. Taking all evidence into consideration, although this variant has been reported in multiple affected individuals, it is also present at a relatively high frequency in the general population, and thus the pathogenicity of this variant is unclear at this moment; hence, this variant is classified as a variant of unknown significance until more information becomes available. -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jun 01, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	Jan 05, 2015	- -

Hypertrophic cardiomyopathy 10 Pathogenic:1 Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Nov 01, 2022	This sequence change replaces glutamic acid, which is acidic and polar, with alanine, which is neutral and non-polar, at codon 134 of the MYL2 protein (p.Glu134Ala). This variant is present in population databases (rs143139258, gnomAD 0.03%). This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 20173211, 24111713, 25524337, 27483260, 27600940). ClinVar contains an entry for this variant (Variation ID: 43475). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C15"). Experimental studies have shown that this missense change affects MYL2 function (PMID: 23343568). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	Nov 21, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Feb 24, 2022	- -

Hypertrophic cardiomyopathy Pathogenic:1 Uncertain:2

Likely pathogenic, criteria provided, single submitter	research	CSER _CC_NCGL, University of Washington	Oct 01, 2016	Found in patient having exome sequencing for an unrelated indication. No known history of hypertrophic cardiomyopathy. This interpretation considers GERP score and allele frequency data, in addition to published reports of the variant in the literature, available at the time of review. -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 05, 2019	Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Gnomad: 0.033 in NFE population, HGMD: Whiffin (2017) Genet Med 19: 1151 PubMed: 28518168 Additional literature report − classed as VUS. See Supplementary Table S1. (only additional report, refers Burghardt et al). %7C ClinVar: VUS by Invitae, Ambry, EGL , LP by University of Washington, Eric and Hanna Klessmann Institute. Reported in multiple individuals with cardiomyopathy but frequency higher than expected for a pathogenic variant. Conflicting information - VUS. -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jan 03, 2024	This missense variant replaces glutamic acid with alanine at codon 134 of the MYL2 protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. Splice site prediction tools suggest that this variant may impact RNA splicing. A functional study using a cardiac papillary muscle fiber system has shown that this variant reduces actin binding in contraction (PMID: 23343568). However, clinical relevance of this observation is not clear. This variant has been reported in at least six unrelated individuals affected with hypertrophic cardiomyopathy (PMID: 20173211, 23396983, 24111713, 31323898, 33495596, 33495597, 33732734). It has also been reported in one individual affected with dilated cardiomyopathy (PMID: 34935411, 35026164), and in one individual affected with respiratory syncytial virus-associated sudden death and an unaffected carrier parent (PMID: 31771554). This variant has been identified in 57/282826 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Cardiomyopathy Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 14, 2023	This missense variant replaces glutamic acid with alanine at codon 134 of the MYL2 protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. Splice site prediction tools suggest that this variant may impact RNA splicing. A functional study using a cardiac papillary muscle fiber system has shown that this variant reduces actin binding in contraction (PMID: 23343568). However, clinical relevance of this observation is not clear. This variant has been reported in at least six unrelated individuals affected with hypertrophic cardiomyopathy (PMID: 20173211, 23396983, 24111713, 31323898, 33495596, 33495597, 33732734). It has also been reported in one individual affected with dilated cardiomyopathy (PMID: 34935411, 35026164), and in one individual affected with respiratory syncytial virus-associated sudden death and an unaffected carrier parent (PMID: 31771554). This variant has been identified in 57/282826 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Feb 24, 2020	- -

Dilated cardiomyopathy 1S Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum Nordrhein-Westfalen

May 01, 2016

- -

Primary dilated cardiomyopathy Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital

Sep 22, 2016

- -

Primary familial hypertrophic cardiomyopathy Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute

Feb 21, 2017

- -

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 30, 2022

The p.E134A variant (also known as c.401A>C), located in coding exon 6 of the MYL2 gene, results from an A to C substitution at nucleotide position 401. The glutamic acid at codon 134 is replaced by alanine, an amino acid with dissimilar properties. This variant has been reported in hypertrophic cardiomyopathy, dilated cardiomyopathy, and sudden cardiac arrest cohorts; however, in several cases clinical detail was limited, this variant was reported to co-occur with other cardiac-related genes, and/or this variant was also detected in unaffected family members (Olivotto I et al. Mayo Clin Proc. 2008;83:630-8; Di Donna P et al. Europace. 2010;12:347-55; Berge KE et al. Clin Genet. 2014;86:355-60; Cecconi M et al. Int J Mol Med. 2016;38(4):1111-24; Stpie-Wojno M et al. Pol Arch Intern Med. 2018;12; Mademont-Soler I et al. PLoS ONE. 2017;12(8):e0181465; Klauke B et al. PLoS One, 2017 Dec;12:e0189489;; Gavotto A et al. BMC Pediatr, 2019 11;19:462). This variant has also been detected in population-based cohorts and exome cohorts with unclear cardiovascular history (Bick AG. Am J Hum Genet. 2012;91(3):513-9; Andreasen C et al. Eur J Hum Genet. 2013;21:918-28; Dorschner MO et al. Am J Hum Genet. 2013 Oct;93:631-40). An in vitro study suggested that this alteration may reduce actin binding (Burghardt TP et al. Biochemistry. 2013;52:1249-59). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.87
CardioboostCm	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.21	D
BayesDel_noAF	Pathogenic	0.37
CADD	Pathogenic	33
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.82	D;.
Eigen	Pathogenic	0.71
Eigen_PC	Pathogenic	0.67
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Pathogenic	0.98	D;D
M_CAP	Pathogenic	0.72	D
MetaRNN	Pathogenic	0.97	D;D
MetaSVM	Uncertain	0.55	D
MutationAssessor	Pathogenic	4.0	H;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.58	T
PROVEAN	Pathogenic	-5.7	D;D
REVEL	Pathogenic	0.94
Sift	Uncertain	0.0010	D;D
Sift4G	Uncertain	0.0020	D;D
Polyphen		0.79	P;.
Vest4		0.93
MVP		0.97
MPC		1.0
ClinPred		0.93	D
GERP RS		5.1
Varity_R		0.88
gMVP		0.83

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	1.0
SpliceAI score (max)		0.070		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: rs143139258; hg19: chr12-111350901;