15-42410633-A-G
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM2PP3_StrongPP5_Very_Strong
The NM_000070.3(CAPN3):c.2230A>G(p.Ser744Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,461,838 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 Pathogenic (★★).
Frequency
Consequence
NM_000070.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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CAPN3 | ENST00000397163.8 | c.2230A>G | p.Ser744Gly | missense_variant | Exon 21 of 24 | 1 | NM_000070.3 | ENSP00000380349.3 | ||
CAPN3 | ENST00000673886.1 | c.235A>G | p.Ser79Gly | missense_variant | Exon 8 of 11 | ENSP00000501155.1 | ||||
CAPN3 | ENST00000673928.1 | c.235A>G | p.Ser79Gly | missense_variant | Exon 8 of 11 | ENSP00000501099.1 | ||||
CAPN3 | ENST00000674146.1 | c.235A>G | p.Ser79Gly | missense_variant | Exon 9 of 12 | ENSP00000501175.1 | ||||
CAPN3 | ENST00000674149.1 | c.235A>G | p.Ser79Gly | missense_variant | Exon 8 of 11 | ENSP00000501112.1 | ||||
CAPN3 | ENST00000673743.1 | c.133A>G | p.Ser45Gly | missense_variant | Exon 8 of 11 | ENSP00000500989.1 | ||||
ENSG00000258461 | ENST00000495723.1 | n.*2666A>G | non_coding_transcript_exon_variant | Exon 23 of 26 | 2 | ENSP00000492063.1 | ||||
ENSG00000258461 | ENST00000495723.1 | n.*2666A>G | 3_prime_UTR_variant | Exon 23 of 26 | 2 | ENSP00000492063.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251302Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135832
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461838Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727218
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2A Pathogenic:2Uncertain:1
Consanguinity: No Clinical Indications: Difficulty climbing stairs and lifting objects since 5 years, waddling gait, Power- weak biceps, weak lower limb adduction Investigations: CPK - 1487 U/L Family history: Sister is similarly affected Clinical Suspicion: Limb Girdle Muscular Dystrophy -
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This variant has been observed to segregate with limb-girdle muscular dystrophy in several families (PMID: 7720071, 8624690, 9655129). ClinVar contains an entry for this variant (Variation ID: 555001). For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change causes constitutive autolysis (PMID: 9642272). This variant is present in population databases (rs750083132, ExAC 0.002%). This sequence change replaces serine with glycine at codon 744 of the CAPN3 protein (p.Ser744Gly). The serine residue is highly conserved and there is a small physicochemical difference between serine and glycine. -
Muscular dystrophy, limb-girdle, autosomal dominant 4 Pathogenic:1
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Autosomal recessive limb-girdle muscular dystrophy Pathogenic:1
Variant summary: CAPN3 c.2230A>G (p.Ser744Gly) results in a non-conservative amino acid change located in the EF-hand domain (IPR002048) 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 8e-06 in 251302 control chromosomes. c.2230A>G has been reported in the literature in at-least three individuals affected with Limb-Girdle Muscular Dystrophy, Autosomal Recessive as being a compound heterozygous state along with two different pathogenic variants, respectively (examples: Anderson_1998, Ono_1998, Penisson-Besnier_1998, Richard_1995). At least two publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in completely loss of proteolysis activity against the substrate fodrin (Richard_1995). Additionally, significantly decreased CAPN3 levels in muscular biopsy, determined by Western blotting, have been found in at-least two patients carrying c.2230A>G and second null alleles, respectively (Anderson_1998). These data indicate that the variant is very likely associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 9777948, 9642272, 9655129, 7720071). Three submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 (Pathogenic n=2; VUS n=1). Based on the evidence outlined above, the variant was classified as pathogenic. -
not provided Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at