chr15-42399641-G-A

Position:

• chr15-42399641-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.1343G>A​(p.Arg448His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000759 in 1,449,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R448C) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000076 (0 hom.)
• Consequence: CAPN3 NM_000070.3 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:12
• 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]

ENSG00000258461 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PM1: In a region_of_interest Domain III (size 168) in uniprot entity CAN3_HUMAN there are 132 pathogenic changes around while only 0 benign (100%) in NM_000070.3
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr15-42399640-C-T is described in Lovd as [Likely_pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.981
• PP5: Variant 15-42399641-G-A is Pathogenic according to our data. Variant chr15-42399641-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 217149.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-42399641-G-A is described in Lovd as [Pathogenic]. Variant chr15-42399641-G-A is described in Lovd as [Pathogenic]. Variant chr15-42399641-G-A is described in Lovd as [Likely_pathogenic]. Variant chr15-42399641-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAPN3	NM_000070.3	c.1343G>A	p.Arg448His	missense_variant	10/24	ENST00000397163.8	NP_000061.1
CAPN3	NM_024344.2	c.1343G>A	p.Arg448His	missense_variant	10/23		NP_077320.1
CAPN3	NM_173087.2	c.1199G>A	p.Arg400His	missense_variant	9/21		NP_775110.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAPN3	ENST00000397163.8	c.1343G>A	p.Arg448His	missense_variant	10/24	1	NM_000070.3	ENSP00000380349.3
ENSG00000258461	ENST00000495723.1	n.*1139G>A		non_coding_transcript_exon_variant	14/26	2		ENSP00000492063.1
ENSG00000258461	ENST00000495723.1	n.*1139G>A		3_prime_UTR_variant	14/26	2		ENSP00000492063.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD3 exomes AF: 0.0000128 AC: 3 AN: 235170 Hom.: 0 AF XY: 0.00000787 AC XY: 1 AN XY: 127016

Gnomad AFR exome AF: 0.0000663

Gnomad AMR exome AF: 0.0000308

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: 0.00000951

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000759 AC: 11 AN: 1449806 Hom.: 0 Cov.: 31 AF XY: 0.0000111 AC XY: 8 AN XY: 719596

Gnomad4 AFR exome AF: 0.0000300

Gnomad4 AMR exome AF: 0.0000231

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000117

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000633

Gnomad4 OTH exome AF: 0.0000167

GnomAD4 genome Cov.: 31

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:12

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Autosomal recessive limb-girdle muscular dystrophy type 2A Pathogenic:6

Pathogenic, criteria provided, single submitter	research	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Dec 03, 2018	The homozygous p.Arg448His variant in CAPN3 was identified by our study in three siblings with Limb-Girdle Muscular Dystrophy. This variant has been identified in 0.001303% (3/230304) of chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs863224956). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. This variant impacts the same residue as the pathogenic p.Arg448Cys variant, supporting the possibility that a missense mutation at this position may not be tolerated (ClinVar Variation ID: 280038). This variant was reported in the compound heterozygous state in 3 individuals with Limb-Girdle Muscular Dystrophy, but no information on other variants in those individuals was available (PMID: 16141003, 10330340). Animal models in mice have shown that this variant causes Limb-Girdle Muscular Dystrophy with evidence of increased protein degredation and decreasing binding to titin (PMID: 21624972, 11371436). This variant has also been reported in ClinVar (Variation ID: 217149). In summary, this variant is pathogenic. ACMG/AMP Criteria applied: PM2, PM5, PS3, PP1, PP3, PM3_Supporting (Richards 2015). -
Pathogenic, criteria provided, single submitter	clinical testing	Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Breakthrough Genomics, Breakthrough Genomics	Oct 01, 2021	This variant was previously reported in individuals with autosomal recessive limb-girdle muscular dystrophy [PMID: 25135358, 20635405, 30919934]. Functional studies using animal models in mice have shown that this variant causes Limb-Girdle Muscular Dystrophy with evidence of increased protein degradation and decreasing binding to titin [PMID: 21624972, 11371436]. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 03, 2023	This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 448 of the CAPN3 protein (p.Arg448His). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with autosomal recessive limb-girdle muscular dystrophy (PMID: 20635405, 25135358, 30919934; Invitae). ClinVar contains an entry for this variant (Variation ID: 217149). 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 CAPN3 protein function. Experimental studies have shown that this missense change affects CAPN3 function (PMID: 15138196, 21624972). This variant disrupts the p.Arg448 amino acid residue in CAPN3. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 7318636, 10330340, 16141003, 16650086, 18854869, 26404900, 27447704). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, no assertion criteria provided	clinical testing	Counsyl	Dec 21, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	The observed missense c.1343G>A(p.Arg448His) variant in CAPN3 gene has been reported in homozygous and compound heterozygous state in individuals affected with CAPN3 related disorder (Piluso G, et. al., 2005; Cerino M, et. al., 2020; Ganaraja VH, et. al., 2021). Experimental studies have shown that this missense change affects CAPN3 function (Ermolova N, et. al., 2011). This p.Arg448His variant is present with an allele frequency of 0.001% in gnomAD Exomes. This variant has been reported to the ClinVar database as Likely pathogenic/ Pathogenic (multiple submissions). The amino acid change p.Arg448His in CAPN3 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Arg at position 448 is changed to a His changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Dec 30, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 01, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2019	- -

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

Pathogenic, flagged submission

clinical testing

Baylor Genetics

Oct 05, 2023

- -

Autosomal recessive limb-girdle muscular dystrophy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Sep 11, 2023

Variant summary: CAPN3 c.1343G>A (p.Arg448His) results in a non-conservative amino acid change located in the Peptidase C2, calpain, large subunit, domain III (IPR022682) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.3e-05 in 235170 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.1343G>A has been reported in the literature in multiple individuals affected with Limb-Girdle Muscular Dystrophy, Autosomal Recessive (e.g., Fanin_2009, Stehlikova_2014, Ten Dam_2019). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 18854869, 25135358, 30919934). Five submitters have reported clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Autosomal recessive limb-girdle muscular dystrophy type 2A;C4748295:Muscular dystrophy, limb-girdle, autosomal dominant 4 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Feb 22, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.94
BayesDel_addAF	Pathogenic	0.47	D
BayesDel_noAF	Pathogenic	0.44
CADD	Pathogenic	33
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.59	D;.;.;D
Eigen	Pathogenic	0.99
Eigen_PC	Pathogenic	0.94
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.97	D;D;D;D
M_CAP	Uncertain	0.27	D
MetaRNN	Pathogenic	0.98	D;D;D;D
MetaSVM	Pathogenic	0.87	D
MutationAssessor	Pathogenic	3.1	.;M;.;M
PrimateAI	Pathogenic	0.87	D
PROVEAN	Pathogenic	-4.8	.;D;D;D
REVEL	Pathogenic	0.90
Sift	Uncertain	0.0010	.;D;D;D
Sift4G	Pathogenic	0.0010	D;D;D;D
Polyphen		1.0	.;D;D;D
Vest4		0.95
MutPred		0.96		.;Loss of methylation at R448 (P = 0.0392);.;Loss of methylation at R448 (P = 0.0392);
MVP		0.97
MPC		0.70
ClinPred		1.0	D
GERP RS		5.4
Varity_R		0.89
gMVP		0.85

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: rs863224956; hg19: chr15-42691839; COSMIC: COSV58826312; COSMIC: COSV58826312;