ClinVar Miner

Submissions for variant NM_000110.4(DPYD):c.299_302del (p.Phe100fs)

dbSNP: rs72549309
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000589260 SCV000695413 pathogenic Dihydropyrimidine dehydrogenase deficiency 2017-04-06 criteria provided, single submitter clinical testing Variant summary: The DPYD c.299_302delTCAT (p.Phe100Serfs) variant results in a premature termination codon, predicted to cause a truncated or absent DPYD protein due to nonsense mediated decay, which are commonly known mechanisms for disease. This variant was found in 11/121318 control chromosomes at a frequency of 0.0000907, which does not exceed the estimated maximal expected allele frequency of a pathogenic DPYD variant (0.0025). Multiple publications have cited the variant in homozygous and compound heterozygous affected individuals. Vreken_1997 reports the variant in one family, 3 homozygous individuals, the proband presented at the age of 4, while the mother didn't present until age of 19 with generalized tonic seizures. The brother, who was also homozygous for the variant was indicated to be normal, although the age of the brother was not provided. All three individuals were found to have no detectable levels of DPD activity. The variant of interest has not, to our knowledge, been cited and classified by other clinical diagnostic laboratories or reputable databases (other than HGMD). Therefore, the variant of interest has been classified as "pathogenic."
Revvity Omics, Revvity RCV000589260 SCV002021753 pathogenic Dihydropyrimidine dehydrogenase deficiency 2019-08-01 criteria provided, single submitter clinical testing
GeneDx RCV001836843 SCV002097432 pathogenic not provided 2025-02-11 criteria provided, single submitter clinical testing Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 34697415, 10071185, 9254861, 19296131, 31589614)
Baylor Genetics RCV000589260 SCV003835440 pathogenic Dihydropyrimidine dehydrogenase deficiency 2024-03-23 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000589260 SCV004049894 pathogenic Dihydropyrimidine dehydrogenase deficiency 2023-04-11 criteria provided, single submitter clinical testing
OMIM RCV000589260 SCV000020612 pathogenic Dihydropyrimidine dehydrogenase deficiency 2009-06-01 no assertion criteria provided literature only

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