NM_000070.3(CAPN3):c.2134C>T (p.Leu712Phe) AND not provided

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Apr 15, 2020
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000597464.6

Allele description [Variation Report for NM_000070.3(CAPN3):c.2134C>T (p.Leu712Phe)]

NM_000070.3(CAPN3):c.2134C>T (p.Leu712Phe)

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.2134C>T (p.Leu712Phe)

HGVS:

NC_000015.10:g.42410446C>T
NG_008660.1:g.67344C>T
NM_000070.3:c.2134C>TMANE SELECT
NM_024344.2:c.2116C>T
NM_173087.2:c.1858C>T
NM_173088.2:c.598C>T
NM_173089.2:c.139C>T
NM_173090.2:c.139C>T
NP_000061.1:p.Leu712Phe
NP_077320.1:p.Leu706Phe
NP_775110.1:p.Leu620Phe
NP_775111.1:p.Leu200Phe
NP_775112.1:p.Leu47Phe
NP_775113.1:p.Leu47Phe
LRG_849t1:c.2134C>T
LRG_849:g.67344C>T
LRG_849p1:p.Leu712Phe
NC_000015.9:g.42702644C>T
NM_000070.2:c.2134C>T

Protein change:

L200F

Links:

dbSNP: rs794727318

NCBI 1000 Genomes Browser:

rs794727318

Molecular consequence:

NM_000070.3:c.2134C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_024344.2:c.2116C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_173087.2:c.1858C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_173088.2:c.598C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_173089.2:c.139C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_173090.2:c.139C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000700773	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions)	Likely pathogenic (Jun 30, 2016)	germline	clinical testing	Citation Link,
SCV001476314	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Likely pathogenic (Apr 15, 2020)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 26886200, 17562833, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000700773

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions)

Likely pathogenic
(Jun 30, 2016)

germline

clinical testing

Citation Link,

SCV001476314

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Likely pathogenic
(Apr 15, 2020)

unknown

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Utility of a next-generation sequencing-based gene panel investigation in German patients with genetically unclassified limb-girdle muscular dystrophy.

Kuhn M, Gläser D, Joshi PR, Zierz S, Wenninger S, Schoser B, Deschauer M.

J Neurol. 2016 Apr;263(4):743-50. doi: 10.1007/s00415-016-8036-0. Epub 2016 Feb 17.

PubMed [citation]

PMID:: 26886200

Limb-girdle muscular dystrophy in the Netherlands: gene defect identified in half the families.

van der Kooi AJ, Frankhuizen WS, Barth PG, Howeler CJ, Padberg GW, Spaans F, Wintzen AR, Wokke JH, van Ommen GJ, de Visser M, Bakker E, Ginjaar HB.

Neurology. 2007 Jun 12;68(24):2125-8.

PubMed [citation]

PMID:: 17562833

See all PubMed Citations (3)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000700773.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		2	not provided	not provided	not provided

From Athena Diagnostics, SCV001476314.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

Not found in the total gnomAD dataset, and the data is high quality. Found in at least one patient with expected phenotype for this gene. Predicted to have a damaging effect on the protein. 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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