chr12-110911094-C-T

Position:

• chr12-110911094-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1 PM2 PM5 PP3 PP5

The NM_000432.4(MYL2):​c.484G>A​(p.Gly162Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/22 in silico tools predict a damaging outcome for this variant. 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. G162E) has been classified as Pathogenic.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: MYL2 NM_000432.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:6 U:1 O:1
• Conservation: PhyloP100: 5.81

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 8 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
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr12-110911093-C-T is described in Lovd as [Pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.816
• PP5: Variant 12-110911094-C-T is Pathogenic according to our data. Variant chr12-110911094-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 132976.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=3, not_provided=1, Uncertain_significance=1, Pathogenic=2}. Variant chr12-110911094-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYL2	NM_000432.4	c.484G>A	p.Gly162Arg	missense_variant	7/7	ENST00000228841.15	NP_000423.2
MYL2	NM_001406745.1	c.442G>A	p.Gly148Arg	missense_variant	6/6		NP_001393674.1
MYL2	NM_001406916.1	c.427G>A	p.Gly143Arg	missense_variant	7/7		NP_001393845.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYL2	ENST00000228841.15	c.484G>A	p.Gly162Arg	missense_variant	7/7	1	NM_000432.4	ENSP00000228841	P1
MYL2	ENST00000548438.1	c.442G>A	p.Gly148Arg	missense_variant	6/6	3		ENSP00000447154
MYL2	ENST00000663220.1	c.427G>A	p.Gly143Arg	missense_variant	7/7			ENSP00000499568

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461790 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 727200

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

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: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Significance: Conflicting classifications of pathogenicity

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

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:3 Other:1

Likely pathogenic, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Mar 12, 2015	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. p.Gly162Arg (p.G162R; c.484G>A) in exon 7 of the MYL2 gene (NM_000432.3) Mutations in the myosin ventricular regulatory light chain 2 (MYL2 gene) have been reported in a small percentage of patients with HCM (estimated range 1-5%). The variant has been reported in one other case of HCM, and it was de novo in that patient. Olivotto et al., 2008 (last author Cecchi) reported the “E162R” variant in one individual with HCM; however, we contacted the authors and learned that this is a typo that actually indicates G162R (as indicated by LMM, ClinVar, HGMD, etc.). Additional details regarding this patient’s phenotype were not given in the paper. The authors report to us by email that the variant was de novo in the young girl with HCM, and that her parents were studied and found to be clinically unaffected, supporting pathogenicity (Francesca Girolami, personal communication). Harvard’s LMM has reported a different variant at the same amino acid in 3 probands with HCM: p.Gly162Glu in the MYL2 gene (Alfares et al. 2015). They classify this p.Gly162Glu variant as “likely pathogenic”. One piece of evidence unique to their lab is that the change to glutamic acid (Glu) was predicted to be pathogenic using a computational tool, validated by the LMM laboratory, which uses a set of cardiomyopathy variants with well-established clinical significance. This tool's pathogenic prediction is estimated to be correct 94% of the time (Jordan 2011). Our patient’s variant at this same position (Gly162Arg) is also predicted to be pathogenic by the same tool (LMM unpublished data). The Gly162Arg variant results in a non-conservative amino acid substitution of a nonpolar Glycine with a positively charged Arginine, which has a much bulkier side chain. It is located in exon 7 out of 7 exons. In silico analysis with PolyPhen-2 predicts the variant to be “probably damaging” with a score of 1.0. The Glycine at codon 162 is entirely conserved across vertebrate species. Neighboring amino acids are also entirely conserved. One other variant listed in HGMD has been associated with disease at a nearby codon (+/- 10): Asp166Val (as of January 2014). In vitro studies of this variant indicate that it results in altered protein function, although these studies do not always mirror effects in vivo (Berghardt et al. 2013). The variant is very rare: In total it has not been seen in ~60,000 laboratory controls, published controls, and individuals from publicly available population datasets. There is no variation at codon 162 listed in the NHLBI Exome Sequencing Project dataset, which currently includes variant calls on ~6,500 Caucasian and African American individuals (as of 2/17/2015). Our patient is Caucasian. It is absent from 1000 Genomes. It is also absent from the ExAC database, which includes 60,000 exomes from disease-specific and population genetic studies (with efforts made to exclude individuals with severe pediatric diseases). The variant was not observed in the following laboratory and published control samples: absent 150 Caucasian individuals of Italian origin (Olivotto et al. 2008). -
not provided, no classification provided	literature only	Leiden Muscular Dystrophy (MYL2)	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jan 26, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Dec 29, 2022	Published in vitro and in vivo functional studies demonstrate a damaging effect on protein function (Manivannan et al., 2020); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Reported in ClinVar but additional evidence is not available (ClinVar Variant ID#132976; ClinVar); This variant is associated with the following publications: (PMID: 23343568, 18533079, 28991257, 32368696, 36291626, 32453731) -

Hypertrophic cardiomyopathy 10 Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Apr 04, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 13, 2023	This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 162 of the MYL2 protein (p.Gly162Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with hypertrophic cardiomyopathy or congenital heart disease (PMID: 18533079, 27532257, 28991257; Invitae). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 132976). 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: 23343568, 32453731). For these reasons, this variant has been classified as Pathogenic. -

Hypertrophic cardiomyopathy Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Apr 06, 2021

The p.Gly162Arg variant in MYL2 has been reported as a de novo occurrence in two individuals with HCM, one of whom was also reported to have AV and RBB block (Olivotto 2008, personal communication, LMM data) and in a third individual with LVH, reduced EF and ST segment abnormality (LMM data). This variant was absent from large population studies, but has been reported in ClinVar (Variation ID: 132976). In vitro functional studies provide some evidence that the p.Gly162Arg variant may impact protein function (Burghardt 2013); however, these types of assays sometimes do not accurately represent biological function. Glycine (Gly) at position 162 is highly conserved in evolution and the change to arginine (Arg) was predicted to be pathogenic using a computational tool clinically validated by our laboratory. This tool's pathogenic prediction is estimated to be correct 94% of the time (Jordan 2011). In summary, although additional studies are required to fully establish its clinical significance, the p.Gly162Arg variant is likely pathogenic. ACMG/AMP Criteria applied: PM6_Strong; PM2; PS3_Supporting; PP3; PS4_Supporting. -

Cardiomyopathy Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Center of Genomic medicine, Geneva, University Hospital of Geneva

Jan 09, 2018

This heterozygous variant in the MYL2 gene was identified in a young patient diagnosed with restrictive cardiomyopathy. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.96
CardioboostCm	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.42	D
BayesDel_noAF	Pathogenic	0.36
CADD	Pathogenic	29
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.83	D;.
Eigen	Pathogenic	0.88
Eigen_PC	Pathogenic	0.79
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Pathogenic	0.99	D;D
M_CAP	Pathogenic	0.61	D
MetaRNN	Pathogenic	0.82	D;D
MetaSVM	Uncertain	0.70	D
MutationAssessor	Pathogenic	3.7	H;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Pathogenic	0.85	D
PROVEAN	Pathogenic	-7.2	D;D
REVEL	Pathogenic	0.90
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Polyphen		1.0	D;.
Vest4		0.57
MutPred		0.59		Loss of glycosylation at K165 (P = 0.1121);.;
MVP		0.95
MPC		1.3
ClinPred		1.0	D
GERP RS		5.0
Varity_R		0.90
gMVP		0.82

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: rs199474814; hg19: chr12-111348898; COSMIC: COSV57406238; COSMIC: COSV57406238;