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NM_004006.3(DMD):c.6290+2T>A AND Duchenne muscular dystrophy

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 23, 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:
RCV001048615.7

Allele description [Variation Report for NM_004006.3(DMD):c.6290+2T>A]

NM_004006.3(DMD):c.6290+2T>A

Gene:
DMD:dystrophin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp21.1
Genomic location:
Preferred name:
NM_004006.3(DMD):c.6290+2T>A
HGVS:
  • NC_000023.11:g.32287527A>T
  • NG_012232.1:g.1057083T>A
  • NM_000109.4:c.6266+2T>A
  • NM_004006.3:c.6290+2T>AMANE SELECT
  • NM_004009.3:c.6278+2T>A
  • NM_004010.3:c.5921+2T>A
  • NM_004011.4:c.2267+2T>A
  • NM_004012.4:c.2258+2T>A
  • LRG_199t1:c.6290+2T>A
  • LRG_199:g.1057083T>A
  • NC_000023.10:g.32305644A>T
  • NM_004006.2:c.6290+2T>A
Links:
dbSNP: rs2097447247
NCBI 1000 Genomes Browser:
rs2097447247
Molecular consequence:
  • NM_000109.4:c.6266+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_004006.3:c.6290+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_004009.3:c.6278+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_004010.3:c.5921+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_004011.4:c.2267+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_004012.4:c.2258+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Duchenne muscular dystrophy (DMD)
Synonyms:
Muscular dystrophy, pseudohypertrophic progressive, Duchenne type
Identifiers:
MONDO: MONDO:0010679; MedGen: C0013264; Orphanet: 98896; OMIM: 310200

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001212629Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 23, 2019) 		germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Entries in the Leiden Duchenne muscular dystrophy mutation database: an overview of mutation types and paradoxical cases that confirm the reading-frame rule.

Aartsma-Rus A, Van Deutekom JC, Fokkema IF, Van Ommen GJ, Den Dunnen JT.

Muscle Nerve. 2006 Aug;34(2):135-44. Review.

PubMed [citation]
PMID:
16770791
See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001212629.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

For these reasons, this variant has been classified as Pathogenic. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in DMD are known to be pathogenic (PMID: 16770791, 25007885). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Disruption of this splice site has been observed in individual(s) with Duchenne or Becker muscular dystrophy (PMID: 28318817, 28859693, 17726484). This variant is not present in population databases (ExAC no frequency). This sequence change affects a donor splice site in intron 43 of the DMD gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product.

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

Last Updated: Sep 29, 2024