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:: RCV003512202.1

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004326630	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 3, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 16770791, 25007885, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004326630

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 3, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

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 Invitae, SCV004326630.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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).

#	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: Feb 20, 2024

ClinVar

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