12-110914287-C-T

Position:

• chr12-110914287-C-T

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1 PM2 PP3 PP5_Very_Strong

The NM_000432.4(MYL2):​c.173G>A​(p.Arg58Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,934 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 Pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: MYL2 NM_000432.4 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:13 O:1
• Conservation: PhyloP100: 7.50

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 13 ACMG points.

• PM1: In a domain EF-hand 1 (size 35) in uniprot entity MLRV_HUMAN there are 7 pathogenic changes around while only 0 benign (100%) in NM_000432.4
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.835
• PP5: Variant 12-110914287-C-T is Pathogenic according to our data. Variant chr12-110914287-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 14067.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110914287-C-T is described in Lovd as [Pathogenic]. Variant chr12-110914287-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.173G>A	p.Arg58Gln	missense_variant	4/7	ENST00000228841.15	NP_000423.2
MYL2	NM_001406745.1	c.131G>A	p.Arg44Gln	missense_variant	3/6		NP_001393674.1
MYL2	NM_001406916.1	c.116G>A	p.Arg39Gln	missense_variant	4/7		NP_001393845.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYL2	ENST00000228841.15	c.173G>A	p.Arg58Gln	missense_variant	4/7	1	NM_000432.4	ENSP00000228841	P1
MYL2	ENST00000548438.1	c.131G>A	p.Arg44Gln	missense_variant	3/6	3		ENSP00000447154
MYL2	ENST00000663220.1	c.116G>A	p.Arg39Gln	missense_variant	4/7			ENSP00000499568
MYL2	ENST00000549029.1	n.4G>A		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000795 AC: 2 AN: 251438 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135898

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000924

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1460934 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 726836

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: 0.0000374

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 32

ExAC AF: 0.00000824 AC: 1

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:13 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jun 13, 2022	Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Published functional studies demonstrate a damaging effect as the p.(R58Q) residue is in a calcium binding site within the human cardiac regulatory light chain; p.(R58Q) eliminates normal calcium binding and increases the calcium sensitivity of myofibrillar ATPase (Szczesna et al., 2001; Szczesna-Cordary et al., 2004; Greenberg et al., 2009; Wang et al., 2013); This variant is associated with the following publications: (PMID: 18929571, 26187847, 26914223, 12404107, 24111713, 25351510, 21723297, 11102452, 23727233, 20855589, 12707239, 21310275, 9535554, 12818575, 27532257, 28166811, 29452157, 29398688, 21835320, 16837010, 26116789, 23283745, 19150977, 30775854, 31104103, 30430732, 29710196, 33673806, 14594949, 34310159, 30796699, 33190526, 32746448, 33731536, 33919432, 26582918) -
Likely pathogenic, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Feb 03, 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.Arg58Gln (p.R58Q; c.173G>A) in the MYL2 gene (NM_000432.3) The variant has been seen in at least 8 unrelated cases of HCM (one of them is another patient at SCICD). There is weak segregation in at least two families. The Arg58Gln variant was first reported in association with HCM in two unrelated individuals and it was also present in an affected relative of one of these individuals (Flavigny et al., 1998). Kabaeva et al., 2002 (last author Osterziel) reported this variant in one individual with HCM. The proband had non-obstructive HCM first diagnosed at the age of 7 years. She underwent implantation of an ICD at age 25 years after VT degenerating into VF was observed. She had recurrent episodes of supraventricular tachycardia. No segregation data was available as her family members with HCM (father and sister) had sudden cardiac deaths at young ages and DNA was not available, however the proband's mother tested negative suggesting that this variant was paternally inherited and therefore more likely to be a disease-causing variant in the family. The pattern of LV hypertrophy was reportedly similar to the cases presented by Flavigny et al. Olivotto et al., 2008 (last author Cecchi) reported this variant in two individuals with HCM. Additional details regarding their phenotype were not given. Richard et al., 2003 reported this variant in one individual with HCM. Additional phenotype or segregation details were not given. Harvard’s Laboratory for Molecular Medicine submitted this variant to ClinVar on 1/29/2015. They classify it as pathogenic, and report seeing it in 5 families. Arg58Gln results in a non-conservative amino acid substitution of a positively charged Arginine with a neutral, polar Glutamine at a residue that is conserved across species. This variant is located in exon 4 of 7 exons. Functional studies of this variant indicate that it is in a calcium binding site within the human cardiac regulatory light chain and Arg58Gln eliminates normal calcium binding and increases the calcium sensitively of myofibrillar ATPase, which is proposed to affect regulation of cardiac muscle contraction (Szczesna-Cordary et al., 2004). In silico analysis with PolyPhen-2 predicts the variant to be probably damaging. The arginine at codon 58 is conserved across vertebrate species, however it is a glutamine in C-elegans. Neighboring amino acids are conserved. No other variants have been associated with disease at this codon. A neighboring codon, p.Gly57Glu, has been reported in one individual with RCM; she was also found to be homozygous for a variant in MYL3, p.Glu143Lys. HGMD also includes a nearby variant (+/- 10) Glu65Lys associated with HCM. In total the variant has been seen in just 1 out of ~60,000 laboratory controls, published controls and individuals from publicly available population datasets. There is no variation at codon 58 listed in the NHLBI Exome Sequencing Project dataset, which currently includes variant calls on ~6,500 Caucasian and African American individuals (as of 1/26/2015). Note that this dataset does not match the patient's ancestry. The variant was not observed in the following laboratory and published control samples: absent 150 individuals (Olivotto et al.), absent in 100 individuals (Morner et al), absent in 105 individuals (Richard et al), and 100 individuals (Kabeava et al.). The ethnicities of these individuals are not known. -
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	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	Jun 15, 2023	- -

Hypertrophic cardiomyopathy 10 Pathogenic:4 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	May 18, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 15, 2024	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 58 of the MYL2 protein (p.Arg58Gln). This variant is present in population databases (rs104894369, gnomAD 0.009%). This missense change has been observed in individuals with hypertrophic cardiomyopathy (HCM) (PMID: 9535554, 12404107, 12818575, 23283745, 24111713). ClinVar contains an entry for this variant (Variation ID: 14067). 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: 14594949, 19150977, 20855589, 21723297, 23727233, 26116789). For these reasons, this variant has been classified as Pathogenic. -
not provided, no classification provided	curation	Leiden Muscular Dystrophy (MYL2)	Mar 26, 2012	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Mar 22, 2022	Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000014067, PMID:9535554). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000532778, PMID:24793961). In silico tool predictions suggest damaging effect of the variant on gene or gene product (3CNET: 0.793>=0.75). A missense variant is a common mechanism . It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000008). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Nov 01, 2002	- -

Cardiomyopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Mar 25, 2021

- -

Primary familial hypertrophic cardiomyopathy Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Blueprint Genetics

Jul 21, 2014

- -

Hypertrophic cardiomyopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Jan 24, 2018

The p.Arg58Gln variant in MYL2 has been reported in at least 16 individuals with HCM and segregated with disease in 11 affected relatives from 6 families (Flavi gny 1998, Kabaeva 2002, Morner 2003, Olivotto 2011, Li 2015, Walsh 2016, LMM dat a). It has also been identified in 2/22298 Finnish chromosomes by the Genome Agg regation Database (gnomAD, http://exac.broadinstitute.org; dbSNP rs104894369). T his variant 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 vitro functional studies provide so me evidence that the p.Arg58Gln variant may impact protein function (Szczesna 20 01,Szczesna-Cordary 2004, Greenberg 2009, Greenberg 2010, Mettikolla 2011, Wang 2013). In summary, this variant meets criteria to be classified as pathogenic fo r HCM in an autosomal dominant manner. ACMG/AMP Criteria applied: PS4; PP1_Stron g; PM2; PS3_Moderate; PP3. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 21, 2022

The p.R58Q pathogenic mutation (also known as c.173G>A), located in coding exon 4 of the MYL2 gene, results from a G to A substitution at nucleotide position 173. The arginine at codon 58 is replaced by glutamine, an amino acid with highly similar properties. This alteration has been reported in multiple individuals with hypertrophic cardiomyopathy (HCM) or from HCM cohorts (Flavigny J et al. J. Mol. Med., 1998 Mar;76:208-14; Kabaeva ZT et al. Eur. J. Hum. Genet., 2002 Nov;10:741-8; Richard P et al. Circulation, 2003 May;107:2227-32; Mörner S et al. J. Mol. Cell. Cardiol., 2003 Jul;35:841-9; Lopes LR et al. Heart, 2015 Feb;101:294-301; Walsh R et al. Genet Med . 2017 02;19(2):192-203; Yin K et al. Mol Genet Genomics. 2019 Oct;294(5):1241-1249; Burstein DS et al. Pediatr Res. 2021 05;89(6):1470-1476). This variant has been reported to segregate with HCM in several affected members from different families (Flavigny J et al. J. Mol. Med., 1998 Mar;76:208-14; Mörner S et al. J. Mol. Cell. Cardiol., 2003 Jul;35:841-9; Yin K et al. Mol Genet Genomics. 2019 Oct;294(5):1241-1249). In addition, a number of in vitro studies suggested that this variant would abolish calcium binding and alter the contraction kinetics of cardiac muscle (Szczesna D et al. J. Biol. Chem., 2001 Mar;276:7086-92; Greenberg MJ et al. J. Mol. Cell. Cardiol., 2009 Jan;46:108-15; Greenberg MJ et al. Proc. Natl. Acad. Sci. U.S.A., 2010 Oct;107:17403-8; Wang Y et al. J. Mol. Biol., 2006 Aug;361:286-99; Mettikolla P et al. J. Theor. Biol., 2011 Sep;284:71-81; Wang L et al. J. Mol. Cell. Cardiol., 2013 Sep;62:153-63). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.35
CardioboostCm	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.080
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.42	T;.
Eigen	Uncertain	0.33
Eigen_PC	Uncertain	0.44
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.95	D;D
M_CAP	Pathogenic	0.51	D
MetaRNN	Pathogenic	0.83	D;D
MetaSVM	Benign	-0.35	T
MutationAssessor	Benign	-0.65	N;.
MutationTaster	Benign	1.0	A;A
PrimateAI	Pathogenic	0.80	T
PROVEAN	Benign	-2.0	N;N
REVEL	Uncertain	0.57
Sift	Benign	0.14	T;T
Sift4G	Benign	0.33	T;T
Polyphen		1.0	D;.
Vest4		0.89
MVP		0.88
MPC		1.1
ClinPred		0.80	D
GERP RS		4.9
Varity_R		0.85
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: rs104894369; hg19: chr12-111352091;