NM_004006.3(DMD):c.2569C>T (p.Pro857Ser) AND not specified

Clinical significance:Benign/Likely benign (Last evaluated: Aug 7, 2017)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000214891.3

Allele description [Variation Report for NM_004006.3(DMD):c.2569C>T (p.Pro857Ser)]

NM_004006.3(DMD):c.2569C>T (p.Pro857Ser)

Gene:
DMD:dystrophin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp21.1
Genomic location:
Preferred name:
NM_004006.3(DMD):c.2569C>T (p.Pro857Ser)
HGVS:
  • NC_000023.11:g.32491330G>A
  • NG_012232.1:g.853280C>T
  • NM_000109.4:c.2545C>T
  • NM_004006.3:c.2569C>TMANE SELECT
  • NM_004009.3:c.2557C>T
  • NM_004010.3:c.2200C>T
  • NP_000100.3:p.Pro849Ser
  • NP_003997.1:p.Pro857Ser
  • NP_003997.2:p.Pro857Ser
  • NP_004000.1:p.Pro853Ser
  • NP_004001.1:p.Pro734Ser
  • LRG_199t1:c.2569C>T
  • LRG_199:g.853280C>T
  • LRG_199p1:p.Pro857Ser
  • NC_000023.10:g.32509447G>A
  • NM_004006.2:c.2569C>T
Protein change:
P734S
Links:
dbSNP: rs552275776
NCBI 1000 Genomes Browser:
rs552275776
Molecular consequence:
  • NM_000109.4:c.2545C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004006.3:c.2569C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004009.3:c.2557C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004010.3:c.2200C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000270126Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Likely benign
(Mar 13, 2015)
germlineclinical testing

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

SCV000707111EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Likely benign
(Mar 23, 2017)
germlineclinical testing

Citation Link,

SCV000714969GeneDxcriteria provided, single submitter
Benign
(Aug 7, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot providednot providednot providedclinical testing
not providedgermlinenot provided11not providednot providednot providedclinical testing
not providedgermlineyesnot providednot 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 Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000270126.2

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

Description

p.Pro857Ser in exon 20 of DMD: This variant is not expected to have clinical sig nificance because it has been identified in 0.9% (92/10124) of South Asian chrom osomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org ; dbSNP rs552275776).

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

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000707111.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000714969.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

Last Updated: Dec 4, 2021

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