NM_000070.3(CAPN3):c.1722del (p.Ser575fs) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 14, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV000599177.2

Allele description [Variation Report for NM_000070.3(CAPN3):c.1722del (p.Ser575fs)]

NM_000070.3(CAPN3):c.1722del (p.Ser575fs)

Gene:

CAPN3:calpain 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

15q15.1

Genomic location:

Preferred name:

NM_000070.3(CAPN3):c.1722del (p.Ser575fs)

HGVS:

NC_000015.10:g.42402979del
NG_008660.1:g.59877del
NM_000070.3:c.1722delMANE SELECT
NM_024344.2:c.1722del
NM_173087.2:c.1578del
NM_173088.2:c.186del
NP_000061.1:p.Ser575fs
NP_077320.1:p.Ser575fs
NP_775110.1:p.Ser527fs
NP_775111.1:p.Ser63fs
LRG_849t1:c.1722del
LRG_849:g.59877del
LRG_849p1:p.Ser575fs
NC_000015.9:g.42695177del
NM_000070.2:c.1722del
NM_000070.2:c.1722delC

Protein change:

S527fs

Links:

dbSNP: rs1366387924

NCBI 1000 Genomes Browser:

rs1366387924

Molecular consequence:

NM_000070.3:c.1722del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024344.2:c.1722del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_173087.2:c.1578del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_173088.2:c.186del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000709911	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Dec 14, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000709911

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Dec 14, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000709911.2

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

Description

The c.1722delC variant in the CAPN3 gene has been previously reported in limb-girdle muscular dystrophy type 2A, in an affected individual who was also reported with a second CAPN3 variant (ChrobÃ¡kovÃ¡ et al., 2004). The c.1722delC variant causes a frameshift starting with codon Serine 575, changes this amino acid to a Leucine residue, and creates a premature Stop codon at position 20 of the new reading frame, denoted Ser575LeufsX20. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1722delC variant is not observed in the homozygous state or at a significant frequency in large population cohorts (Lek et al., 2016). We interpret c.1722delC as a likely pathogenic variant.

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

Last Updated: Sep 29, 2024

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