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NM_000258.3(MYL3):c.427G>A (p.Glu143Lys) AND Hypertrophic cardiomyopathy 8

Germline classification:
Conflicting interpretations of pathogenicity (5 submissions)
Last evaluated:
Apr 14, 2022
Review status:
criteria provided, conflicting classifications
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000015107.29

Allele description [Variation Report for NM_000258.3(MYL3):c.427G>A (p.Glu143Lys)]

NM_000258.3(MYL3):c.427G>A (p.Glu143Lys)

Gene:
MYL3:myosin light chain 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.31
Genomic location:
Preferred name:
NM_000258.3(MYL3):c.427G>A (p.Glu143Lys)
Other names:
p.E143K:GAG>AAG
HGVS:
  • NC_000003.12:g.46859529C>T
  • NG_007555.2:g.27641G>A
  • NM_000258.3:c.427G>AMANE SELECT
  • NP_000249.1:p.Glu143Lys
  • NP_000249.1:p.Glu143Lys
  • LRG_395t1:c.427G>A
  • LRG_395:g.27641G>A
  • LRG_395p1:p.Glu143Lys
  • NC_000003.11:g.46901019C>T
  • NM_000258.2:c.427G>A
  • P08590:p.Glu143Lys
  • c.427G>A
  • p.(Glu143Lys)
Protein change:
E143K; GLU143LYS
Links:
Leiden Muscular Dystrophy (MYL3): MYL3_00009; UniProtKB: P08590#VAR_019843; OMIM: 160790.0003; dbSNP: rs104893750
NCBI 1000 Genomes Browser:
rs104893750
Molecular consequence:
  • NM_000258.3:c.427G>A - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
functional variant [Sequence Ontology: SO:0001536]

Condition(s)

Name:
Hypertrophic cardiomyopathy 8
Synonyms:
CARDIOMYOPATHY, HYPERTROPHIC, MID-LEFT VENTRICULAR CHAMBER TYPE, 1; Familial hypertrophic cardiomyopathy 8; MYL3-Related Familial Hypertrophic Cardiomyopathy
Identifiers:
MONDO: MONDO:0012111; MedGen: C1837471; OMIM: 608751

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000035364OMIM
no assertion criteria provided
Pathogenic
(Sep 1, 2011)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000045775Leiden Muscular Dystrophy (MYL3)
no classification provided
not providedgermlinecuration

PubMed (1)
[See all records that cite this PMID]

SCV000885788ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)
Uncertain significance
(Apr 6, 2022)
germlineclinical testing

Citation Link,

SCV003836291Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Apr 14, 2022)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV003920244Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Mar 30, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only, curation
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Furthering the link between the sarcomere and primary cardiomyopathies: restrictive cardiomyopathy associated with multiple mutations in genes previously associated with hypertrophic or dilated cardiomyopathy.

Caleshu C, Sakhuja R, Nussbaum RL, Schiller NB, Ursell PC, Eng C, De Marco T, McGlothlin D, Burchard EG, Rame JE.

Am J Med Genet A. 2011 Sep;155A(9):2229-35. doi: 10.1002/ajmg.a.34097. Epub 2011 Aug 5.

PubMed [citation]
PMID:
21823217
PMCID:
PMC3158811

Myosin light chain mutation causes autosomal recessive cardiomyopathy with mid-cavitary hypertrophy and restrictive physiology.

Olson TM, Karst ML, Whitby FG, Driscoll DJ.

Circulation. 2002 May 21;105(20):2337-40.

PubMed [citation]
PMID:
12021217
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000035364.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

Olson et al. (2002) reported a consanguineous family in which 3 sibs had presented with childhood-onset CMH characterized by midcavitary left-ventricular hypertrophy (CMH8; 608751). Both parents had completely normal hearts in their 40s. Mutation screening in a surviving affected sib revealed a homozygous missense G-to-A point mutation at codon 143 of the MYL3 gene, resulting in a glutamic acid-to-lysine (E143K) substitution. Heterozygotes had normal hearts. Sequence alignment of myosin essential light chains demonstrated high conservation of glutamic acid at position 143 across species. The E143K mutation was absent from 150 normal control DNA samples. The authors concluded that this was a true autosomal recessive form of CMH8.

In a 22-year-old woman from El Salvador with cardiomyopathy, Caleshu et al. (2011) sequenced the exons and exon-intron boundaries of 8 known cardiomyopathy-associated genes and identified homozygosity for the E143K mutation in the MYL3 gene. The patient was also found to be heterozygous for a G57E polymorphism in the MYL2 gene (160781); her asymptomatic 45-year-old mother, who had a normal transthoracic echocardiogram, electrocardiogram, and physical examination, was heterozygous for both the E143K mutation in MYL3 and the G57E polymorphism in MYL2. The patient, who had a prior diagnosis of childhood asthma, presented with worsening dyspnea and fatigue over the previous year, and transthoracic echocardiogram revealed severe biatrial enlargement with preserved biventricular systolic function and no left ventricular hypertrophy or valvular disease; Doppler evaluation suggested advanced left ventricular diastolic dysfunction. Left and right heart catheterization showed elevated filling pressures bilaterally, with a prominent y-descent, a suggestion of a 'dip-and-plateau,' and ventricular concordance, all features described in restrictive cardiomyopathy (RCM). Right ventricular endomyocardial biopsy revealed marked myocyte hypertrophy and myofiber disarray with interstitial fibrosis. The patient went on to develop recurrent syncope and had an automatic implantable cardiac defibrillator placed; she underwent orthotopic heart transplantation 6 months after diagnosis with cardiomyopathy.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Leiden Muscular Dystrophy (MYL3), SCV000045775.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000885788.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The p.Glu143Lys variant (rs104893750) has been previously identified in two families of Latin American ethnicity (Caleshu 2011 and Olson 2002), and in a large cohort of patients referred for testing due to cardiomyopathy (Walsh 2017). Pathogenic variants in MYHL3 are typically associated with dominantly inherited hypertrophic cardiomyopathy (HCM8; MIM: 608751). However, in the two families described in Caleshu et al (2011) and Olson et al (2002), affected individuals were homozygous for the p.Glu143Lys, whereas a total of five heterozygous carriers between both families (ages 7-70) were clinically unaffected. Consanguinity was confirmed in the family described in Olsen et al (2002), and the authors suggested the p.Glu143Lys variant acts in a recessive manner, likely through a mechanism distinct from other dominantly inherited pathogenic MYL3 variants. At least one functional study of several pathogenic variants in MYL3, including p.Glu143Lys, revealed similar defects compared to wild-type in the binding of variant MYL3 protein to myosin heavy chain. However, these functional observations are difficult to interpretation, as the exact molecular mechanisms underlying the physiological defects associated with MYL3 remain unknown. Furthermore, to our knowledge, no other recessive-acting pathogenic alleles have been identified in MYL3, and all clinical laboratories submitting to ClinVar also classify the p.Glu143Lys variant as being of uncertain clinical significance (Variation ID: 14063). The glutamic acid at codon 143 is highly conserved considering 14 species up to C. elegans (Alamut software v2.9), and computational analyses suggest this variant has a significant effect on MYL3 protein structure/function (SIFT: damaging, PolyPhen2: possibly damaging, and Mutation Taster: disease causing). In summary, based on the available information, the clinical significance of the p.Glu143Lys variant cannot be determined with certainty.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV003836291.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV003920244.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

MYL3 NM_000258.2 exon 4 p.Glu143Lys (c.427G>A): This variant has been reported in the literature in the heterozygous state in at least 5 individuals with HCM, in the homozygous state in two siblings with early-onset HCM, and in the homozygous state in one individual with RCM (Olson 2002 PMID:12021217, Caleshu 2011 PMID:21823217, Gomez 2014 PMID:25342278, McNamara 2017 PMID:28658286, Walsh 2017 PMID:27532257). Of note, at least one of these individuals was also identified to carry an additional clinically significant cardiogenetic variant (McNamara 2017 PMID:28658286). This variant is present in 0.008% (3/34420) of Latino alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/3-46901019-C-T) and is present in ClinVar, with multiple labs classifying this variant as pathogenic or likely pathogenic (Variation ID:14063). Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. An in vitro functional study on rat cardiomyocytes demonstrated significantly reduced binding affinity of this protein to myosin heavy chains when compared to the wildtype, supporting that this variant impacts the protein (Lossie 2012 PMID:22131351). However, this study may not accurately represent in vivo biological function. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 23, 2024