NM_000070.3(CAPN3):c.2305C>T (p.Arg769Trp) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Feb 25, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000711016.3

Allele description [Variation Report for NM_000070.3(CAPN3):c.2305C>T (p.Arg769Trp)]

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

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.2305C>T (p.Arg769Trp)
HGVS:
  • NC_000015.10:g.42410925C>T
  • NG_008660.1:g.67823C>T
  • NM_000070.3:c.2305C>TMANE SELECT
  • NM_024344.1:c.2287C>T
  • NM_173087.1:c.2029C>T
  • NM_173088.1:c.769C>T
  • NM_173089.1:c.310C>T
  • NM_173090.1:c.310C>T
  • NP_000061.1:p.Arg769Trp
  • NP_077320.1:p.Arg763Trp
  • NP_775110.1:p.Arg677Trp
  • NP_775111.1:p.Arg257Trp
  • NP_775112.1:p.Arg104Trp
  • NP_775113.1:p.Arg104Trp
  • LRG_849t1:c.2305C>T
  • LRG_849:g.67823C>T
  • LRG_849p1:p.Arg769Trp
  • NC_000015.9:g.42703123C>T
  • NM_000070.2:c.2305C>T
Protein change:
R104W
Links:
dbSNP: rs868791726
NCBI 1000 Genomes Browser:
rs868791726
Molecular consequence:
  • NM_000070.3:c.2305C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024344.1:c.2287C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_173087.1:c.2029C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_173088.1:c.769C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_173089.1:c.310C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_173090.1:c.310C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
4

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000333873EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Likely pathogenic
(Apr 12, 2017)
germlineclinical testing

Citation Link,

SCV000841334Athena Diagnostics Inccriteria provided, single submitter
Likely pathogenic
(Feb 25, 2020)
unknownclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown4not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Expanding genotype/phenotype of neuromuscular diseases by comprehensive target capture/NGS.

Tian X, Liang WC, Feng Y, Wang J, Zhang VW, Chou CH, Huang HD, Lam CW, Hsu YY, Lin TS, Chen WT, Wong LJ, Jong YJ.

Neurol Genet. 2015 Aug;1(2):e14. doi: 10.1212/NXG.0000000000000015.

PubMed [citation]
PMID:
27066551
PMCID:
PMC4807910

Clinical applications of next-generation sequencing-based gene panel in patients with muscular dystrophy: Korean experience.

Seong MW, Cho A, Park HW, Seo SH, Lim BC, Seol D, Cho SI, Park SS, Chae JH.

Clin Genet. 2016 Apr;89(4):484-488. doi: 10.1111/cge.12621. Epub 2015 Jun 29.

PubMed [citation]
PMID:
26060040
See all PubMed Citations (4)

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000333873.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided4not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided4not providednot providednot provided

From Athena Diagnostics Inc, SCV000841334.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

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. Predicted to have a damaging effect on the protein. One other pathogenic or likely pathogenic variant affects the same amino acid. In multiple individuals, this variant has been seen with a single recessive pathogenic variant in the same gene, suggesting this variant may also be pathogenic.

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

Last Updated: May 27, 2021

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