rs587780290

chr15-42410646-G-A

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM5 PP3_Strong PP5_Very_Strong

The NM_000070.3(CAPN3):c.2243G>A(p.Arg748Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,734 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R748G) has been classified as Pathogenic.

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000011 (0 hom.)
• Consequence: CAPN3 NM_000070.3 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:15
• Conservation: PhyloP100: 10.0

Genes affected

CAPN3 (HGNC:1480): (calpain 3) Calpain, a heterodimer consisting of a large and a small subunit, is a major intracellular protease, although its function has not been well established. This gene encodes a muscle-specific member of the calpain large subunit family that specifically binds to titin. Mutations in this gene are associated with limb-girdle muscular dystrophies type 2A. Alternate promoters and alternative splicing result in multiple transcript variants encoding different isoforms and some variants are ubiquitously expressed. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 9 uncertain in NM_000070.3
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr15-42410645-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 548138.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.968
• PP5: Variant 15-42410646-G-A is Pathogenic according to our data. Variant chr15-42410646-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 128570.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-42410646-G-A is described in Lovd as [Pathogenic]. Variant chr15-42410646-G-A is described in Lovd as [Pathogenic]. Variant chr15-42410646-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAPN3	NM_000070.3	c.2243G>A	p.Arg748Gln	missense_variant	21/24	ENST00000397163.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAPN3	ENST00000397163.8	c.2243G>A	p.Arg748Gln	missense_variant	21/24	1	NM_000070.3	P2

Frequencies

GnomAD3 genomes AF: 0.0000197 AC: 3 AN: 152022 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000199 AC: 5 AN: 251118 Hom.: 0 AF XY: 0.00000737 AC XY: 1 AN XY: 135726

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000145

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000109 AC: 16 AN: 1461712 Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6 AN XY: 727148

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000179

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000540

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome AF: 0.0000197 AC: 3 AN: 152022 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 74246

Gnomad4 AFR AF: 0.0000242

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000529

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:15

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Autosomal recessive limb-girdle muscular dystrophy type 2A Pathogenic:9

Likely pathogenic, criteria provided, single submitter	reference population	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	Mar 18, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Nov 07, 2013	- -
Pathogenic, no assertion criteria provided	clinical testing	Counsyl	Nov 21, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	This c.2243G>A (p.Arg748Gln) missense variant in CAPN3 gene has been reported in the homozygous or compound heterozygous state in many individuals affected with limb girdle muscular dystrophy (LGMD) (Fanin et al., 2009; Fadaee et al., 2016; Sáenz et al., 2005), and in one affected family it was shown to cosegregate with LGMD (Richard et al., 1997). Experimental studies have shown that this missense substitution reduces CAPN3 catalytic activity as measured by cleavage of an exogenous peptide, which was attributed to an increased rate of autoproteolytic degradation (Garnham et al., 2009). This variant is reported with the allele frequency (0.0051%) in the gnomAD and novel in 1000 genome database. This variant has been submitted to ClinVar with varying interpretations: Pathogenic/ Likely Pathogenic. The amino acid Arg at position 748 is changed to a Gln changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Arg748Gln in CAPN3 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Feb 19, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	May 18, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 07, 2023	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 748 of the CAPN3 protein (p.Arg748Gln). This variant is present in population databases (rs587780290, gnomAD 0.01%). This missense change has been observed in individuals with autosomal recessive limb-girdle muscular dystrophy (PMID: 9150160, 9762961, 9777948, 10330340, 12461690, 15689361, 18563459, 18854869, 19015733, 22443334, 26404900, 27020652, 30028523). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 128570). 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 not expected to disrupt CAPN3 protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects CAPN3 function (PMID: 19226146). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Pathogenic, criteria provided, single submitter	research	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Dec 03, 2018	The homozygous p.Arg748Gln variant in CAPN3 was identified by our study in one individual with limb-girdle muscular dystrophy (LGMD) This variant has been identified in 0.01455% (5/34372) of Latino chromosomes and 0.004166% (1/24006) of African chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs587780290). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. One study that examined a rat model with an analagous protein suggested that this variant affects protein catalytic activity (PMID: 19226146). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enought to determine pathogenicity. The p.Arg748Gln variant in CAPN3 has been reported in many individuals with LGMD in the homozygous and compound heterozygous states in ClinVar and the literature (Variation ID: 128570). This variant segregated with disease in 2 affected relatives from 1 family (PMID: 9150160). There are many reports of individuals with LGMD and this variant (in either the homozygous or compound heterozygous state) in ClinVar and the literature. Animal models in rats have shown that this variant causes LGMD via a deleterious effect on calpain protein catalytic activity (PMID: 19226146). In summary, the p.Arg748Gln variant is pathogenic based off of our findings, multiple reports in ClinVar, and the literature. ACMG/AMP Criteria applied: PM2, PP3, PS3, PP1, PM3_Strong (Richards 2015). -

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 06, 2017	The R748Q variant in the CAPN3 gene has been reported previously in association with limb-girdle muscular dystrophy, type 2A. The affected individuals had onset within the first two decades of life, ranging from 2.5 years to 15 years of age and all had elevated creatine phosphokinase levels (Richards et al., 1997; Fattahi et al., 2017). The R748Q variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The R748Q variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species. Functional studies in rat calpain 2 showed that R748Q, using the alternate nomenclature R628Q, reduced initial enzyme activity and catalytic activity, suggesting R748Q in human CAPN3 is damaging (Garnham et al., 2009). We interpret R748Q as a pathogenic variant. -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Sep 01, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Oct 01, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 10, 2017	- -

Muscular dystrophy, limb-girdle, autosomal dominant 4 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Sep 30, 2023

- -

Abnormality of the musculature Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Kariminejad - Najmabadi Pathology & Genetics Center

Jul 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.53
BayesDel_addAF	Pathogenic	0.19	D
BayesDel_noAF	Pathogenic	0.29
Cadd	Pathogenic	34
Dann	Pathogenic	1.0
DEOGEN2	Benign	0.073	T;.;.;T;.;.;.;.;.;.;.;.
Eigen	Pathogenic	0.80
Eigen_PC	Pathogenic	0.76
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	1.0	D;D;D;D;D;D;.;D;.;D;.;D
M_CAP	Uncertain	0.19	D
MetaRNN	Pathogenic	0.97	D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	-0.028	T
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.74	T
REVEL	Pathogenic	0.72
Sift4G	Pathogenic	0.0	D;D;D;D;D;D;T;T;T;D;T;T
Polyphen		1.0	.;D;D;D;.;.;.;.;.;.;.;.
Vest4		0.96
MutPred		0.92		.;.;.;Gain of disorder (P = 0.1607);.;.;.;.;.;.;.;.;
MVP		0.89
MPC		0.68
ClinPred		0.98	D
GERP RS		4.5
Varity_R		0.88
gMVP		0.87

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: rs587780290; hg19: chr15-42702844; COSMIC: COSV55522473; COSMIC: COSV55522473;