DGKI

diacylglycerol kinase iota, the group of Ankyrin repeat domain containing|Diacylglycerol kinases

Basic information

Region (hg38): 7:137381037-137847092

Links

ENSG00000157680

∙ NCBI:9162 ∙ OMIM:604072 ∙ HGNC:2855 ∙ Uniprot:O75912 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DGKI gene.

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.

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			69 clinvar	1 clinvar		70
nonsense			1 clinvar			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	70	1	0

Variants in DGKI

This is a list of pathogenic ClinVar variants found in the DGKI region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
7-137391263-T-C	not specified	Uncertain significance (Jul 05, 2022)	2292174
7-137391269-C-T	not specified	Uncertain significance (Feb 16, 2023)	2460473
7-137391270-G-A	not specified	Uncertain significance (Sep 09, 2021)	2348986
7-137391270-G-T	not specified	Uncertain significance (Apr 26, 2023)	2540884
7-137391285-C-T	not specified	Uncertain significance (Feb 28, 2024)	3081942
7-137395696-C-T	not specified	Uncertain significance (Apr 18, 2023)	2538469
7-137407879-G-T	not specified	Uncertain significance (Sep 22, 2022)	2369887
7-137407905-C-T	not specified	Uncertain significance (Jan 03, 2024)	3081941
7-137463496-C-T	not specified	Uncertain significance (Jul 14, 2024)	3501352
7-137463501-G-A	not specified	Uncertain significance (Apr 16, 2024)	3271736
7-137463522-T-C	not specified	Uncertain significance (Dec 28, 2023)	3081939
7-137463530-C-G	not specified	Uncertain significance (Jul 20, 2021)	2240129
7-137463547-T-C	not specified	Uncertain significance (Mar 07, 2024)	3081938
7-137463563-G-C	not specified	Uncertain significance (Oct 05, 2022)	2317100
7-137463570-A-T	not specified	Uncertain significance (Jan 30, 2024)	3081936
7-137465911-G-A	not specified	Uncertain significance (Mar 18, 2024)	3271735
7-137465951-T-C	not specified	Uncertain significance (Nov 03, 2024)	3501360
7-137469568-G-A	not specified	Uncertain significance (Jan 23, 2023)	2477048
7-137485396-C-T	not specified	Uncertain significance (Jul 09, 2024)	3501350
7-137487621-G-A	not specified	Uncertain significance (Dec 04, 2024)	3501349
7-137487627-T-C	not specified	Uncertain significance (Aug 19, 2024)	3501356
7-137487662-C-T	not specified	Uncertain significance (Aug 10, 2024)	2341608
7-137487672-G-T	not specified	Uncertain significance (Aug 02, 2021)	2395321
7-137521902-C-T	not specified	Uncertain significance (Aug 08, 2022)	2305884
7-137521907-T-C	not specified	Uncertain significance (Nov 14, 2024)	2318472

GnomAD

Source: gnomAD

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: dbNSFP

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