3-46860813-G-T

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 8P and 1B. PM1PM2PM5PP3_ModerateBS1_Supporting

The NM_000258.3(MYL3):c.170C>A(p.Ala57Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000118 in 1,614,056 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic 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. A57G) has been classified as Likely pathogenic.

Frequency

Genomes: 𝑓 0.00013 ( 1 hom., cov: 32)

Exomes 𝑓: 0.00012 ( 0 hom. )

Consequence

MYL3
NM_000258.3 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2U:15B:1

Conservation

PhyloP100: 8.15

Variant links:

Genes affected

MYL3 (HGNC:7584): (myosin light chain 3) MYL3 encodes myosin light chain 3, an alkali light chain also referred to in the literature as both the ventricular isoform and the slow skeletal muscle isoform. Mutations in MYL3 have been identified as a cause of mid-left ventricular chamber type hypertrophic cardiomyopathy. [provided by RefSeq, Jul 2008]

MYL3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

PM1

In a domain EF-hand 1 (size 37) in uniprot entity MYL3_HUMAN there are 8 pathogenic changes around while only 0 benign (100%) in NM_000258.3

PM2

Very rare variant in population databases, with high coverage;

PM5

Other missense variant is known to change same aminoacid residue: Variant chr3-46860813-G-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 31780.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=2, Uncertain_significance=8, Likely_pathogenic=3, not_provided=1}.

PP3

MetaRNN computational evidence supports a deleterious effect, 0.86

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.000116 (170/1461860) while in subpopulation MID AF= 0.00156 (9/5768). AF 95% confidence interval is 0.000814. There are 0 homozygotes in gnomad4_exome. There are 101 alleles in male gnomad4_exome subpopulation. Median coverage is 33. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYL3	NM_000258.3 linkuse as main transcript	c.170C>A	p.Ala57Asp	missense_variant	3/7	ENST00000292327.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYL3	ENST00000292327.6 linkuse as main transcript	c.170C>A	p.Ala57Asp	missense_variant	3/7	1	NM_000258.3	P1

Frequencies

GnomAD3 genomes

AF:

0.000132

AC:

AN:

152078

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000242

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000524

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000882

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.000171

AC:

AN:

251470

Hom.:

AF XY:

0.000221

AC XY:

AN XY:

135914

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000289

Gnomad ASJ exome

AF:

0.000397

Gnomad EAS exome

AF:

0.000489

Gnomad SAS exome

AF:

0.000555

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000967

Gnomad OTH exome

AF:

0.000163

GnomAD4 exome

AF:

0.000116

AC:

170

AN:

1461860

Hom.:

Cov.:

AF XY:

0.000139

AC XY:

101

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.0000299

Gnomad4 AMR exome

AF:

0.0000224

Gnomad4 ASJ exome

AF:

0.000230

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.000626

Gnomad4 FIN exome

AF:

0.0000187

Gnomad4 NFE exome

AF:

0.0000647

Gnomad4 OTH exome

AF:

0.000281

GnomAD4 genome

AF:

0.000131

AC:

AN:

152196

Hom.:

Cov.:

AF XY:

0.000108

AC XY:

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.0000241

Gnomad4 AMR

AF:

0.000523

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000882

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.000200

Hom.:

Bravo

AF:

0.000128

ExAC

AF:

0.000115

AC:

EpiCase

AF:

0.000327

EpiControl

AF:

0.000237

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2Uncertain:15Benign:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Hypertrophic cardiomyopathy

Uncertain:4Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 23, 2022	The p.Ala57Asp variant in MYL3 has been reported in heterozygous state in at least 4 individuals with hypertrophic cardiomyopathy (Fokstuen 2011 PMID: 21239446, Almaas 2013 PMID: 23426552, Berge 2014 PMID: 24111713, Norrish 2019 PMID: 31006259, LMM data); two of these individuals were heterozygous for pathogenic variants in another gene. This variant has been identified in homozygous state in at least 2 individuals with cardiomyopathy (Osborn 2021 PMID: 33288880, LMM data). It has also been identified in 0.06% (17/30616) of South Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant has also been reported in ClinVar (Variation ID 43121). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In vitro functional studies provide conflicting evidence regarding the impact of this variant on protein function (Ma 2018 PMID: 29914921 , Osborn 2021 PMID: 33288880); however, these types of assays may not accurately represent biological function. Another variant involving this codon (p.Ala57Gly) has been identified in individuals with hypertrophic cardiomyopathy and is classified as uncertain significance by this laboratory. In summary, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PP3, BP5. -
Uncertain significance, criteria provided, single submitter	research	Genetics and Genomics Program, Sidra Medicine	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jan 11, 2024	This missense variant replaces alanine with aspartic acid at codon 57 of the MYL3 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). A functional study with human-induced pluripotent stem cells has shown that this variant has no significant impact on MYL3 protein as determined by gene expression, sarcomere structure, cell size, contractility, action potentials and calcium handling (PMID: 29914921). However, another study with zebrafish knockdown model has shown that this variant is unable to rescue the compromised cardiac function as wild-type MYL3 does (PMID: 33288880). This variant has been reported in multiple individuals affected with hypertrophic cardiomyopathy (PMID: 21239446, 23426552, 24111713, 27483260, 27574918, 33288880, 34137518), including three unrelated homozygotes (PMID: 27574918, 33288880, 34137518). This variant has also been identified in 46/282810 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, this is a variant with uncertain functional impact that has been observed in the control population as well as in affected individuals. 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. -
Likely benign, criteria provided, single submitter	research	Agnes Ginges Centre for Molecular Cardiology, Centenary Institute	Jun 19, 2018	The MYL3 Ala57Asp has been previously identified in HCM cases (Jaafar N, et al., 2016; Almaas VM, et al., 2013; Vazquez-Alvarez MC, et al., 2012; Fokstuen S et al., 2011; Calore C, et al., 2011; Choi JO, et al., 2010). The cases reported by Vazquez-Alvarez MC, et al. (2012) included a prenatal HCM case, however the patient was also diagnosed with Noonan syndrome. An iPSC-CM model showed that both heterozygous and homozygous cardiac cells did not produce an HCM phenotype (Ma N, et al., 2018). Interestingly a different change at this position (Ala57Gly) has been reported in multiple HCM cases, suggesting that an amino acid substitution at this site may not be tolerated. Computational tools SIFT, PolyPhen2 and MutationTaster predict this variant to have a deleterious effect. The variant is present in the Genome Aggregation Database (http://gnomad.broadinstitute.org/), at an allele frequency of 0.0001588, which is higher then expected for HCM. We identified this variant in an HCM patient with a family history of HCM. A second variant (ACTC1 Ala323Val) was also identified in this patient. The ACTC1 variant was found to segregate to an affected fourth degree relative but MYL3 Ala57Asp did not segregate. The variant has been found to segregate with disease in two homozygous siblings reported by LMM (ClinVar: SCV000208872). In summary, based on the lack of phenotype in iPSC-CM, high allele frequency and non-segregation in affected family members, we classify MYL3 Ala57Asp (in the heterozygous form) as "likely benign". -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Jan 29, 2024	This sequence change replaces alanine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 57 of the MYL3 protein (p.Ala57Asp). This variant is present in population databases (rs139794067, gnomAD 0.06%). This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 21239446, 23426552, 24111713, 27483260). ClinVar contains an entry for this variant (Variation ID: 43121). 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 does not substantially affect MYL3 function (PMID: 29914921). 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. -

not provided

Pathogenic:1Uncertain:3

Uncertain significance, no assertion criteria provided	provider interpretation	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Jun 29, 2016	MYL3 p.Ala57Asp (c.170C>A) (NM_000258.1) There is moderate case data with some segregation demonstrated, but the variant is also seen at relatively high frequency in population databases and has been seen in combination with a pathogenic variant and in a homozygous state in an unaffected individual. We consider this conflicting data and deem the variant to be a variant of uncertain significance. We do not feel that this variant is suitable for assessing risk in healthy relatives ("predictive genetic testing"). We have seen this variant in an individual with HCM. Testing was performed by Familion. The variant has been seen in at least 5 unrelated cases of HCM (not including this patient's family). There is conflicting case data. This variant has been reported in 1 individual with HCM by Fokstuen et al., 2011, and in 1 individual with HCM by Almaas et al., 2013. It has also been reported in a Korean family, segregating with disease in 5 individuals with HCM by Choi et al., 2010. Controls/Population data: The variant has not been seen in 400 Familion laboratory controls. The variant was reported online in 14 of 60,669 (0.023%) individuals in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/), which currently includes variant calls on ~64,000 individuals of European, African, Latino and Asian descent (as of 6/25/16). Specifically, the variant was observed in following ethnicities European (Non-Finnish) 5/33,342; East Asian 3/4,323; Latino 1/5,787; South Asian 5/8,256. The phenotype of those individuals is not publicly available. The dataset is comprised of multiple cohorts, some of which were recruited from the general population, others were enriched for common cardiovascular disease. -
Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Mar 10, 2022	BS1, PP3 -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	May 03, 2023	In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Functional studies using human induced pluripotent stem cell (iPSC) lines demonstrated that p.(A57D) expressed in the heterozygous and homozygous state did not produce an HCM phenotype (PMID: 29914921); This variant is associated with the following publications: (PMID: 29687901, 24111713, 27483260, 21239446, 27574918, 28971120, 28518168, 29914921, 30624779, 31006259, 23426552, 31019283, 33288880, 34636345, 34509299, 34137518, 33935716, 29710196, 26779504, 29343803, 35653365) -

Hypertrophic cardiomyopathy 8

Pathogenic:1Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	Nov 21, 2018	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago	Mar 30, 2021	MYL3 NM_000258.2 exon 3 p.Ala57Asp (c.170C>A): This variant has been reported in the literature in several individuals with HCM (Fokstuen 2011 PMID:21239446, Almaas 2013 PMID:23426552, Berge 2014 PMID:24111713, Jaafar 2015 PMID:26779504, Rubatta 2016 PMID:27483260, Dejgaard 2017 PMID:28971120). This variant is present in 0.05% (17/30616) of South Asian alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/3-46902303-G-T) and is present in ClinVar (Variation ID:43121). Please note, disease causing variants may be present in control databases at low frequencies, reflective of the general population, autosomal recessive inheritance carrier status, and/or variable expressivity. Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. Additionally, another variant at the same amino acid (p.Ala57Gly) has been reported in association with disease. In summary, data on this variant is highly suspicious for disease, but requires further evidence for pathogenicity. Therefore, this variant is classified as likely pathogenic. -

Cardiomyopathy

Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 17, 2023	This missense variant replaces alanine with aspartic acid at codon 57 of the MYL3 protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. A functional study with human-induced pluripotent stem cells has shown that this variant has no significant impact on MYL3 protein as determined by gene expression, sarcomere structure, cell size, contractility, action potentials and calcium handling (PMID: 29914921). However, another study with zebrafish knockdown model has shown that this variant is unable to rescue the compromised cardiac function as wild-type MYL3 does (PMID: 33288880). This variant has been reported in heterozygous multiple individuals affected with hypertrophic cardiomyopathy (PMID: 21239446, 23426552, 24111713, 27483260, 27574918, 33288880, 34137518, 37431535), as well as in five unrelated homozygous individuals (PMID: 27574918, 33288880, 34137518, 37431535). This variant has also been identified in 46/282810 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, this is a variant with uncertain functional impact that has been observed in the control population as well as in affected individuals. 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	Dec 03, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	Nov 30, 2015	- -

Long QT syndrome

Uncertain:1

Uncertain significance, criteria provided, single submitter

research

Dept of Medical Biology, Uskudar University

Jan 08, 2024

Criteria: PP2, PP3, BS3 -

Primary familial hypertrophic cardiomyopathy

Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Blueprint Genetics

Jul 07, 2014

- -

Cardiovascular phenotype

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 01, 2023

The p.A57D variant (also known as c.170C>A), located in coding exon 3 of the MYL3 gene, results from a C to A substitution at nucleotide position 170. The alanine at codon 57 is replaced by aspartic acid, an amino acid with dissimilar properties. This alteration has been detected in individuals from hypertrophic cardiomyopathy (HCM) cohorts (Fokstuen S et al. J Med Genet. 2011;48:572-6; Almaas VM et al. Europace. 2013;15:1319-27; Berge KE et al. Clin Genet. 2014;86:355-60; Rubattu S et al. Int J Mol Sci, 2016 Jul;17:1239). This variant has also been identified in two unrelated homozygous individuals with HCM, both of whom had consanguineous parents and family histories of sudden death; heterozygous family members were reportedly unaffected, and one proband had three homozygous young children who had normal echocardiograms at the time of evaluation (Jaafar N et al. Genet Test Mol Biomarkers. 2016;20:674-679; Osborn DPS et al. Genet Med, 2021 Apr;23:787-792). In addition, multiple probands with this variant have had additional pathogenic variants in other HCM-associated genes (Ambry internal data; Broendberg AK et al. Eur J Hum Genet, 2018 03;26:303-313). Furthermore, this variant did not demonstrate a deleterious impact in several functional assays performed in human induced pluripotent stem cells heterozygous or homozygous for this alteration, although zebrafish models showed only partial rescue; given that the molecular mechanisms underlying HCM are not fully understood, the physiological significance of these results is unclear (Ma N et al. Circulation. 2018;138:2666-2681; Osborn DPS et al. Genet Med, 2021 Apr;23:787-792). Based on data from gnomAD, the frequency for this variant is above the maximum credible frequency for a disease-causing variant in this gene based on internally established thresholds (Karczewski et al. Nature. 2020 May;581(7809):434-443; Whiffin et al. Genet Med. 2017 10;19:1151-1158). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.99

CardioboostCm

Uncertain

0.38

BayesDel_addAF

Uncertain

0.089

BayesDel_noAF

Pathogenic

0.24

Cadd

Pathogenic

Dann

Uncertain

1.0

DEOGEN2

Pathogenic

0.83

D;D

Eigen

Pathogenic

1.1

Eigen_PC

Pathogenic

0.90

FATHMM_MKL

Pathogenic

0.98

M_CAP

Pathogenic

0.33

MetaRNN

Pathogenic

0.86

D;D

MetaSVM

Pathogenic

1.0

MutationAssessor

Pathogenic

4.7

H;H

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.74

PROVEAN

Pathogenic

-5.2

D;D

REVEL

Pathogenic

0.89

Sift

Pathogenic

0.0

D;D

Sift4G

Pathogenic

0.0010

D;D

Polyphen

1.0

D;D

Vest4

0.95

MutPred

0.61

Gain of disorder (P = 0.0453);Gain of disorder (P = 0.0453);

MVP

0.91

MPC

1.4

ClinPred

0.84

GERP RS

4.4

Varity_R

0.95

gMVP

0.92

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over