NM_004006.3(DMD):c.3189G>A (p.Trp1063Ter) AND Duchenne muscular dystrophy

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 9, 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:: RCV002541132.10

Allele description [Variation Report for NM_004006.3(DMD):c.3189G>A (p.Trp1063Ter)]

NM_004006.3(DMD):c.3189G>A (p.Trp1063Ter)

Gene:

DMD:dystrophin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp21.1

Genomic location:

Preferred name:

NM_004006.3(DMD):c.3189G>A (p.Trp1063Ter)

HGVS:

NC_000023.11:g.32464673C>T
NG_012232.1:g.879937G>A
NM_000109.4:c.3165G>A
NM_004006.3:c.3189G>AMANE SELECT
NM_004009.3:c.3177G>A
NM_004010.3:c.2820G>A
NP_000100.3:p.Trp1055Ter
NP_003997.2:p.Trp1063Ter
NP_004000.1:p.Trp1059Ter
NP_004001.1:p.Trp940Ter
LRG_199t1:c.3189G>A
LRG_199:g.879937G>A
NC_000023.10:g.32482790C>T

Protein change:

W1055*

Links:

dbSNP: rs2148428124

NCBI 1000 Genomes Browser:

rs2148428124

Molecular consequence:

NM_000109.4:c.3165G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_004006.3:c.3189G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_004009.3:c.3177G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_004010.3:c.2820G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

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

Recent activity

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Gemella taiwanensis strain NTUH_2196 RNA polymerase beta subunit (rpoB) gene, pa...
Gemella taiwanensis strain NTUH_2196 RNA polymerase beta subunit (rpoB) gene, partial cds
gi|308194106|gb|HM103927.1|

Nucleotide
Gemella taiwanensis strain NTUH_2196 16S ribosomal RNA gene, partial sequence
Gemella taiwanensis strain NTUH_2196 16S ribosomal RNA gene, partial sequence
gi|308194100|gb|HM103932.1|

Nucleotide
syntaxin-6 isoform X1 [Tursiops truncatus]
syntaxin-6 isoform X1 [Tursiops truncatus]
gi|1835157847|ref|XP_033709793.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003445037	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 9, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 28318817, 16770791, 25007885, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003445037

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 9, 2022)

germline

clinical testing

PubMed (4)
[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

Clinical and mutational characteristics of Duchenne muscular dystrophy patients based on a comprehensive database in South China.

Wang DN, Wang ZQ, Yan L, He J, Lin MT, Chen WJ, Wang N.

Neuromuscul Disord. 2017 Aug;27(8):715-722. doi: 10.1016/j.nmd.2017.02.010. Epub 2017 Feb 21.

PubMed [citation]

PMID:: 28318817

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 (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003445037.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1322689). This premature translational stop signal has been observed in individual(s) with Duchenne muscular dystrophy (PMID: 28318817). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp1063*) 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: Oct 26, 2024

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