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NM_000110.4(DPYD):c.1503G>A (p.Trp501Ter) AND Dihydropyrimidine dehydrogenase deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 15, 2018
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:
RCV000778264.4

Allele description [Variation Report for NM_000110.4(DPYD):c.1503G>A (p.Trp501Ter)]

NM_000110.4(DPYD):c.1503G>A (p.Trp501Ter)

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.1503G>A (p.Trp501Ter)
HGVS:
  • NC_000001.11:g.97549581C>T
  • NG_008807.2:g.376479G>A
  • NM_000110.4:c.1503G>AMANE SELECT
  • NP_000101.2:p.Trp501Ter
  • NP_000101.2:p.Trp501Ter
  • LRG_722t1:c.1503G>A
  • LRG_722:g.376479G>A
  • LRG_722p1:p.Trp501Ter
  • NC_000001.10:g.98015137C>T
  • NM_000110.3:c.1503G>A
Protein change:
W501*
Links:
dbSNP: rs1557790713
NCBI 1000 Genomes Browser:
rs1557790713
Molecular consequence:
  • NM_000110.4:c.1503G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Dihydropyrimidine dehydrogenase deficiency (DPYDD)
Synonyms:
DPYD DEFICIENCY; DPD deficiency; Pyrimidinemia familial; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010130; MedGen: C1959620; Orphanet: 1675; OMIM: 274270

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000914436Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)		Uncertain significance
(Oct 15, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000914436.1

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

Description

This variant is a stop-gained variant, which was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018) and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score for this variant, it could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. Due to the potential impact of stop-gained variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for this disease.

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

Last Updated: Nov 4, 2023