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NM_004006.3(DMD):c.5048del (p.Thr1683fs) AND Duchenne muscular dystrophy

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 3, 2023
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:
RCV003512202.2

Allele description [Variation Report for NM_004006.3(DMD):c.5048del (p.Thr1683fs)]

NM_004006.3(DMD):c.5048del (p.Thr1683fs)

Gene:
DMD:dystrophin [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xp21.1
Genomic location:
Preferred name:
NM_004006.3(DMD):c.5048del (p.Thr1683fs)
HGVS:
  • NC_000023.11:g.32364688del
  • NG_012232.1:g.979922del
  • NM_000109.4:c.5024del
  • NM_004006.3:c.5048delMANE SELECT
  • NM_004009.3:c.5036del
  • NM_004010.3:c.4679del
  • NM_004011.4:c.1025del
  • NM_004012.4:c.1016del
  • NP_000100.3:p.Thr1675fs
  • NP_003997.1:p.Thr1683Ilefs
  • NP_003997.2:p.Thr1683fs
  • NP_004000.1:p.Thr1679fs
  • NP_004001.1:p.Thr1560fs
  • NP_004002.3:p.Thr342fs
  • NP_004003.2:p.Thr339fs
  • LRG_199t1:c.5048del
  • LRG_199:g.979922del
  • LRG_199p1:p.Thr1683Ilefs
  • NC_000023.10:g.32382805del
  • NC_000023.10:g.32382805del
  • NM_004006.2:c.5048delC
Protein change:
T1560fs
Molecular consequence:
  • NM_000109.4:c.5024del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004006.3:c.5048del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004009.3:c.5036del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004010.3:c.4679del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004011.4:c.1025del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004012.4:c.1016del - frameshift variant - [Sequence Ontology: SO:0001589]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004326630Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jun 3, 2023)
germlineclinical testing

PubMed (3)
[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

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

New variants, challenges and pitfalls in DMD genotyping: implications in diagnosis, prognosis and therapy.

Santos R, Gonçalves A, Oliveira J, Vieira E, Vieira JP, Evangelista T, Moreno T, Santos M, Fineza I, Bronze-da-Rocha E.

J Hum Genet. 2014 Aug;59(8):454-64. doi: 10.1038/jhg.2014.54. Epub 2014 Jul 10.

PubMed [citation]
PMID:
25007885
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004326630.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 2502344). This variant has not been reported in the literature in individuals affected with DMD-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Thr1683Ilefs*38) in the DMD gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DMD are known to be pathogenic (PMID: 16770791, 25007885).

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

Last Updated: Sep 29, 2024