Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_000070.3(CAPN3):c.1543G>A (p.Gly515Arg)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jul 4, 2021)
Last evaluated:
Oct 25, 2019
Accession:
VCV000254861.8
Variation ID:
254861
Description:
single nucleotide variant
Help

NM_000070.3(CAPN3):c.1543G>A (p.Gly515Arg)

Allele ID
255187
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q15.1
Genomic location
15: 42402800 (GRCh38) GRCh38 UCSC
15: 42694998 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.42402800G>A
NC_000015.9:g.42694998G>A
NM_000070.3:c.1543G>A MANE Select NP_000061.1:p.Gly515Arg missense
... more HGVS
Protein change
G515R, G3R, G467R
Other names
-
Canonical SPDI
NC_000015.10:42402799:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00009
Trans-Omics for Precision Medicine (TOPMed) 0.00030
Exome Aggregation Consortium (ExAC) 0.00011
The Genome Aggregation Database (gnomAD) 0.00029
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00023
1000 Genomes Project 0.00040
Links
dbSNP: rs150226817
ClinGen: CA7511431
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Aug 1, 2019 RCV000724737.2
Uncertain significance 2 criteria provided, single submitter Oct 25, 2019 RCV000692602.4
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 31, 2016 RCV000245397.3
Help
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

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000301870.1
Submitted: (Apr 28, 2016)
Evidence details
Uncertain significance
(Dec 31, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000612636.1
Submitted: (Aug 17, 2017)
Evidence details
Uncertain significance
(Aug 10, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000331893.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Oct 25, 2019)
criteria provided, single submitter
Method: clinical testing
Limb-girdle muscular dystrophy, type 2A
Allele origin: germline
Invitae
Accession: SCV000820432.3
Submitted: (Feb 06, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces glycine with arginine at codon 515 of the CAPN3 protein (p.Gly515Arg). The glycine residue is highly conserved and there is a … (more)
Uncertain significance
(Aug 01, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001247172.5
Submitted: (Jul 04, 2021)
Evidence details
Uncertain significance
(Apr 17, 2020)
no assertion criteria provided
Method: clinical testing
Limb-girdle muscular dystrophy type 2A
Allele origin: germline
Natera, Inc.
Accession: SCV001460837.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

Help
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

Help
Title Author Journal Year Link
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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CAPN3 - - - -

Text-mined citations for rs150226817...

Help
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 Aug 27, 2021