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NM_000070.3(CAPN3):c.2305C>T (p.Arg769Trp)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: May 6, 2021)
Last evaluated:
Apr 26, 2021
Accession:
VCV000282411.6
Variation ID:
282411
Description:
single nucleotide variant
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NM_000070.3(CAPN3):c.2305C>T (p.Arg769Trp)

Allele ID
266648
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q15.1
Genomic location
15: 42410925 (GRCh38) GRCh38 UCSC
15: 42703123 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.42410925C>T
NC_000015.9:g.42703123C>T
NM_000070.3:c.2305C>T MANE Select NP_000061.1:p.Arg769Trp missense
... more HGVS
Protein change
R769W, R677W, R257W, R763W, R104W
Other names
-
Canonical SPDI
NC_000015.10:42410924:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
ClinGen: CA10604167
dbSNP: rs868791726
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Feb 25, 2020 RCV000711016.3
Pathogenic 2 criteria provided, single submitter Jul 13, 2020 RCV000295812.7
Pathogenic 1 criteria provided, single submitter Apr 26, 2021 RCV001420333.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CAPN3 - - GRCh38
GRCh37
999 1011

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Apr 12, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000333873.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely pathogenic
(Feb 25, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV000841334.2
Submitted: (Dec 30, 2020)
Evidence details
Publications
PubMed (3)
Comment:
The frequency of this variant in the general population is consistent with pathogenicity. Found in at least one patient with expected phenotype for this gene. … (more)
Pathogenic
(Jul 13, 2020)
criteria provided, single submitter
Method: clinical testing
Limb-girdle muscular dystrophy, type 2A
Allele origin: germline
Invitae
Accession: SCV000645494.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (10)
Comment:
This sequence change replaces arginine with tryptophan at codon 769 of the CAPN3 protein (p.Arg769Trp). The arginine residue is highly conserved and there is a … (more)
Pathogenic
(Apr 26, 2021)
criteria provided, single submitter
Method: clinical testing
See cases
(Autosomal recessive inheritance)
Allele origin: unknown
Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli
Accession: SCV001622753.1
Submitted: (May 06, 2021)
Evidence details
Comment:
PP5_strong;PM1_moderate;PM2_supporting;PM3_moderate;PM5_moderate;PP3_supporting;BP1_supporting
Likely pathogenic
(May 16, 2017)
no assertion criteria provided
Method: clinical testing
Limb-girdle muscular dystrophy, type 2A
Allele origin: unknown
Counsyl
Accession: SCV000791434.2
Submitted: (Aug 05, 2019)
Evidence details
Publications
PubMed (4)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
European muscle MRI study in limb girdle muscular dystrophy type R1/2A (LGMDR1/LGMD2A). Barp A Journal of neurology 2020 PMID: 31555977
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Mutational spectrum of Chinese LGMD patients by targeted next-generation sequencing. Yu M PloS one 2017 PMID: 28403181
Clinical applications of next-generation sequencing-based gene panel in patients with muscular dystrophy: Korean experience. Seong MW Clinical genetics 2016 PMID: 26060040
Expanding genotype/phenotype of neuromuscular diseases by comprehensive target capture/NGS. Tian X Neurology. Genetics 2015 PMID: 27066551
[Clinical-genetic characteristics of limb girdle-muscular dystrophy type 2A]. Dadali EL Zhurnal nevrologii i psikhiatrii imeni S.S. Korsakova 2010 PMID: 20517216
Calpainopathy: how broad is the spectrum of clinical variability? Starling A Journal of molecular neuroscience : MN 2003 PMID: 14645990
Clinical variability in calpainopathy: what makes the difference? de Paula F European journal of human genetics : EJHG 2002 PMID: 12461690
Genetic heterogeneity of autosomal recessive limb-girdle muscular dystrophy in a genetic isolate (Amish) and evidence for a new locus. Allamand V Human molecular genetics 1995 PMID: 7795603
Preferential localization of the limb-girdle muscular dystrophy type 2A gene in the proximal part of a 1-cM 15q15.1-q15.3 interval. Allamand V American journal of human genetics 1995 PMID: 7762565
Mutations in the proteolytic enzyme calpain 3 cause limb-girdle muscular dystrophy type 2A. Richard I Cell 1995 PMID: 7720071
- - - - PMID: 205172126
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CAPN3 - - - -

Text-mined citations for rs868791726...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated May 27, 2021