DPYS
Basic information
Region (hg38): 8:104330324-104467055
Links
Phenotypes
GenCC
Source:
- dihydropyrimidinuria (Strong), mode of inheritance: AR
- dihydropyrimidinuria (Supportive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Dihydropyriminidase deficiency | AR | Pharmacogenomic | Affected individuals could theoretically have severe toxicity with 5-fluorouracil; Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Biochemical; Neurologic | 1770794; 9323563; 9266350; 9718352; 17383919; 20362666; 29054612 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (9 variants)
- Dihydropyrimidinase deficiency (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPYS gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 24 | 37 | ||||
missense | 90 | 102 | ||||
nonsense | 5 | |||||
start loss | 1 | |||||
frameshift | 7 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 1 | 3 | 4 | |||
non coding | 11 | 24 | ||||
Total | 9 | 11 | 103 | 39 | 15 |
Highest pathogenic variant AF is 0.0000460
Variants in DPYS
This is a list of pathogenic ClinVar variants found in the DPYS region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
8-104348556-G-C | not specified | Uncertain significance (Mar 31, 2023) | ||
8-104348607-G-A | not specified | Uncertain significance (Mar 19, 2024) | ||
8-104348676-A-C | not specified | Uncertain significance (Jul 19, 2023) | ||
8-104348747-G-T | not specified | Uncertain significance (Oct 25, 2022) | ||
8-104348755-C-A | not specified | Uncertain significance (Sep 21, 2023) | ||
8-104348773-G-T | not specified | Uncertain significance (Dec 20, 2021) | ||
8-104348774-C-G | not specified | Uncertain significance (Mar 20, 2024) | ||
8-104348778-A-G | not specified | Uncertain significance (May 05, 2023) | ||
8-104348862-G-A | not specified | Uncertain significance (Oct 26, 2021) | ||
8-104348868-G-A | not specified | Uncertain significance (Aug 08, 2023) | ||
8-104348883-G-A | not specified | Uncertain significance (Mar 19, 2024) | ||
8-104348914-T-G | not specified | Uncertain significance (Apr 27, 2022) | ||
8-104348962-A-G | not specified | Uncertain significance (Dec 21, 2023) | ||
8-104349070-T-C | not specified | Uncertain significance (May 14, 2024) | ||
8-104349106-A-G | not specified | Uncertain significance (Aug 07, 2024) | ||
8-104349138-G-A | not specified | Likely benign (Feb 10, 2023) | ||
8-104349177-T-C | not specified | Uncertain significance (Nov 29, 2021) | ||
8-104349223-T-C | not specified | Uncertain significance (Jul 31, 2024) | ||
8-104349289-A-G | not specified | Uncertain significance (Jan 23, 2024) | ||
8-104349304-T-A | not specified | Uncertain significance (May 13, 2024) | ||
8-104349361-A-G | not specified | Likely benign (Apr 18, 2024) | ||
8-104349406-C-T | not specified | Likely benign (May 11, 2022) | ||
8-104349438-T-C | not specified | Uncertain significance (May 20, 2024) | ||
8-104349496-A-T | not specified | Uncertain significance (Mar 01, 2023) | ||
8-104349520-C-T | not specified | Uncertain significance (Sep 09, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
DPYS | protein_coding | protein_coding | ENST00000351513 | 9 | 136730 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.78e-11 | 0.269 | 125457 | 3 | 288 | 125748 | 0.00116 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.335 | 272 | 288 | 0.944 | 0.0000154 | 3369 |
Missense in Polyphen | 124 | 137.09 | 0.90448 | 1589 | ||
Synonymous | -0.604 | 115 | 107 | 1.07 | 0.00000623 | 1036 |
Loss of Function | 0.921 | 19 | 23.9 | 0.797 | 0.00000144 | 256 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00769 | 0.00765 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00109 | 0.00109 |
Finnish | 0.0000924 | 0.0000924 |
European (Non-Finnish) | 0.000766 | 0.000756 |
Middle Eastern | 0.00109 | 0.00109 |
South Asian | 0.00101 | 0.00101 |
Other | 0.000652 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the second step of the reductive pyrimidine degradation, the reversible hydrolytic ring opening of dihydropyrimidines. Can catalyze the ring opening of 5,6- dihydrouracil to N-carbamyl-alanine and of 5,6-dihydrothymine to N-carbamyl-amino isobutyrate.;
- Disease
- DISEASE: Dihydropyrimidinase deficiency (DPYSD) [MIM:222748]: An autosomal recessive disorder of pyrimidine metabolism characterized by dihydropyrimidinuria. It is associated with a variable clinical phenotype characterized by epileptic or convulsive attacks, dysmorphic features and severe developmental delay, and congenital microvillous atrophy. Most patients are, however, asymptomatic. {ECO:0000269|PubMed:9718352}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Pyrimidine metabolism - Homo sapiens (human);beta-Alanine metabolism - Homo sapiens (human);Pantothenate and CoA biosynthesis - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Fluoropyrimidine Pathway, Pharmacokinetics;Carnosinuria, carnosinemia;Ureidopropionase deficiency;GABA-Transaminase Deficiency;Pyrimidine Metabolism;Beta-Alanine Metabolism;UMP Synthase Deiciency (Orotic Aciduria);MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy);Beta Ureidopropionase Deficiency;Dihydropyrimidinase Deficiency;Fluoropyrimidine Activity;pyrimidine ribonucleosides degradation;Pyrimidine metabolism;Pyrimidine catabolism;Nucleobase catabolism;Metabolism of nucleotides;Metabolism;uracil degradation;thymine degradation;Pyrimidine nucleotides nucleosides metabolism
(Consensus)
Recessive Scores
- pRec
- 0.303
Intolerance Scores
- loftool
- 0.267
- rvis_EVS
- -1.04
- rvis_percentile_EVS
- 7.71
Haploinsufficiency Scores
- pHI
- 0.145
- hipred
- Y
- hipred_score
- 0.528
- ghis
- 0.448
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.857
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dpys
- Phenotype
Gene ontology
- Biological process
- pyrimidine nucleobase catabolic process;thymine catabolic process;uracil catabolic process;beta-alanine metabolic process;pyrimidine nucleoside catabolic process;protein homotetramerization
- Cellular component
- cytosol;extracellular exosome
- Molecular function
- uracil binding;thymine binding;dihydropyrimidinase activity;zinc ion binding;amino acid binding;phosphoprotein binding