rs774685118
Variant summary
Our verdict is Uncertain significance. Variant got 6 ACMG points: 6P and 0B. PP3PP4PM3_Strong
This summary comes from the ClinGen Evidence Repository: The NM_000070.3: c.398C>T variant in CAPN3 is a missense variant predicted to cause substitution of alanine by valine at position 133, p.(Ala133Val). This variant has been reported in two unrelated individuals with a clinical diagnosis of LGMD, where it was confirmed in trans with a likely pathogenic or pathogenic variant (c.598_612del p.(Phe200_Leu204del), 1.0 pt x2, PMID:16141003, LOVD individuals #00214184, #00214185; PM3_Strong, PP4). However, it has also been observed in a homozygous state or in trans with a second presumed diagnostic CAPN3 variant (c.133G>A p.(Ala45Thr), c.1303G>A (p.Glu435Lys)) in three individuals without a clear LGMD phenotype (ClinVar SCV001985435.3, SCV003509679.1 internal data communication). The filtering allele frequency of this variant is 0.0001855 (the upper threshold of the 95% CI of 16/86246 exome chromosomes) in the South Asian population in gnomAD v4.1.0, which is greater than the ClinGen LGMD VCEP threshold (≤0.0001) (PM2_Supporting not met). Of note, the South Asian population also includes one homozygous individual of unknown age. The computational predictor REVEL gives a score of 0.959, which is above the LGMD VCEP threshold of ≥0.70, evidence that correlates with impact to CAPN3 function (PP3). In summary, while 6 Bayesian points were awarded to this variant based on the ACMG/AMP criteria applied, as specified by the ClinGen LGMD VCEP (PM3_Strong, PP3, PP4), given the conflicting evidence, the VCEP has opted to classify it as a variant of uncertain significance for autosomal recessive limb girdle muscular dystrophy (LGMD VCEP specifications version 1.0.0; 03/25/2025). LINK:https://erepo.genome.network/evrepo/ui/classification/CA7511008/MONDO:0015152/187
Frequency
Consequence
NM_000070.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPN3 | NM_000070.3 | c.398C>T | p.Ala133Val | missense_variant | Exon 3 of 24 | ENST00000397163.8 | NP_000061.1 | |
CAPN3 | NM_024344.2 | c.398C>T | p.Ala133Val | missense_variant | Exon 3 of 23 | NP_077320.1 | ||
CAPN3 | NM_173087.2 | c.398C>T | p.Ala133Val | missense_variant | Exon 3 of 21 | NP_775110.1 | ||
LOC105370794 | XR_932178.3 | n.-154G>A | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAPN3 | ENST00000397163.8 | c.398C>T | p.Ala133Val | missense_variant | Exon 3 of 24 | 1 | NM_000070.3 | ENSP00000380349.3 | ||
ENSG00000258461 | ENST00000495723.1 | n.*194C>T | non_coding_transcript_exon_variant | Exon 7 of 26 | 2 | ENSP00000492063.1 | ||||
ENSG00000258461 | ENST00000495723.1 | n.*194C>T | 3_prime_UTR_variant | Exon 7 of 26 | 2 | ENSP00000492063.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251410Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135870
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461364Hom.: 1 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727050
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74348
ClinVar
Submissions by phenotype
not provided Uncertain:4
Identified in a patient with limb-girdle muscular dystrophy who also harbored a second variant in CAPN3, however, it is unknown if these variants were on the same (in cis) or opposite (in trans) CAPN3 allele (PMID: 16141003); 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: 16141003) -
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CAPN3: PM2, PM3:Supporting, PP3 -
Autosomal recessive limb-girdle muscular dystrophy type 2A Uncertain:3
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This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 133 of the CAPN3 protein (p.Ala133Val). This variant is present in population databases (rs774685118, gnomAD 0.02%). This missense change has been observed in individual(s) with clinical features of autosomal recessive limb-girdle muscular dystrophy (PMID: 16141003). ClinVar contains an entry for this variant (Variation ID: 290335). 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. 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 specified Uncertain:1
Variant summary: CAPN3 c.398C>T (p.Ala133Val) results in a non-conservative amino acid change located in the catalytic domain (IPR001300) 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 6e-05 in 251410 control chromosomes (gnomAD). This frequency is not higher than the estimated maximum expected for a pathogenic variant in CAPN3 causing Limb-Girdle Muscular Dystrophy, Autosomal Recessive (0.0032), allowing no conclusion about variant significance. The variant, c.398C>T, has been reported in the literature in 2 individuals affected with Limb-Girdle Muscular Dystrophy, who were described as compound heterozygotes, however no 2nd variant was specified (Piluso_2005). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014, and all of them classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -
Autosomal recessive limb-girdle muscular dystrophy Uncertain:1
The NM_000070.3: c.398C>T variant in CAPN3 is a missense variant predicted to cause substitution of alanine by valine at position 133, p.(Ala133Val). This variant has been reported in two unrelated individuals with a clinical diagnosis of LGMD, where it was confirmed in trans with a likely pathogenic or pathogenic variant (c.598_612del p.(Phe200_Leu204del), 1.0 pt x2, PMID: 16141003, LOVD individuals #00214184, #00214185; PM3_Strong, PP4). However, it has also been observed in a homozygous state or in trans with a second presumed diagnostic CAPN3 variant (c.133G>A p.(Ala45Thr), c.1303G>A (p.Glu435Lys)) in three individuals without a clear LGMD phenotype (ClinVar SCV001985435.3, SCV003509679.1 internal data communication). The filtering allele frequency of this variant is 0.0001855 (the upper threshold of the 95% CI of 16/86246 exome chromosomes) in the South Asian population in gnomAD v4.1.0, which is greater than the ClinGen LGMD VCEP threshold (≤0.0001) (PM2_Supporting not met). Of note, the South Asian population also includes one homozygous individual of unknown age. The computational predictor REVEL gives a score of 0.959, which is above the LGMD VCEP threshold of ≥0.70, evidence that correlates with impact to CAPN3 function (PP3). In summary, while 6 Bayesian points were awarded to this variant based on the ACMG/AMP criteria applied, as specified by the ClinGen LGMD VCEP (PM3_Strong, PP3, PP4), given the conflicting evidence, the VCEP has opted to classify it as a variant of uncertain significance for autosomal recessive limb girdle muscular dystrophy (LGMD VCEP specifications version 1.0.0; 03/25/2025). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at