NM_004006.3(DMD):c.7398del (p.Met2466fs) AND Duchenne muscular dystrophy

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 21, 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:: RCV003623184.2

Allele description [Variation Report for NM_004006.3(DMD):c.7398del (p.Met2466fs)]

NM_004006.3(DMD):c.7398del (p.Met2466fs)

Gene:

DMD:dystrophin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xp21.1

Genomic location:

Preferred name:

NM_004006.3(DMD):c.7398del (p.Met2466fs)

HGVS:

NC_000023.11:g.31774104del
NG_012232.1:g.1570506del
NM_000109.4:c.7374del
NM_004006.3:c.7398delMANE SELECT
NM_004009.3:c.7386del
NM_004010.3:c.7029del
NM_004011.4:c.3375del
NM_004012.4:c.3366del
NM_004013.3:c.18del
NM_004020.4:c.18del
NM_004021.3:c.18del
NM_004022.3:c.18del
NM_004023.3:c.18del
NP_000100.3:p.Met2458fs
NP_003997.1:p.Met2466Ilefs
NP_003997.2:p.Met2466fs
NP_004000.1:p.Met2462fs
NP_004001.1:p.Met2343fs
NP_004002.3:p.Met1125fs
NP_004003.2:p.Met1122fs
NP_004004.2:p.Met6fs
NP_004011.3:p.Met6fs
NP_004012.2:p.Met6fs
NP_004013.2:p.Met6fs
NP_004014.2:p.Met6fs
LRG_199t1:c.7398del
LRG_199:g.1570506del
LRG_199p1:p.Met2466Ilefs
NC_000023.10:g.31792221del
NM_004006.2:c.7398delG

Protein change:

M1122fs

Molecular consequence:

NM_000109.4:c.7374del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004006.3:c.7398del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004009.3:c.7386del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004010.3:c.7029del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004011.4:c.3375del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004012.4:c.3366del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004013.3:c.18del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004020.4:c.18del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004021.3:c.18del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004022.3:c.18del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004023.3:c.18del - 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
SCV004448316	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 21, 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

SCV004448316

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 21, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004448316.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with DMD-related conditions. This sequence change creates a premature translational stop signal (p.Met2466Ilefs*28) 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: Nov 10, 2024

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