DGKZ
Basic information
Region (hg38): 11:46332905-46380554
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (383 variants)
- not_specified (155 variants)
- atypical_cerebral_palsy (2 variants)
- Autism (1 variants)
- Inborn_genetic_diseases (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DGKZ gene is commonly pathogenic or not. These statistics are base on transcript: NM_001199267.2. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 65 | 74 | ||||
| missense | 167 | 11 | 180 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 169 | 76 | 9 |
Highest pathogenic variant AF is 0.0001130349
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DGKZ | protein_coding | protein_coding | ENST00000454345 | 31 | 47650 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0395 | 0.960 | 125698 | 1 | 23 | 125722 | 0.0000955 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.76 | 493 | 698 | 0.706 | 0.0000460 | 7089 |
| Missense in Polyphen | 120 | 276.48 | 0.43403 | 2913 | ||
| Synonymous | -0.0469 | 288 | 287 | 1.00 | 0.0000192 | 2261 |
| Loss of Function | 5.73 | 17 | 68.0 | 0.250 | 0.00000404 | 679 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000186 | 0.000182 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000282 | 0.000231 |
| European (Non-Finnish) | 0.0000940 | 0.0000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000103 | 0.0000980 |
| Other | 0.000329 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Displays a strong preference for 1,2-diacylglycerols over 1,3-diacylglycerols, but lacks substrate specificity among molecular species of long chain diacylglycerols. Isoform 2 but not isoform 1 regulates RASGRP1 activity (PubMed:11257115). Positively regulates insulin-induced translocation of SLC2A4 to the cell membrane in adipocytes (By similarity). Activates PIP5K1A activity via generation of phosphatidic acid (PubMed:15157668). {ECO:0000250|UniProtKB:Q80UP3, ECO:0000269|PubMed:11257115, ECO:0000269|PubMed:15157668}.;
- Pathway
- Glycerolipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Myometrial Relaxation and Contraction Pathways;Leptin Insulin Overlap;Signaling by GPCR;Signal Transduction;Effects of PIP2 hydrolysis;Platelet activation, signaling and aggregation;Glycerophospholipid metabolism;Hemostasis;G alpha (q) signalling events;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.238
Intolerance Scores
- loftool
- 0.606
- rvis_EVS
- 0.27
- rvis_percentile_EVS
- 70.69
Haploinsufficiency Scores
- pHI
- 0.130
- hipred
- Y
- hipred_score
- 0.790
- ghis
- 0.464
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.991
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dgkz
- Phenotype
- immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- phosphatidic acid biosynthetic process;protein kinase C-activating G protein-coupled receptor signaling pathway;cell migration;platelet activation;intracellular signal transduction;diacylglycerol metabolic process;glycerolipid metabolic process;lipid phosphorylation;positive regulation of 1-phosphatidylinositol-4-phosphate 5-kinase activity
- Cellular component
- nucleus;cytoplasm;plasma membrane;postsynaptic density;nuclear speck;lamellipodium;glutamatergic synapse
- Molecular function
- NAD+ kinase activity;diacylglycerol kinase activity;protein binding;ATP binding;kinase activity;metal ion binding