rs146923842

chr15-42410660-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM1 PM5 PP5 BP4

The NM_000070.3(CAPN3):c.2257G>A(p.Asp753Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000912 in 1,613,422 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign 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. D753K?) has been classified as Pathogenic.

• Frequency:
  • Genomes: 𝑓 0.00076 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00093 (2 hom.)
• Consequence: CAPN3 NM_000070.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:13
• Conservation: PhyloP100: 5.79

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 Uncertain_significance. Variant got 4 ACMG points.

• PM1: In a helix (size 9) in uniprot entity CAN3_HUMAN there are 17 pathogenic changes around while only 0 benign (100%) in NM_000070.3
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr15-42410660-G-AA is described in ClinVar as [Pathogenic]. Clinvar id is 1285364.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP5: Variant 15-42410660-G-A is Pathogenic according to our data. Variant chr15-42410660-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 281081.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=11, Likely_pathogenic=2}. Variant chr15-42410660-G-A is described in Lovd as [Pathogenic]. Variant chr15-42410660-G-A is described in Lovd as [Pathogenic]. Variant chr15-42410660-G-A is described in Lovd as [Likely_pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.08944106).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAPN3	NM_000070.3	c.2257G>A	p.Asp753Asn	missense_variant	21/24	ENST00000397163.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAPN3	ENST00000397163.8	c.2257G>A	p.Asp753Asn	missense_variant	21/24	1	NM_000070.3	P2

Frequencies

GnomAD3 genomes AF: 0.000756 AC: 115 AN: 152052 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00262

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.0000944

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000882

Gnomad OTH AF: 0.00144

GnomAD3 exomes AF: 0.000785 AC: 197 AN: 250800 Hom.: 0 AF XY: 0.000797 AC XY: 108 AN XY: 135558

Gnomad AFR exome AF: 0.0000618

Gnomad AMR exome AF: 0.00110

Gnomad ASJ exome AF: 0.000795

Gnomad EAS exome AF: 0.000218

Gnomad SAS exome AF: 0.000131

Gnomad FIN exome AF: 0.000277

Gnomad NFE exome AF: 0.00116

Gnomad OTH exome AF: 0.000653

GnomAD4 exome AF: 0.000929 AC: 1357 AN: 1461252 Hom.: 2 Cov.: 32 AF XY: 0.000898 AC XY: 653 AN XY: 726948

Gnomad4 AFR exome AF: 0.0000896

Gnomad4 AMR exome AF: 0.000986

Gnomad4 ASJ exome AF: 0.000880

Gnomad4 EAS exome AF: 0.000101

Gnomad4 SAS exome AF: 0.000151

Gnomad4 FIN exome AF: 0.000318

Gnomad4 NFE exome AF: 0.00106

Gnomad4 OTH exome AF: 0.000961

GnomAD4 genome AF: 0.000756 AC: 115 AN: 152170 Hom.: 0 Cov.: 31 AF XY: 0.000753 AC XY: 56 AN XY: 74392

Gnomad4 AFR AF: 0.000145

Gnomad4 AMR AF: 0.00262

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.0000944

Gnomad4 NFE AF: 0.000882

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.00112 Hom.: 1

Bravo AF: 0.000839

TwinsUK AF: 0.000539 AC: 2

ALSPAC AF: 0.000519 AC: 2

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.00116 AC: 10

ExAC AF: 0.000758 AC: 92

EpiCase AF: 0.00207

EpiControl AF: 0.00155

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:13

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Autosomal recessive limb-girdle muscular dystrophy type 2A Pathogenic:1 Uncertain:5

Uncertain significance, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Dec 17, 2019	NM_000070.2(CAPN3):c.2257G>A(D753N) is classified as a variant of uncertain significance in the context of calpainopathy. Sources cited for classification include the following: PMID 17318636, 17994539, 17897828, 18854869, 20044116, 16141003, 27884173 and 30564623. Classification of NM_000070.2(CAPN3):c.2257G>A(D753N) is based on the following criteria: At this time, there is insufficient or conflicting evidence to classify this variant as pathogenic or benign. Please note: this variant was assessed in the context of healthy population screening. -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	May 18, 2021	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 09, 2019	Across a selection of the available literature, the CAPN3 c.2257G>A (p.Arg753Asn) is identified in six probands described to have limb girdle muscular dystrophy in a heterozygous state and five probands in a compound heterozygous state (Fanin et al. 2004; Piluso et al. 2005; Saenz et al. 2005; Todorova et al. 2007; Fanin et al. 2009). The p.Arg753Asn variant absent from at least 400 controls and is reported at a frequency of 0.00118 in the European (non-Finnish) population of the Exome Aggregation Consortium. Todorova et al. (2007) noted that the variant, when observed in a heterozygous state in probands with limb girdle muscular dystrophy, seemed to confer a later onset and milder phenotype. Based on the evidence, the p.Asp753Asn variant is classified as likely pathogenic for calpainopathy. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 26, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Oct 25, 2022	This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 753 of the CAPN3 protein (p.Asp753Asn). This variant is present in population databases (rs146923842, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individuals with limb girdle muscular dystrophy (PMID: 16141003, 18854869). ClinVar contains an entry for this variant (Variation ID: 281081). 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. 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 Uncertain:5

Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jan 11, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jul 27, 2023	Reported, without a second identifiable CAPN3 variant, in an individual with LGMD2A who had complete calpain-3 deficiency on Western blot (Fanin et al., 2004); Reported in the heterozygous and compound heterozygous state in association with LGMD2A; however, parental testing was not completed and functional characterization of the variant was not performed (Piluso et al., 2005; Senz et al., 2005; Todorova et al., 2007); Reported previously in five patients with LGMD and two of these patients harbored a second variant (phase unknown). No further clinical or segregation information was provided (Fanin et al., 2009; Nallamilli et al., 2018); 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: 17994539, 15689361, 31937337, 17318636, 15221789, 27884173, 32403337, 31931849, 30564623, 18854869, Koken_2022[Poster], 32528171, 16141003, 34720847, 35157181) -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Oct 27, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	May 25, 2023	PM3_supporting -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The CAPN3 p.D753N variant was identified in the heterozygous or compound heterozygous state in 9 of 2194 proband chromosomes (frequency: 0.004) from individuals with Limb girdle muscular dystrophy (LGMD) type 2A (LGMD2A) and unspecified muscular dystrophy (Todorova_2007_PMID:17318636; Piluso_2005_PMID:16141003; Fanin_2009_PMID:18854869). The variant was identified in dbSNP (ID: rs146923842), ClinVar (classified as uncertain significance by EGL Genetics, GeneDx and Invitae and as likely pathogenic by Counsyl and Illumina) and LOVD 3.0 (classified as pathogenic and a VUS). The variant was identified in control databases in 210 of 282180 chromosomes (0 homozygous) at a frequency of 0.0007442 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: Latino in 39 of 35324 chromosomes (freq: 0.001104), European (non-Finnish) in 142 of 128804 chromosomes (freq: 0.001102), Ashkenazi Jewish in 8 of 10354 chromosomes (freq: 0.000773), Other in 4 of 7212 chromosomes (freq: 0.000555), European (Finnish) in 6 of 25108 chromosomes (freq: 0.000239), East Asian in 4 of 19914 chromosomes (freq: 0.000201), South Asian in 4 of 30576 chromosomes (freq: 0.000131), and African in 3 of 24888 chromosomes (freq: 0.000121). The p.Asp661 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and three of four in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. Fanin et al. (2009) identified the p.D753N variant in two heterozygous and two compound heterozygous patients with Limb girdle muscular dystrophy; these patients had varying degrees of calpain levels and autolytic activity ranging from normal to absent (Fanin_2009_PMID:18854869). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -

Muscular dystrophy, limb-girdle, autosomal dominant 4 Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Jun 29, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 30, 2022	- -

CAPN3-related disorder Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

DASA

Feb 05, 2022

The c.2257G>A;p.(Asp753Asn) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (PMID: 31517061; 18854869) - PS4_moderate. The variant is present at low allele frequencies population databases (rs146923842 – gnomAD 0.007563%; ABraOM 0.000854 frequency - http://abraom.ib.usp.br/) - PM2_supporting. The p.(Asp753Asn) was detected in trans with a pathogenic variant (PMID: 31517061; 18854869) - PM3. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. In summary, the currently available evidence indicates that the variant is likely pathogenic. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Sep 22, 2023

Variant summary: CAPN3 c.2257G>A (p.Asp753Asn) results in a conservative amino acid change located in the EF-hand domain of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00079 in 250800 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in CAPN3 causing Limb-Girdle Muscular Dystrophy, Autosomal Recessive (0.00079 vs 0.0032), allowing no conclusion about variant significance. c.2257G>A has been reported in the literature in the heterozygous or compound heterozygous state in individuals affected with Limb-Girdle Muscular Dystrophy without strong evidence for causality (eg. Fanin_2004, Piluso_2005, Saenz_2005, Todorova_2007, Guglieri_2008, Fanin_2009, Nallamilli_2018, Macias_2021, Ozyilmaz_2022). These reports do not provide unequivocal conclusions about association of the variant with autosomal recessive Limb-Girdle Muscular Dystrophy. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 30564623, 17994539, 31931849, 18854869, 16141003, 15221789, 32528171, 15689361, 32403337, 34720847, 31517061, 17318636, 35157181). Ten submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as either VUS (n=8) or likely pathogenic (n=2). Based on the evidence outlined above, the variant was classified as uncertain significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.096
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Uncertain	-0.020
Cadd	Pathogenic	32
Dann	Pathogenic	1.0
DEOGEN2	Benign	0.022	T;.;.;T;.;.;.;.;.;.;.;.
Eigen	Uncertain	0.48
Eigen_PC	Uncertain	0.44
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.93	D;D;D;D;D;D;.;D;.;D;.;D
M_CAP	Uncertain	0.19	D
MetaRNN	Benign	0.089	T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Pathogenic	0.82	D
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.75	T
REVEL	Pathogenic	0.65
Sift4G	Benign	0.45	T;T;T;T;T;T;T;T;T;T;T;T
Polyphen		1.0	.;D;D;D;.;.;.;.;.;.;.;.
Vest4		0.61
MVP		0.97
MPC		0.62
ClinPred		0.19	T
GERP RS		4.5
Varity_R		0.62
gMVP		0.64

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: rs146923842; hg19: chr15-42702858; COSMIC: COSV55515591; COSMIC: COSV55515591;