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NM_004006.3(DMD):c.4093C>T (p.Leu1365Phe) AND not specified

Germline classification:
Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:
Mar 6, 2023
Review status:
criteria provided, conflicting classifications
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:
RCV000235165.14

Allele description [Variation Report for NM_004006.3(DMD):c.4093C>T (p.Leu1365Phe)]

NM_004006.3(DMD):c.4093C>T (p.Leu1365Phe)

Gene:
DMD:dystrophin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp21.1
Genomic location:
Preferred name:
NM_004006.3(DMD):c.4093C>T (p.Leu1365Phe)
Other names:
p.L1365F:CTT>TTT
HGVS:
  • NC_000023.11:g.32411892G>A
  • NG_012232.1:g.932718C>T
  • NM_000109.4:c.4069C>T
  • NM_004006.3:c.4093C>TMANE SELECT
  • NM_004009.3:c.4081C>T
  • NM_004010.3:c.3724C>T
  • NM_004011.4:c.70C>T
  • NM_004012.4:c.61C>T
  • NP_000100.3:p.Leu1357Phe
  • NP_003997.1:p.Leu1365Phe
  • NP_003997.2:p.Leu1365Phe
  • NP_004000.1:p.Leu1361Phe
  • NP_004001.1:p.Leu1242Phe
  • NP_004002.3:p.Leu24Phe
  • NP_004003.2:p.Leu21Phe
  • LRG_199t1:c.4093C>T
  • LRG_199:g.932718C>T
  • LRG_199p1:p.Leu1365Phe
  • NC_000023.10:g.32430009G>A
  • NM_004006.2:c.4093C>T
Protein change:
L1242F
Links:
dbSNP: rs148781346
NCBI 1000 Genomes Browser:
rs148781346
Molecular consequence:
  • NM_000109.4:c.4069C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004006.3:c.4093C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004009.3:c.4081C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004010.3:c.3724C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004011.4:c.70C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004012.4:c.61C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000112502Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)		Likely benign
(Jan 13, 2016) 		germlineclinical testing

Citation Link,

SCV000711684Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)		Uncertain significance
(May 22, 2017) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV003922913Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely benign
(Mar 6, 2023) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing
not providedgermlineunknown3not providednot providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Eurofins Ntd Llc (ga), SCV000112502.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided3not providednot providednot provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000711684.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

Variant classified as Uncertain Significance - Favor Benign. The p.Leu1365Phe va riant in DMD has not been previously reported in individuals with muscular dystr ophy, but has been identified in 0.19% (35/18082) of African chromosomes by the genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org/; dbSNP rs 148781346). This variant has been reported in ClinVar (Variation ID: 94611). Ple ase note that for diseases with clinical variability, reduced penetrance, or rec essive inheritance, pathogenic variants may be present at a low frequency in the general population. Computational prediction tools and conservation analysis su ggest that the p.Leu1365Phe variant may impact the protein, though this informat ion is not predictive enough to determine pathogenicity. In summary, while the c linical significance of the p.Leu1365Phe variant is uncertain, its frequency sug gests that it is more likely to be benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003922913.1

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

Last Updated: Jan 13, 2025