rs193922385

chr11-47349899-G-Achr11-47349899-G-Cchr11-47349899-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3

The NM_000256.3(MYBPC3):c.529C>T(p.Arg177Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000964 in 1,607,078 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R177P) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000099 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000096 (0 hom.)
• Consequence: MYBPC3 NM_000256.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:17 B:1
• Conservation: PhyloP100: 4.75

Genes affected

MYBPC3 (HGNC:7551): (myosin binding protein C3) MYBPC3 encodes the cardiac isoform of myosin-binding protein C. Myosin-binding protein C is a myosin-associated protein found in the cross-bridge-bearing zone (C region) of A bands in striated muscle. MYBPC3 is expressed exclusively in heart muscle and is a key regulator of cardiac contraction. Mutations in this gene are a frequent cause of familial hypertrophic cardiomyopathy. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PP3: MetaRNN computational evidence supports a deleterious effect, 0.813

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYBPC3	NM_000256.3	c.529C>T	p.Arg177Cys	missense_variant	5/35	ENST00000545968.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYBPC3	ENST00000545968.6	c.529C>T	p.Arg177Cys	missense_variant	5/35	5	NM_000256.3	P4
MYBPC3	ENST00000399249.6	c.529C>T	p.Arg177Cys	missense_variant	5/34	5		A2
MYBPC3	ENST00000544791.1	c.529C>T	p.Arg177Cys	missense_variant, NMD_transcript_variant	5/27	5

Frequencies

GnomAD3 genomes AF: 0.0000988 AC: 15 AN: 151796 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000725

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000658

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000132

Gnomad OTH AF: 0.000480

GnomAD3 exomes AF: 0.0000685 AC: 16 AN: 233730 Hom.: 0 AF XY: 0.0000549 AC XY: 7 AN XY: 127454

Gnomad AFR exome AF: 0.000223

Gnomad AMR exome AF: 0.0000905

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000232

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000569

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000962 AC: 140 AN: 1455282 Hom.: 0 Cov.: 31 AF XY: 0.0000954 AC XY: 69 AN XY: 723300

Gnomad4 AFR exome AF: 0.000270

Gnomad4 AMR exome AF: 0.000114

Gnomad4 ASJ exome AF: 0.0000386

Gnomad4 EAS exome AF: 0.0000254

Gnomad4 SAS exome AF: 0.0000118

Gnomad4 FIN exome AF: 0.0000190

Gnomad4 NFE exome AF: 0.000105

Gnomad4 OTH exome AF: 0.0000832

GnomAD4 genome AF: 0.0000988 AC: 15 AN: 151796 Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8 AN XY: 74120

Gnomad4 AFR AF: 0.0000725

Gnomad4 AMR AF: 0.0000658

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000132

Gnomad4 OTH AF: 0.000480

Alfa AF: 0.000190 Hom.: 0

Bravo AF: 0.000113

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000119 AC: 1

ExAC AF: 0.0000579 AC: 7

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:17 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:6

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Sep 07, 2023	Identified in patients with cardiomyopathy in published literature (Miller et al., 2013; Pugh et al., 2014; Walsh et al., 2017; van Waning et al., 2018; Aljeaid et al., 2019; Verdonschot et al., 2020; Burstein et al., 2021; van der Meulen et al., 2022 ); of note, several patients harbored pathogenic or likely pathogenic variants in other cardiomyopathy-related genes; Identified in a family with a history of DCM and congenital heart abnormalities; however, the proband from this family and other affected relatives also harbored a missense variant in the VCL gene, and the most severely affected individuals harbored both the MYBPC3 and VCL variants (Wells et al., 2011); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 21415409, 27532257, 30762279, 25637381, 23299917, 22555271, 28518168, 33782553, 32880476, 32746448, 36178741, 34097875, 24503780, 24062880, 29447731, 23054336) -
Uncertain significance, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Uncertain significance, no assertion criteria provided	provider interpretation	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Oct 24, 2017	Found on postmortem testing of a 17-year-old with a negative autopsy and a history of 2 seizures in one day and then a sudden death a few months later. A 148-gene Arrhythmia and Cardiomyopathy Comprehensive Panel was done by the Invitae laboratory. This included Sudden Death in Epilepsy genes. Results included 3 variants: -p.Thr368Ile (c.1103C>T) in the DSC2 gene -p.Ala647Val (c.1940C>T) in the LAMA4 gene -p.Arg177Cys (c.529C>T) in the MYBPC3 gene p.Arg177Cys (c.529C>T) in exon 5 of the MYBPC3 gene (NM_000256.3) Chromosome location 11:47371450 G / A Based on the information reviewed below, we classify Arg177Cys as a Variant of Uncertain Significance, Probably Benign, concluding that there is not sufficient evidence for its pathogenicity to warrant using it for predictive genetic testing. A different variant at this same location, Arg177His, has been classified in ClinVar as Benign by multiple labs. This variant has previously been reported in at least 3 unrelated families with cardiomyopathy, however in a family with hypertrophic cardiomyopathy there was also a pathogenic truncating variant in MYBPC3, suggesting that the Arg177Cys variant was not the primary cause of disease. LMM in ClinVar reports seeing Arg177Cys in two families with DCM; in one of these families a VUS in the VCL gene was also present. There were no affected relatives who harbored only the Arg177Cys, but there was one relative with DCM who had only the VUS in VCL, suggesting that Arg177Cys failed to segregate with disease (it was present in 3 out of 4 affected family members tested). However, the most severely affected family members each had both the MYBPC3 and VCL variants, so it is possible that they both play a role (Wells et al., 2011). This is a nonconservative amino acid change, resulting in the replacement of a positively-charged Arginine with a polar Cysteine capable of forming disulfide bridges. Arginine at this location is poorly conserved across ~100 vertebrate species for which we have data. It is most frequently changed to another positively-charged amino acid, but Valine and Glutamine are other alternatives. There are no Likely Pathogenic or Pathogenic missense variants listed in ClinVar within 10 amino acids to either side, indicating that this region of the protein might be tolerant of change. LMM’s computational algorithm designed to assess the pathogenicity of variants in MYBPC3 with regard to hypertrophic cardiomyopathy predicted this sequence change to be tolerated. The algorithm has a sensitivity of 94% and a specificity of 89% (PMID: 21310275). This variant was reported in 17 individuals in the gnomAD database, which includes variant calls on ~140,000 individuals of European, African, Latino, South Asian, Ashkenazi, and East Asian descent. Specifically, the variant was observed in 4 East Asian ancestry individuals (for the highest allele frequency: 0.02%), 3 African, 3 Latino, and 7 non-Finnish European ancestry individuals. Overall MAF 0.0065%. Of note: Whiffin et al (2017) proposed that variants with frequency greater than 0.004% are unlikely to be pathogenic in HCM. A different variant at this same location, Arg177His, is present in 305 individuals in gnomAD, with a MAF of 1.3% among individuals with African ancestry and 0.05% among Latinos. 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. The curators made an effort to exclude individuals with severe pediatric diseases. -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Aug 18, 2021	- -

Hypertrophic cardiomyopathy 4 Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	Sep 21, 2015	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Phosphorus, Inc.	Aug 01, 2017	- -
Uncertain significance, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Cardiomyopathy Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Apr 25, 2023	This missense variant replaces arginine with cysteine at codon 177 of the MYBPC3 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in two individuals affected with hypertrophic cardiomyopathy (PMID: 22555271, 30762279). One of these individuals carried a pathogenic truncating variant in the same gene (PMID: 22555271). This variant has been reported in individuals affected with dilated cardiomyopathy (PMID: 24503780, 24062880, 24503780, 27532257, 32746448, 32880476, 36178741). One of these individuals also carried a pathogenic variant in the MYH7 gene (PMID: 36178741). This variant has also been reported in an individual affected with non-compaction cardiomyopathy (PMID: 29447731). This variant has been identified in 17/265018 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	Mar 17, 2023	- -

Hypertrophic cardiomyopathy Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Dec 31, 2023	This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 177 of the MYBPC3 protein (p.Arg177Cys). This variant is present in population databases (rs193922385, gnomAD 0.02%). This missense change has been observed in individual(s) with dilated or hypertrophic cardiomyopathy (PMID: 22555271, 24062880, 27532257, 30762279, 32746448, 32880476, 33782553, 36178741). ClinVar contains an entry for this variant (Variation ID: 36613). 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. 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Dec 13, 2023	This missense variant replaces arginine with cysteine at codon 177 of the MYBPC3 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in two individuals affected with hypertrophic cardiomyopathy (PMID: 22555271, 30762279). One of these individuals carried a pathogenic truncating variant in the same gene (PMID: 22555271). This variant has been reported in individuals affected with dilated cardiomyopathy (PMID: 24503780, 24062880, 24503780, 27532257, 32746448, 32880476, 36178741). One of these individuals also carried a pathogenic variant in the MYH7 gene (PMID: 36178741). This variant has also been reported in an individual affected with non-compaction cardiomyopathy (PMID: 29447731). This variant has been identified in 17/265018 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. -

not specified Uncertain:1 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jul 16, 2018	Variant classified as Uncertain Significance - Favor Benign. The Arg177Cys varia nt in MYBPC3 has been reported in 1 adult with HCM who carried another pathogeni c variant in the MYBPC3 gene(Cardiogenomics) and was identified by our laborator y in 2 individuals with DCM (Wells 2011, LMM unpublished data), one of whom carr ied a second variant of unknown significance in VCL. In 1 family with DCM this v ariant was found to segregate with disease in 2/3 affected family members. The A rg177Cys variant has been identified in 1/8398 European American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs19 3922385). Arginine (Arg) at position 177 not well conserved in mammals or evolut ionarily distant species and the change to cysteine (Cys) was predicted to be be nign using a computational tool clinically validated by our laboratory. This too l's benign prediction is estimated to be correct 89% of the time (Jordan 2011). In addition, another change at the same position (Arg177His) is present in 1% of the general population (42/4088 African American chromosomes, NHLBI Exome Seque ncing Project), suggesting that changes at this position may not affect the prot ein. In summary, while these data argue against a disease-causing role when pres ent in isolation, a modifying effect cannot be ruled out and additional studies are needed to fully establish the clinical significance of this variant. -
Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 11, 2023	Variant summary: MYBPC3 c.529C>T (p.Arg177Cys) results in a non-conservative amino acid change located in the Immunoglobulin subtype domain (IPR003599) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 6.8e-05 in 233730 control chromosomes in gnomAD. This frequency is not significantly higher than estimated for a pathogenic variant in MYBPC3 causing Hypertrophic Cardiomyopathy (6.8e-05 vs 0.001), allowing no conclusion about variant significance. However, another variant at the same residue (p.Arg177His) is present at allele frequency of 1.3% in African subpopulation in gnomAD, strongly suggesting it to be a likely benign polymorphism, thus the residue p.Arg177 may not be critical for protein function. c.529C>T has been reported in the literature in individuals affected with Hypertrophic Cardiomyopathy or Dilated Cardiomyopathy (example: Kindel_2012, Wells_2011, Waning_2018, Alijeaid_2019, Verdonschot_2020, Bursetein_2021, Suay-Corredara_2021). These data do not allow any conclusion about variant significance. Co-occurrences with other pathogenic variants have been reported in our internal data or publications (MYPBC3 c.3811C>T, p.R1271*; MYPBC3 c.1235_1236delTT, p.Ile411_Phe412insTer; RAF1 c.769T>C, p.Ser257Pro) (Kindel_2012, Alijeaid_2019), providing supporting evidence for a benign role. Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as likely benign. -

Left ventricular noncompaction 10 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Phosphorus, Inc.

Aug 01, 2017

- -

Primary familial hypertrophic cardiomyopathy Uncertain:1

Uncertain significance, no assertion criteria provided

research

CSER _CC_NCGL, University of Washington

Jun 01, 2014

- -

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 04, 2022

The c.529C>T (p.R177C) alteration is located in exon 5 (coding exon 5) of the MYBPC3 gene. This alteration results from a C to T substitution at nucleotide position 529, causing the arginine (R) at amino acid position 177 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.37
CardioboostCm	Benign	0.049
BayesDel_addAF	Benign	-0.0091	T
BayesDel_noAF	Uncertain	0.040
Cadd	Uncertain	26
Dann	Pathogenic	1.0
DEOGEN2	Uncertain	0.65	D;T;T
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.53
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Pathogenic	0.98	D;D;D
M_CAP	Pathogenic	0.53	D
MetaRNN	Pathogenic	0.81	D;D;D
MetaSVM	Benign	-0.37	T
MutationAssessor	Benign	1.4	L;.;.
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Benign	0.43	T
PROVEAN	Pathogenic	-4.7	D;D;D
REVEL	Uncertain	0.53
Sift	Uncertain	0.0010	D;D;D
Sift4G	Pathogenic	0.0	D;D;D
Polyphen		1.0	D;.;.
Vest4		0.87
MVP		0.89
MPC		0.90
ClinPred		0.73	D
GERP RS		4.8
Varity_R		0.37
gMVP		0.75

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: rs193922385; hg19: chr11-47371450;