NM_004006.3(DMD):c.10141C>T (p.Arg3381Ter) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: May 1, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000437942.13

Allele description [Variation Report for NM_004006.3(DMD):c.10141C>T (p.Arg3381Ter)]

NM_004006.3(DMD):c.10141C>T (p.Arg3381Ter)

Gene:

DMD:dystrophin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp21.2

Genomic location:

Preferred name:

NM_004006.3(DMD):c.10141C>T (p.Arg3381Ter)

Other names:

NP_003997.1:p.Arg3381*

HGVS:

NC_000023.11:g.31178751G>A
NG_012232.1:g.2165859C>T
NM_000109.4:c.10117C>T
NM_004006.3:c.10141C>TMANE SELECT
NM_004009.3:c.10129C>T
NM_004010.3:c.9772C>T
NM_004011.4:c.6118C>T
NM_004012.4:c.6109C>T
NM_004013.3:c.2761C>T
NM_004014.3:c.1954C>T
NM_004015.3:c.937C>T
NM_004016.3:c.937C>T
NM_004017.3:c.937C>T
NM_004018.3:c.937C>T
NM_004019.3:c.937C>T
NM_004020.4:c.2761C>T
NM_004021.3:c.2761C>T
NM_004022.3:c.2761C>T
NM_004023.3:c.2761C>T
NP_000100.3:p.Arg3373Ter
NP_003997.1:p.Arg3381Ter
NP_003997.2:p.Arg3381Ter
NP_004000.1:p.Arg3377Ter
NP_004001.1:p.Arg3258Ter
NP_004002.3:p.Arg2040Ter
NP_004003.2:p.Arg2037Ter
NP_004004.2:p.Arg921Ter
NP_004005.2:p.Arg652Ter
NP_004006.1:p.Arg313Ter
NP_004007.1:p.Arg313Ter
NP_004008.1:p.Arg313Ter
NP_004009.1:p.Arg313Ter
NP_004010.1:p.Arg313Ter
NP_004011.3:p.Arg921Ter
NP_004012.2:p.Arg921Ter
NP_004013.2:p.Arg921Ter
NP_004014.2:p.Arg921Ter
LRG_199t1:c.10141C>T
LRG_199:g.2165859C>T
LRG_199p1:p.Arg3381Ter
NC_000023.10:g.31196868G>A
NM_004006.2:c.10141C>T

Protein change:

R2037*; ARG3381TER

Links:

OMIM: 300377.0067; dbSNP: rs104894790

NCBI 1000 Genomes Browser:

rs104894790

Molecular consequence:

NM_000109.4:c.10117C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004006.3:c.10141C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004009.3:c.10129C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004010.3:c.9772C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004011.4:c.6118C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004012.4:c.6109C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004013.3:c.2761C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004014.3:c.1954C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004015.3:c.937C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004016.3:c.937C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004017.3:c.937C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004018.3:c.937C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004019.3:c.937C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004020.4:c.2761C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004021.3:c.2761C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004022.3:c.2761C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004023.3:c.2761C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000112313	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Jun 23, 2017)	germline	clinical testing	Citation Link,
SCV000516731	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Dec 14, 2023)	germline	clinical testing	Citation Link,
SCV005051403	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (May 1, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000112313

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Pathogenic
(Jun 23, 2017)

germline

clinical testing

Citation Link,

SCV000516731

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Dec 14, 2023)

germline

clinical testing

Citation Link,

SCV005051403

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(May 1, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	5	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000112313.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	5	not provided	not provided	clinical testing	not provided

#	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		5	not provided	not provided	not provided

From GeneDx, SCV000516731.5

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

Description

Reported previously in association with dystrophinopathy in published literature, the Leiden Open Variation Database, the UMD-DMD database and in individuals referred for genetic testing at GeneDx (PMID: 27425820, 8281150, 10320864, 19783145); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Based on the understanding of this genetic alteration, it may be amenable to nonsense read-through therapy that is currently available or in clinical trial; Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 19783145, 27425820, 27593222, 30833962, 23148581, 10320864, 25525159, 26886021, 20409719, 33773883, 32358784, 8281150)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV005051403.5

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

Description

DMD: PVS1, PM2, PS4:Moderate

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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