15-42410660-G-A

Variant names:

• chr15-42410660-G-A
• rs146923842
• NM_000070.3:c.2257G>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 5P and 5B. PM1 PM5 PP5 BP4 BS2

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 Likely 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:14
• 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]

ENSG00000258461 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 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 chr15-42410660-G-AA is described in ClinVar as [no_classifications_from_unflagged_records]. Clinvar id is 1285364.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=1}.
• 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=12, 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.
• BS2: High Homozygotes in GnomAdExome4 at 2 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAPN3	NM_000070.3	c.2257G>A	p.Asp753Asn	missense_variant	Exon 21 of 24	ENST00000397163.8	NP_000061.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAPN3	ENST00000397163.8	c.2257G>A	p.Asp753Asn	missense_variant	Exon 21 of 24	1	NM_000070.3	ENSP00000380349.3
CAPN3	ENST00000673886.1	c.262G>A	p.Asp88Asn	missense_variant	Exon 8 of 11			ENSP00000501155.1
CAPN3	ENST00000673928.1	c.262G>A	p.Asp88Asn	missense_variant	Exon 8 of 11			ENSP00000501099.1
CAPN3	ENST00000674146.1	c.262G>A	p.Asp88Asn	missense_variant	Exon 9 of 12			ENSP00000501175.1
CAPN3	ENST00000674149.1	c.262G>A	p.Asp88Asn	missense_variant	Exon 8 of 11			ENSP00000501112.1
CAPN3	ENST00000673743.1	c.160G>A	p.Asp54Asn	missense_variant	Exon 8 of 11			ENSP00000500989.1
ENSG00000258461	ENST00000495723.1	n.*2693G>A		non_coding_transcript_exon_variant	Exon 23 of 26	2		ENSP00000492063.1
ENSG00000258461	ENST00000495723.1	n.*2693G>A		3_prime_UTR_variant	Exon 23 of 26	2		ENSP00000492063.1

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

GnomAD2 exomes AF: 0.000785 AC: 197 AN: 250800 AF XY: 0.000797

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 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 AC: 3 AN: 33472

Gnomad4 AMR exome AF: 0.000986 AC: 44 AN: 44646

Gnomad4 ASJ exome AF: 0.000880 AC: 23 AN: 26134

Gnomad4 EAS exome AF: 0.000101 AC: 4 AN: 39692

Gnomad4 SAS exome AF: 0.000151 AC: 13 AN: 86212

Gnomad4 FIN exome AF: 0.000318 AC: 17 AN: 53408

Gnomad4 NFE exome AF: 0.00106 AC: 1175 AN: 1111540

Gnomad4 Remaining exome AF: 0.000961 AC: 58 AN: 60382

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 AC: 0.000144557 AN: 0.000144557

Gnomad4 AMR AF: 0.00262 AC: 0.00261712 AN: 0.00261712

Gnomad4 ASJ AF: 0.000288 AC: 0.000288018 AN: 0.000288018

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.000415 AC: 0.000415455 AN: 0.000415455

Gnomad4 FIN AF: 0.0000944 AC: 0.0000943752 AN: 0.0000943752

Gnomad4 NFE AF: 0.000882 AC: 0.000882275 AN: 0.000882275

Gnomad4 OTH AF: 0.00142 AC: 0.0014218 AN: 0.0014218

Alfa AF: 0.00102 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:14

Revision: criteria provided, conflicting classifications

Submissions by phenotype

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

Sep 16, 2020

Natera, Inc.

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 autosomal recessive limb girdle muscular dystrophy (PMID: 16141003, 18854869). ClinVar contains an entry for this variant (Variation ID: 281081). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt CAPN3 protein function with a negative predictive value of 80%. 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. -

Mar 26, 2024

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 09, 2019

Illumina Laboratory Services, Illumina

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

May 18, 2021

Genome-Nilou Lab

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 17, 2019

Myriad Genetics, Inc.

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

not provided Uncertain:6

Jan 11, 2018

Eurofins Ntd Llc (ga)

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 25, 2023

Mayo Clinic Laboratories, Mayo Clinic

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM3_supporting -

Feb 08, 2025

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Reported as a single heterozygous variant and with a second CAPN3 variant in patients with limb-girdle muscular dystrophy; however it is unknown if the variants were in cis or trans for some cases with two CAPN3 variants dectected (PMID: 18854869, 30564623, 15221789, 16141003, 15689361, 17318636, 38391941); 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, 27884173, 31931849, 30564623, Koken_2022[Poster], 32528171, 34720847, 38391941, 16141003, 36575883, 20044116, 32403337, 35157181, 39457051, 18854869, 15221789, 31517061) -

Oct 27, 2023

Revvity Omics, Revvity

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 23, 2024

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM3, BS1 -

-

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

Jun 29, 2022

MGZ Medical Genetics Center

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 30, 2022

Baylor Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

CAPN3-related disorder Pathogenic:1

Feb 05, 2022

DASA

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Sep 22, 2023

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

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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
MutationAssessor	Benign	1.2	.;.;.;L;.;.;.;.;.;.;.;.
PrimateAI	Uncertain	0.75	T
PROVEAN	Benign	-1.5	.;N;N;N;N;N;N;D;N;N;N;N
REVEL	Pathogenic	0.65
Sift	Benign	0.44	.;T;T;T;T;T;T;T;T;T;T;T
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
Mutation Taster		=28/72	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
Splicevardb		2.0
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;