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NM_000070.3(CAPN3):c.338T>C (p.Ile113Thr)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Mar 5, 2021)
Last evaluated:
Jul 3, 2018
Accession:
VCV000283107.4
Variation ID:
283107
Description:
single nucleotide variant
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NM_000070.3(CAPN3):c.338T>C (p.Ile113Thr)

Allele ID
267344
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q15.1
Genomic location
15: 42384511 (GRCh38) GRCh38 UCSC
15: 42676709 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.42384511T>C
NC_000015.9:g.42676709T>C
NM_000070.3:c.338T>C MANE Select NP_000061.1:p.Ile113Thr missense
... more HGVS
Protein change
I113T
Other names
-
Canonical SPDI
NC_000015.10:42384510:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00014
Exome Aggregation Consortium (ExAC) 0.00007
The Genome Aggregation Database (gnomAD), exomes 0.00009
The Genome Aggregation Database (gnomAD) 0.00022
Links
ClinGen: CA7510921
dbSNP: rs747026964
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 3 criteria provided, multiple submitters, no conflicts May 3, 2018 RCV000675143.3
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jul 3, 2018 RCV000440617.3
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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
Uncertain significance
(Jul 03, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000335003.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely pathogenic
(Feb 01, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000533388.3
Submitted: (Jan 29, 2019)
Evidence details
Comment:
A variant that is likely pathogenic has been identified in the CAPN3 gene. The I113T variant has been previously reported in a patient with LGMD2A … (more)
Uncertain significance
(Jan 29, 2018)
criteria provided, single submitter
Method: clinical testing
Limb-girdle muscular dystrophy, type 2A
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000914667.1
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (1)
Comment:
The CAPN3 c.338T>C (p.Ile113Thr) variant has been reported in a compound heterozygous state with a second missense variant in one patient with limb-girdle muscular dystrophy … (more)
Uncertain significance
(May 03, 2018)
criteria provided, single submitter
Method: clinical testing
Limb-girdle muscular dystrophy, type 2A
Allele origin: unknown
Baylor Genetics
Accession: SCV001529404.1
Submitted: (Mar 05, 2021)
Evidence details
Comment:
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Uncertain significance
(Sep 15, 2017)
criteria provided, single submitter
Method: clinical testing
Limb-girdle muscular dystrophy, type 2A
Allele origin: unknown
Counsyl
Accession: SCV000800733.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (1)

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
Redox state and mitochondrial respiratory chain function in skeletal muscle of LGMD2A patients. Nilsson MI PloS one 2014 PMID: 25079074
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CAPN3 - - - -

Text-mined citations for rs747026964...

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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 Mar 28, 2021