NM_004006.3(DMD):c.10098AGA[1] (p.Glu3367del) AND Duchenne muscular dystrophy

Clinical significance:Likely pathogenic (Last evaluated: Aug 23, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000312055.5

Allele description [Variation Report for NM_004006.3(DMD):c.10098AGA[1] (p.Glu3367del)]

NM_004006.3(DMD):c.10098AGA[1] (p.Glu3367del)

Gene:
DMD:dystrophin [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
Xp21.2
Genomic location:
Preferred name:
NM_004006.3(DMD):c.10098AGA[1] (p.Glu3367del)
HGVS:
  • NC_000023.11:g.31178789TCT[1]
  • NG_012232.1:g.2165816AGA[1]
  • NM_000109.4:c.10074AGA[1]
  • NM_004006.3:c.10098AGA[1]MANE SELECT
  • NM_004009.3:c.10086AGA[1]
  • NM_004010.3:c.9729AGA[1]
  • NM_004011.4:c.6075AGA[1]
  • NM_004012.4:c.6066AGA[1]
  • NM_004013.3:c.2718AGA[1]
  • NM_004014.3:c.1911AGA[1]
  • NM_004015.3:c.894AGA[1]
  • NM_004016.3:c.894AGA[1]
  • NM_004017.3:c.894AGA[1]
  • NM_004018.3:c.894AGA[1]
  • NM_004019.3:c.894AGA[1]
  • NM_004020.4:c.2718AGA[1]
  • NM_004021.3:c.2718AGA[1]
  • NM_004022.3:c.2718AGA[1]
  • NM_004023.3:c.2718AGA[1]
  • NP_000100.3:p.Glu3359del
  • NP_003997.2:p.Glu3367del
  • NP_004000.1:p.Glu3363del
  • NP_004001.1:p.Glu3244del
  • NP_004002.3:p.Glu2026del
  • NP_004003.2:p.Glu2023del
  • NP_004004.2:p.Glu907del
  • NP_004005.2:p.Glu638del
  • NP_004006.1:p.Glu299del
  • NP_004007.1:p.Glu299del
  • NP_004008.1:p.Glu299del
  • NP_004009.1:p.Glu299del
  • NP_004010.1:p.Glu299del
  • NP_004011.3:p.Glu907del
  • NP_004012.2:p.Glu907del
  • NP_004013.2:p.Glu907del
  • NP_004014.2:p.Glu907del
  • LRG_199t1:c.10101_10103del
  • LRG_199:g.2165816AGA[1]
  • NC_000023.10:g.31196906TCT[1]
  • NC_000023.10:g.31196906_31196908del
  • NM_004006.2:c.10101_10103del
  • NM_004006.2:c.10101_10103delAGA
Protein change:
E2023del
Links:
dbSNP: rs886042840
NCBI 1000 Genomes Browser:
rs886042840
Molecular consequence:
  • NM_000109.4:c.10074AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004006.3:c.10098AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004009.3:c.10086AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004010.3:c.9729AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004011.4:c.6075AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004012.4:c.6066AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004013.3:c.2718AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004014.3:c.1911AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004015.3:c.894AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004016.3:c.894AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004017.3:c.894AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004018.3:c.894AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004019.3:c.894AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004020.4:c.2718AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004021.3:c.2718AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004022.3:c.2718AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004023.3:c.2718AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV000692218Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospitalno assertion criteria providedPathogenic
(Apr 11, 2014)
germlineclinical testing

SCV001395018Invitaecriteria provided, single submitter
Likely pathogenic
(Aug 23, 2019)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Small mutation screening in the DMD gene by whole exome sequencing of an argentine Duchenne/Becker muscular dystrophies cohort.

Luce LN, Carcione M, Mazzanti C, Ferrer M, Szijan I, Giliberto F.

Neuromuscul Disord. 2018 Dec;28(12):986-995. doi: 10.1016/j.nmd.2018.08.012. Epub 2018 Sep 6.

PubMed [citation]
PMID:
30342905

Loss of a single amino acid from dystrophin resulting in Duchenne muscular dystrophy with retention of dystrophin protein.

Becker K, Robb SA, Hatton Z, Yau SC, Abbs S, Roberts RG.

Hum Mutat. 2003 Jun;21(6):651.

PubMed [citation]
PMID:
14961551
See all PubMed Citations (6)

Details of each submission

From Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital, SCV000692218.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001395018.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This variant, c.10101_10103del, results in the deletion of 1 amino acid(s) of the DMD protein (p.Glu3367del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has been observed in a family (PMID: 30342905) and in several individuals with Duchenne muscular dystrophy (DMD) and/or Becker muscular dystrophy (BMD) (PMID: 14961551, 23536893, 19959795, 21515508). ClinVar contains an entry for this variant (Variation ID: 284288). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Aug 17, 2021

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