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NM_000110.4(DPYD):c.1898del (p.Pro633fs) AND Dihydropyrimidine dehydrogenase deficiency

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Jun 11, 2023
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:
RCV002267740.2

Allele description [Variation Report for NM_000110.4(DPYD):c.1898del (p.Pro633fs)]

NM_000110.4(DPYD):c.1898del (p.Pro633fs)

Gene:
DPYD:dihydropyrimidine dehydrogenase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1p21.3
Genomic location:
Preferred name:
NM_000110.4(DPYD):c.1898del (p.Pro633fs)
HGVS:
  • NC_000001.11:g.97450067del
  • NG_008807.2:g.475994del
  • NM_000110.4:c.1898delMANE SELECT
  • NP_000101.2:p.Pro633fs
  • LRG_722:g.475994del
  • NC_000001.10:g.97915622delG
  • NC_000001.10:g.97915623del
  • NC_000001.10:g.97915623del
Protein change:
P633fs
Links:
PharmGKB: 1447989671PA128406956; OMIM: 612779.0005; dbSNP: rs72549303
NCBI 1000 Genomes Browser:
rs72549303
Molecular consequence:
  • NM_000110.4:c.1898del - frameshift variant - [Sequence Ontology: SO:0001589]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000020614OMIM
no assertion criteria provided
Pathogenic
(Aug 1, 1997)
germlineliterature only

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

SCV004194109Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 11, 2023)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Identification of a four-base deletion (delTCAT296-299) in the dihydropyrimidine dehydrogenase gene with variable clinical expression.

Vreken P, Van Kuilenburg AB, Meinsma R, De Abreu RA, Van Gennip AH.

Hum Genet. 1997 Aug;100(2):263-5.

PubMed [citation]
PMID:
9254861

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From OMIM, SCV000020614.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a child with DPD deficiency (274270), born of consanguineous parents, Vreken et al. (1997) identified a homozygous 1-bp deletion (1897delC) in the DPYD gene, resulting in a frameshift and premature termination. At the age of 9 months the patient showed febrile convulsions, severe neuromotor retardation, and spastic tetraplegia. Cerebral MRI showed ventriculomegaly with white matter hypodensity. At the age of 6 years, thymine-uraciluria was noted and DPD deficiency was demonstrated in fibroblasts. An earlier-born child had died before her first birthday with severe neuromotor retardation and febrile convulsions. Surprisingly, the father of the patient was also completely DPD deficient, although he had no history of convulsions. The mother of the patient showed intermediate DPD activity consistent with obligate carrier status. The patient was heterozygous for this 1-bp deletion, whereas the father was thought to be homozygous. The nature of the heterozygous mutation carried by the mother and transmitted to the son was not determined.

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

From Baylor Genetics, SCV004194109.1

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

Last Updated: Oct 26, 2024