NM_000070.3(CAPN3):c.2079A>G (p.Thr693=) AND Autosomal recessive limb-girdle muscular dystrophy type 2A

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 3, 2024
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:: RCV000665576.8

Allele description [Variation Report for NM_000070.3(CAPN3):c.2079A>G (p.Thr693=)]

NM_000070.3(CAPN3):c.2079A>G (p.Thr693=)

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.2079A>G (p.Thr693=)

HGVS:

NC_000015.10:g.42409959A>G
NG_008660.1:g.66857A>G
NM_000070.3:c.2079A>GMANE SELECT
NM_024344.2:c.2061A>G
NM_173087.2:c.1803A>G
NM_173088.2:c.543A>G
NM_173089.2:c.84A>G
NM_173090.2:c.84A>G
NP_000061.1:p.Thr693=
NP_077320.1:p.Thr687=
NP_775110.1:p.Thr601=
NP_775111.1:p.Thr181=
NP_775112.1:p.Thr28=
NP_775113.1:p.Thr28=
LRG_849t1:c.2079A>G
LRG_849:g.66857A>G
LRG_849p1:p.Thr693=
NC_000015.9:g.42702157A>G
NM_000070.2:c.2079A>G

Links:

dbSNP: rs540561728

NCBI 1000 Genomes Browser:

rs540561728

Molecular consequence:

NM_000070.3:c.2079A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_024344.2:c.2061A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_173087.2:c.1803A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_173088.2:c.543A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_173089.2:c.84A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_173090.2:c.84A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

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

Recent activity

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Taxonomy Links for Protein (Select 46015944) (1)
Taxonomy
Gene neighbors for Gene (Select 89511189) (5)
Gene
Chain G, Galactose-binding lectin
Chain G, Galactose-binding lectin
gi|46015948|pdb|1V6M|G

Protein
Chain C, Galactose-binding lectin
Chain C, Galactose-binding lectin
gi|46015944|pdb|1V6M|C

Protein
esv2759189 (1)
dbVar

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000789722	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely benign (Feb 10, 2017)	unknown	clinical testing	Citation Link,
SCV001701434	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 3, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000789722

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Likely benign
(Feb 10, 2017)

unknown

clinical testing

Citation Link,

SCV001701434

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 3, 2024)

germline

clinical testing

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

Help

Summary from all submissions

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Counsyl, SCV000789722.1

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001701434.4

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

#	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		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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