NM_000110.4(DPYD):c.1601G>A (p.Ser534Asn) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(2);Uncertain significance(1) (Last evaluated: Mar 26, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000086477.3

Allele description [Variation Report for NM_000110.4(DPYD):c.1601G>A (p.Ser534Asn)]

NM_000110.4(DPYD):c.1601G>A (p.Ser534Asn)

Gene:
DPYD:dihydropyrimidine dehydrogenase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p21.3
Genomic location:
Preferred name:
NM_000110.4(DPYD):c.1601G>A (p.Ser534Asn)
HGVS:
  • NC_000001.11:g.97515865C>T
  • NG_008807.2:g.410195G>A
  • NM_000110.3:c.1601G>A
  • NM_000110.4:c.1601G>AMANE SELECT
  • NP_000101.2:p.Ser534Asn
  • NP_000101.2:p.Ser534Asn
  • LRG_722t1:c.1601G>A
  • LRG_722:g.410195G>A
  • LRG_722p1:p.Ser534Asn
  • NC_000001.10:g.97981421C>T
  • NC_000001.9:g.97754009C>T
  • Q12882:p.Ser534Asn
Protein change:
S534N
Links:
UniProtKB: Q12882#VAR_005175; dbSNP: rs1801158
NCBI 1000 Genomes Browser:
rs1801158
Molecular consequence:
  • NM_000110.3:c.1601G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_000110.4:c.1601G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000118643Diasio Lab, Mayo Clinicno assertion providednot providedunknownnot provided

SCV000574775CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Uncertain significance
(Jan 1, 2017)
germlineclinical testing

Citation Link,

SCV000841878Athena Diagnostics Inccriteria provided, single submitter
Likely benign
(Sep 8, 2017)
germlineclinical testing

PubMed (57)
[See all records that cite these PMIDs]

SCV000977480GeneDxcriteria provided, single submitter
Likely benign
(Mar 26, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownnot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Pretreatment serum uracil concentration as a predictor of severe and fatal fluoropyrimidine-associated toxicity.

Meulendijks D, Henricks LM, Jacobs BAW, Aliev A, Deenen MJ, de Vries N, Rosing H, van Werkhoven E, de Boer A, Beijnen JH, Mandigers CMPW, Soesan M, Cats A, Schellens JHM.

Br J Cancer. 2017 May 23;116(11):1415-1424. doi: 10.1038/bjc.2017.94. Epub 2017 Apr 20.

PubMed [citation]
PMID:
28427087
PMCID:
PMC5520099

Highlight on DPYD gene polymorphisms and treatment by capecitabine (.).

Milano G.

Scand J Clin Lab Invest Suppl. 2016;245:S30-3. doi: 10.1080/00365513.2016.1208438. Epub 2016 Jul 25.

PubMed [citation]
PMID:
27454530
See all PubMed Citations (57)

Details of each submission

From Diasio Lab, Mayo Clinic, SCV000118643.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot providednot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownnot providednot providednot providednot providednot providednot providednot providednot provided

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV000574775.11

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

From Athena Diagnostics Inc, SCV000841878.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (57)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV000977480.1

#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: Sep 6, 2021

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