DGKI
Basic information
Region (hg38): 7:137381037-137847092
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (112 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DGKI gene is commonly pathogenic or not. These statistics are base on transcript: NM_001321708.2. 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 | 0 | |||||
| missense | 111 | 112 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 112 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DGKI | protein_coding | protein_coding | ENST00000288490 | 34 | 466056 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.931 | 0.0687 | 125728 | 0 | 20 | 125748 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.08 | 340 | 542 | 0.627 | 0.0000294 | 6909 |
| Missense in Polyphen | 115 | 243.09 | 0.47307 | 2861 | ||
| Synonymous | 0.00432 | 190 | 190 | 1.00 | 0.00000976 | 2056 |
| Loss of Function | 6.03 | 13 | 65.8 | 0.197 | 0.00000343 | 766 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000994 | 0.0000992 |
| East Asian | 0.0000602 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000126 | 0.000123 |
| Middle Eastern | 0.0000602 | 0.0000544 |
| South Asian | 0.000137 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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);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
- 0.128
Intolerance Scores
- loftool
- 0.327
- rvis_EVS
- -1.04
- rvis_percentile_EVS
- 7.77
Haploinsufficiency Scores
- pHI
- 0.0995
- hipred
- Y
- hipred_score
- 0.667
- ghis
- 0.546
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.688
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dgki
- Phenotype
- neoplasm;
Gene ontology
- Biological process
- protein kinase C-activating G protein-coupled receptor signaling pathway;neurotransmitter secretion;platelet activation;negative regulation of GTPase activity;intracellular signal transduction;diacylglycerol metabolic process;glycerolipid metabolic process;positive regulation of Ras protein signal transduction;lipid phosphorylation;habituation;regulation of synaptic transmission, glutamatergic;excitatory postsynaptic potential;regulation of long-term synaptic depression;regulation of synaptic vesicle exocytosis
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane;synaptic vesicle;guanyl-nucleotide exchange factor complex;protein-containing complex;neuronal cell body;dendritic spine;axon terminus;synapse;perinuclear region of cytoplasm;excitatory synapse;Schaffer collateral - CA1 synapse;extrinsic component of presynaptic active zone membrane;glutamatergic synapse;extrinsic component of postsynaptic density membrane
- Molecular function
- NAD+ kinase activity;diacylglycerol kinase activity;GTPase inhibitor activity;protein binding;ATP binding;Ras GTPase binding;metal ion binding