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NM_000426.4(LAMA2):c.4682del (p.Lys1561fs) AND Congenital Muscular Dystrophy, LAMA2-related

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 10, 2022
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:
RCV002279724.1

Allele description [Variation Report for NM_000426.4(LAMA2):c.4682del (p.Lys1561fs)]

NM_000426.4(LAMA2):c.4682del (p.Lys1561fs)

Gene:
LAMA2:laminin subunit alpha 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
6q22.33
Genomic location:
Preferred name:
NM_000426.4(LAMA2):c.4682del (p.Lys1561fs)
HGVS:
  • NC_000006.12:g.129353322del
  • NG_008678.1:g.475182del
  • NM_000426.4:c.4682delMANE SELECT
  • NM_001079823.2:c.4682del
  • NP_000417.2:p.Lys1561fs
  • NP_000417.3:p.Lys1561fs
  • NP_001073291.2:p.Lys1561fs
  • LRG_409t1:c.4682del
  • LRG_409:g.475182del
  • LRG_409p1:p.Lys1561fs
  • NC_000006.11:g.129674466del
  • NC_000006.11:g.129674467del
  • NM_000426.3:c.4682del
  • NM_000426.3:c.4682delA
Protein change:
K1561fs
Links:
dbSNP: rs1246940477
NCBI 1000 Genomes Browser:
rs1246940477
Molecular consequence:
  • NM_000426.4:c.4682del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001079823.2:c.4682del - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Name:
Congenital Muscular Dystrophy, LAMA2-related
Identifiers:
MedGen: CN239326

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002567985DASA
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Aug 10, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From DASA, SCV002567985.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The c.4682del;p.(Lys1561Serfs*34) is a null frameshift variant (NMD) in the LAMA2 gene and predicts alteration of the nonsense-mediate decay - NMD is present in a relevant exon to the transcript - PVS1.ClinVar contains an entry for this variant (ClinVar: ID 504010) - PS4_supporting. This variant is not present in population databases (rs1246940477- gnomAD; ABraOM no frequency - http://abraom.ib.usp.br) - PM2. In summary, the currently available evidence indicates that the variant is pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Feb 20, 2024