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NM_000070.3(CAPN3):c.1662C>G (p.Tyr554Ter) AND Autosomal recessive limb-girdle muscular dystrophy type 2A

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 28, 2019
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:
RCV000812975.3

Allele description [Variation Report for NM_000070.3(CAPN3):c.1662C>G (p.Tyr554Ter)]

NM_000070.3(CAPN3):c.1662C>G (p.Tyr554Ter)

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.1662C>G (p.Tyr554Ter)
HGVS:
  • NC_000015.10:g.42402919C>G
  • NG_008660.1:g.59817C>G
  • NM_000070.3:c.1662C>GMANE SELECT
  • NM_024344.2:c.1662C>G
  • NM_173087.2:c.1518C>G
  • NM_173088.2:c.126C>G
  • NP_000061.1:p.Tyr554Ter
  • NP_077320.1:p.Tyr554Ter
  • NP_775110.1:p.Tyr506Ter
  • NP_775111.1:p.Tyr42Ter
  • LRG_849t1:c.1662C>G
  • LRG_849:g.59817C>G
  • LRG_849p1:p.Tyr554Ter
  • NC_000015.9:g.42695117C>G
  • NM_000070.2:c.1662C>G
Protein change:
Y42*
Links:
dbSNP: rs752848213
NCBI 1000 Genomes Browser:
rs752848213
Molecular consequence:
  • NM_000070.3:c.1662C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_024344.2:c.1662C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_173087.2:c.1518C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_173088.2:c.126C>G - nonsense - [Sequence Ontology: SO:0001587]

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000953305Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Aug 28, 2019)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Clinical, molecular, and protein correlations in a large sample of genetically diagnosed Italian limb girdle muscular dystrophy patients.

Guglieri M, Magri F, D'Angelo MG, Prelle A, Morandi L, Rodolico C, Cagliani R, Mora M, Fortunato F, Bordoni A, Del Bo R, Ghezzi S, Pagliarani S, Lucchiari S, Salani S, Zecca C, Lamperti C, Ronchi D, Aguennouz M, Ciscato P, Di Blasi C, Ruggieri A, et al.

Hum Mutat. 2008 Feb;29(2):258-66.

PubMed [citation]
PMID:
17994539

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000953305.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Tyr554*) in the CAPN3 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in an individual affected with limb-girdle muscular dystrophy (PMID: 17994539). ClinVar contains an entry for this variant (Variation ID: 290348). Loss-of-function variants in CAPN3 are known to be pathogenic (PMID: 10330340, 15689361). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024