NM_000070.3(CAPN3):c.338T>C (p.Ile113Thr) AND Limb-girdle muscular dystrophy, type 2A

Clinical significance:Uncertain significance (Last evaluated: May 3, 2018)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000675143.3

Allele description [Variation Report for NM_000070.3(CAPN3):c.338T>C (p.Ile113Thr)]

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

Gene:
CAPN3:calpain 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q15.1
Genomic location:
Preferred name:
NM_000070.3(CAPN3):c.338T>C (p.Ile113Thr)
HGVS:
  • NC_000015.10:g.42384511T>C
  • NG_008660.1:g.41409T>C
  • NM_000070.3:c.338T>CMANE SELECT
  • NM_024344.1:c.338T>C
  • NM_173087.1:c.338T>C
  • NP_000061.1:p.Ile113Thr
  • NP_077320.1:p.Ile113Thr
  • NP_775110.1:p.Ile113Thr
  • LRG_849t1:c.338T>C
  • LRG_849:g.41409T>C
  • LRG_849p1:p.Ile113Thr
  • NC_000015.9:g.42676709T>C
  • NM_000070.2:c.338T>C
Protein change:
I113T
Links:
dbSNP: rs747026964
NCBI 1000 Genomes Browser:
rs747026964
Molecular consequence:
  • NM_000070.3:c.338T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024344.1:c.338T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_173087.1:c.338T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Limb-girdle muscular dystrophy, type 2A (LGMDR1)
Synonyms:
Limb-girdle muscular dystrophy type 2; Muscular dystrophy, pelvofemoral; Leyden-Moebius muscular dystrophy; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009675; MedGen: C1869123; Orphanet: 267; OMIM: 253600

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000800733Counsylcriteria provided, single submitter
Uncertain significance
(Sep 15, 2017)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV000914667Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Jan 29, 2018)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV001529404Baylor Geneticscriteria provided, single submitter
Uncertain significance
(May 3, 2018)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Redox state and mitochondrial respiratory chain function in skeletal muscle of LGMD2A patients.

Nilsson MI, Macneil LG, Kitaoka Y, Alqarni F, Suri R, Akhtar M, Haikalis ME, Dhaliwal P, Saeed M, Tarnopolsky MA.

PLoS One. 2014;9(7):e102549. doi: 10.1371/journal.pone.0102549.

PubMed [citation]
PMID:
25079074
PMCID:
PMC4117472

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Counsyl, SCV000800733.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Clinical Services Laboratory,Illumina, SCV000914667.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

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 type 2A (LGMD2A) (Nilsson et al. 2014). The p.Ile113Thr is reported at a frequency of 0.000213 in the European (non-Finnish) population from the Genome Aggregation Database. The evidence for this variant is limited. The p.Ile113Thr variant is therefore considered to be of unknown clinical significance but suspicious for pathogenicity for calpainopathy. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV001529404.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 28, 2021

Support Center