DPEP1
Basic information
Region (hg38): 16:89613308-89638456
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPEP1 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 | 0 | |||||
missense | 17 | 18 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 17 | 1 | 0 |
Variants in DPEP1
This is a list of pathogenic ClinVar variants found in the DPEP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
16-89630421-G-C | not specified | Uncertain significance (Sep 17, 2021) | ||
16-89635967-G-C | not specified | Uncertain significance (Jun 30, 2022) | ||
16-89636023-G-A | not specified | Uncertain significance (Feb 03, 2022) | ||
16-89636282-C-T | not specified | Uncertain significance (Jun 16, 2024) | ||
16-89636348-A-C | not specified | Uncertain significance (Feb 06, 2023) | ||
16-89636355-G-A | not specified | Likely benign (May 26, 2022) | ||
16-89636625-G-A | not specified | Uncertain significance (Aug 08, 2023) | ||
16-89636626-C-A | not specified | Uncertain significance (Aug 08, 2023) | ||
16-89637225-C-T | not specified | Uncertain significance (May 04, 2023) | ||
16-89637316-A-G | not specified | Uncertain significance (Dec 03, 2021) | ||
16-89637348-C-T | not specified | Uncertain significance (Jun 02, 2024) | ||
16-89637541-C-T | not specified | Uncertain significance (Apr 22, 2024) | ||
16-89637665-C-T | not specified | Uncertain significance (Mar 01, 2023) | ||
16-89637855-G-T | not specified | Uncertain significance (Dec 19, 2022) | ||
16-89637858-G-A | not specified | Uncertain significance (May 12, 2024) | ||
16-89637882-G-A | not specified | Uncertain significance (Jan 04, 2022) | ||
16-89637907-C-T | not specified | Uncertain significance (Jan 09, 2024) | ||
16-89637936-G-T | not specified | Uncertain significance (Jul 25, 2023) | ||
16-89638099-C-A | not specified | Uncertain significance (Sep 08, 2023) | ||
16-89638160-C-T | not specified | Uncertain significance (May 03, 2023) | ||
16-89638215-T-A | not specified | Uncertain significance (Oct 05, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
DPEP1 | protein_coding | protein_coding | ENST00000393092 | 10 | 25124 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.47e-10 | 0.175 | 125414 | 1 | 99 | 125514 | 0.000398 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -1.11 | 318 | 267 | 1.19 | 0.0000172 | 2663 |
Missense in Polyphen | 134 | 123.41 | 1.0858 | 1268 | ||
Synonymous | -2.90 | 161 | 121 | 1.34 | 0.00000875 | 847 |
Loss of Function | 0.543 | 16 | 18.5 | 0.864 | 7.95e-7 | 198 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000362 | 0.000359 |
Ashkenazi Jewish | 0.000703 | 0.000696 |
East Asian | 0.000272 | 0.000272 |
Finnish | 0.000555 | 0.000554 |
European (Non-Finnish) | 0.000470 | 0.000459 |
Middle Eastern | 0.000272 | 0.000272 |
South Asian | 0.000394 | 0.000359 |
Other | 0.000656 | 0.000653 |
dbNSFP
Source:
- Function
- FUNCTION: Hydrolyzes a wide range of dipeptides. Implicated in the renal metabolism of glutathione and its conjugates. Converts leukotriene D4 to leukotriene E4; it may play an important role in the regulation of leukotriene activity.;
- Pathway
- Busulfan Pathway, Pharmacodynamics;Eicosanoid Synthesis;Metabolism of lipids;Synthesis of Leukotrienes (LT) and Eoxins (EX);Arachidonic acid metabolism;Leukotriene metabolism;Biological oxidations;Metabolism;Fatty acid metabolism;leukotriene biosynthesis;Aflatoxin activation and detoxification
(Consensus)
Recessive Scores
- pRec
- 0.268
Intolerance Scores
- loftool
- 0.857
- rvis_EVS
- -0.77
- rvis_percentile_EVS
- 13.1
Haploinsufficiency Scores
- pHI
- 0.149
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.440
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.844
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dpep1
- Phenotype
- normal phenotype;
Gene ontology
- Biological process
- proteolysis;leukotriene metabolic process;glutathione metabolic process;xenobiotic metabolic process;apoptotic process;antibiotic metabolic process;negative regulation of cell migration;cellular response to drug;negative regulation of apoptotic process;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;homocysteine metabolic process;cellular response to calcium ion;cellular response to nitric oxide;cellular lactam catabolic process
- Cellular component
- extracellular space;nucleus;plasma membrane;apical plasma membrane;cell junction;anchored component of membrane;microvillus membrane;apical part of cell;extracellular exosome
- Molecular function
- protein binding;metalloexopeptidase activity;dipeptidyl-peptidase activity;zinc ion binding;dipeptidase activity;GPI anchor binding;cysteine-type endopeptidase inhibitor activity involved in apoptotic process;metallodipeptidase activity;modified amino acid binding