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NM_004006.3(DMD):c.6290G>T (p.Gly2097Val) AND Duchenne muscular dystrophy

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 27, 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:
RCV003084929.3

Allele description [Variation Report for NM_004006.3(DMD):c.6290G>T (p.Gly2097Val)]

NM_004006.3(DMD):c.6290G>T (p.Gly2097Val)

Gene:
DMD:dystrophin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp21.1
Genomic location:
Preferred name:
NM_004006.3(DMD):c.6290G>T (p.Gly2097Val)
HGVS:
  • NC_000023.11:g.32287529C>A
  • NG_012232.1:g.1057081G>T
  • NM_000109.4:c.6266G>T
  • NM_004006.3:c.6290G>TMANE SELECT
  • NM_004009.3:c.6278G>T
  • NM_004010.3:c.5921G>T
  • NM_004011.4:c.2267G>T
  • NM_004012.4:c.2258G>T
  • NP_000100.3:p.Gly2089Val
  • NP_003997.1:p.Gly2097Val
  • NP_003997.2:p.Gly2097Val
  • NP_004000.1:p.Gly2093Val
  • NP_004001.1:p.Gly1974Val
  • NP_004002.3:p.Gly756Val
  • NP_004003.2:p.Gly753Val
  • LRG_199t1:c.6290G>T
  • LRG_199:g.1057081G>T
  • LRG_199p1:p.Gly2097Val
  • NC_000023.10:g.32305646C>A
  • NM_004006.2:c.6290G>T
Protein change:
G1974V
Molecular consequence:
  • NM_000109.4:c.6266G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004006.3:c.6290G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004009.3:c.6278G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004010.3:c.5921G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004011.4:c.2267G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004012.4:c.2258G>T - missense variant - [Sequence Ontology: SO:0001583]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003483590Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Jun 27, 2022) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

[Application of next-generation sequencing in the molecular diagnosis of Duchenne muscular dystrophy].

Tian PC, Wang Y, Shi DD, Chen Z, Luo Q, Wang HL.

Zhongguo Dang Dai Er Ke Za Zhi. 2019 Mar;21(3):244-248. Chinese.

PubMed [citation]
PMID:
30907348
PMCID:
PMC7389351

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003483590.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This missense change has been observed in individual(s) with Becker/Duchenne muscular dystrophy (PMID: 30907348). In at least one individual the variant was observed to be de novo. 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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 2097 of the DMD protein (p.Gly2097Val). This variant also falls at the last nucleotide of exon 43, which is part of the consensus splice site for this exon.

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

Last Updated: Sep 29, 2024