rs397516881

Positions:

• chr10-119676917-G-A

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2 PP3_Moderate PP5_Very_Strong

The NM_004281.4(BAG3):​c.1363G>A​(p.Glu455Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. E455E) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BAG3 NM_004281.4 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:6
• Conservation: PhyloP100: 9.48

Genes affected

BAG3 (HGNC:939): (BAG cochaperone 3) BAG proteins compete with Hip for binding to the Hsc70/Hsp70 ATPase domain and promote substrate release. All the BAG proteins have an approximately 45-amino acid BAG domain near the C terminus but differ markedly in their N-terminal regions. The protein encoded by this gene contains a WW domain in the N-terminal region and a BAG domain in the C-terminal region. The BAG domains of BAG1, BAG2, and BAG3 interact specifically with the Hsc70 ATPase domain in vitro and in mammalian cells. All 3 proteins bind with high affinity to the ATPase domain of Hsc70 and inhibit its chaperone activity in a Hip-repressible manner. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.937
• PP5: Variant 10-119676917-G-A is Pathogenic according to our data. Variant chr10-119676917-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 44778.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAG3	NM_004281.4	c.1363G>A	p.Glu455Lys	missense_variant	4/4	ENST00000369085.8
BAG3	XM_005270287.2	c.1360G>A	p.Glu454Lys	missense_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAG3	ENST00000369085.8	c.1363G>A	p.Glu455Lys	missense_variant	4/4	1	NM_004281.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Blueprint Genetics	Feb 21, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 17, 2021	Not observed in large population cohorts (Lek et al., 2016); 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: 21459883, 25008357, 22337857, 27474739, 28737513, 31737537, 32458740, 32472079) -

Myofibrillar myopathy 6 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

Mar 25, 2024

- -

Myofibrillar myopathy 6;C3151293:Dilated cardiomyopathy 1HH Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Dec 19, 2023

This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 455 of the BAG3 protein (p.Glu455Lys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with dilated cardiomyopathy (PMID: 2159883, 25008357). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 44778). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt BAG3 protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic. -

Primary dilated cardiomyopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Aug 07, 2017

The p.Glu455Lys variant in BAG3 has been identified in 4 individuals with DCM, s egregated with disease in 6 affected relatives from 3 families (Villard 2011, Fr anaszczyk 2014, LMM unpublished data), and was absent from large population stud ies. Additionally, a mouse model harboring this variant presented with DCM (Fang 2017). In summary, this variant meets criteria to be classified as pathogenic f or DCM in an autosomal dominant manner based upon segregation studies, absence f rom controls, and functional evidence. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 26, 2020

The p.E455K pathogenic mutation (also known as c.1363G>A), located in coding exon 4 of the BAG3 gene, results from a G to A substitution at nucleotide position 1363. The glutamic acid at codon 455 is replaced by lysine, an amino acid with similar properties. This alteration has been reported in individuals with dilated cardiomyopathy (DCM), and shown to segregate with disease in multiple families (Villard E et al. Eur Heart J. 2011;32(9):1065-76; Dominguez et al. J Am Coll Cardiol. 2018;72(20):2471-2481; Franaszczyk M et al. J Transl Med. 2014;12:192). Furthermore, mice with cardiac-specific BAG3 knockdown or cardiac-specific BAG3-E455K knock-in developed DCM; decreased levels of small heat shock proteins were observed, and the E455K-BAG3 protein demonstrated defective interaction with HSP70, consistent with loss-of-function as the mechanism of disease (Fang X et al. J. Clin. Invest., 2017 Aug;127:3189-3200). In addition, other loss of function alterations in the BAG domain have been reported with strong segregation in numerous cases of familial DCM (Norton N et al. Am J Hum Genet. 2011;88(3):273-82; Villard E et al. Eur Heart J. 2011;32(9):1065-76; Franaszczyk M et al. J Transl Med. 2014;12:192). 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	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.46	D
BayesDel_noAF	Pathogenic	0.43
CADD	Pathogenic	30
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.90	D
Eigen	Pathogenic	0.92
Eigen_PC	Pathogenic	0.90
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.97	D
M_CAP	Uncertain	0.097	D
MetaRNN	Pathogenic	0.94	D
MetaSVM	Uncertain	0.78	D
MutationAssessor	Uncertain	2.9	M
MutationTaster	Benign	1.0	D
PrimateAI	Pathogenic	0.86	D
PROVEAN	Uncertain	-3.7	D
REVEL	Pathogenic	0.86
Sift	Uncertain	0.0010	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		1.0
MutPred		0.68		Gain of methylation at E455 (P = 0.0138);
MVP		0.99
MPC		0.077
ClinPred		0.99	D
GERP RS		5.6
Varity_R		0.95
gMVP		0.67

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: rs397516881; hg19: chr10-121436429; COSMIC: COSV64841649; COSMIC: COSV64841649;