DGKQ

diacylglycerol kinase theta, the group of Diacylglycerol kinases

Basic information

Region (hg38): 4:958886-986895

Previous symbols: [ "DAGK4" ]

Links

ENSG00000145214 ∙ NCBI:1609 ∙ OMIM:601207 ∙ HGNC:2856 ∙ Uniprot:P52824 ∙ 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 DGKQ gene.

• Inborn genetic diseases (66 variants)
• not provided (7 variants)
• Usher syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DGKQ 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				2	2	4
missense			64	4		68
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	64	6	4

Variants in DGKQ

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

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

Position	Type	Phenotype	Significance	ClinVar
4-960667-C-T		not specified	Uncertain significance (Jul 12, 2022)
4-961105-C-T		not specified	Uncertain significance (Dec 04, 2023)
4-961139-G-T		DGKQ-related disorder	Likely benign (Jun 19, 2019)
4-961147-A-G		not specified	Uncertain significance (Apr 19, 2023)
4-961189-C-T		not specified	Uncertain significance (Oct 14, 2023)
4-961208-C-T		DGKQ-related disorder	Likely benign (Jul 11, 2019)
4-961459-C-G		DGKQ-related disorder	Likely benign (May 28, 2019)
4-961469-T-C		not specified	Uncertain significance (Apr 28, 2022)
4-961475-C-T		DGKQ-related disorder	Benign (Jan 21, 2021)
4-961478-C-T		not specified	Uncertain significance (Dec 17, 2023)
4-961483-G-A		not specified	Uncertain significance (Jan 09, 2024)
4-961742-C-T		not specified	Likely benign (Aug 30, 2022)
4-961746-C-G		not specified	Uncertain significance (Jul 08, 2022)
4-961779-G-A		not specified	Uncertain significance (Sep 27, 2022)
4-961784-T-C		not specified	Uncertain significance (Nov 30, 2022)
4-961800-G-T		not specified	Uncertain significance (Oct 18, 2021)
4-961812-C-T		not specified	Uncertain significance (Oct 06, 2021)
4-961844-G-A			Benign (Aug 15, 2017)
4-962042-G-A		not specified	Uncertain significance (Oct 13, 2023)
4-962063-T-C		not specified	Uncertain significance (Mar 22, 2023)
4-962443-G-A		not specified	Uncertain significance (Dec 15, 2023)
4-962457-G-A		not specified	Uncertain significance (Jul 11, 2022)
4-962459-G-A			Benign (Aug 15, 2017)
4-962522-G-A			Likely benign (Nov 01, 2022)
4-962524-C-T		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DGKQ	protein_coding	protein_coding	ENST00000273814	23	28009

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.76e-9	1.00	125489	0	34	125523	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.104	570	577	0.988	0.0000397	5913
Missense in Polyphen		205	241.14	0.85011		2414
Synonymous	-2.29	310	263	1.18	0.0000197	1996
Loss of Function	3.14	22	44.7	0.493	0.00000237	473

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000207
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000202	0.000194
Middle Eastern	0.000112	0.000109
South Asian	0.000137	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphorylates diacylglycerol (DAG) to generate phosphatidic acid (PA). May regulate the activity of protein kinase C by controlling the balance between these two signaling lipids. Activated in the nucleus in response to alpha-thrombin and nerve growth factor (By similarity). May be involved in cAMP- induced activation of NR5A1 and subsequent steroidogenic gene transcription by delivering PA as ligand for NR5A1. Acts synergistically with NR5A1 on CYP17 transcriptional activity. {ECO:0000250, ECO:0000269|PubMed:17664281}.
• 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: 0.139

Intolerance Scores

• loftool: 0.367
• rvis_EVS: -2.68
• rvis_percentile_EVS: 0.74

Haploinsufficiency Scores

• pHI: 0.0850
• hipred: Y
• hipred_score: 0.505
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.590

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dgkq

Gene ontology

• Biological process: regulation of gluconeogenesis;regulation of transcription by RNA polymerase II;phosphatidic acid biosynthetic process;activation of transmembrane receptor protein tyrosine kinase activity;G protein-coupled receptor signaling pathway;protein kinase C-activating G protein-coupled receptor signaling pathway;regulation of G protein-coupled receptor signaling pathway;positive regulation of gene expression;negative regulation of gene expression;negative regulation of peptidyl-threonine phosphorylation;peptidyl-serine phosphorylation;cAMP-mediated signaling;platelet activation;response to ATP;intracellular signal transduction;diacylglycerol metabolic process;glycerolipid metabolic process;lipid phosphorylation;positive regulation of peptidyl-tyrosine phosphorylation;response to cAMP;thrombin-activated receptor signaling pathway;protein kinase C signaling;regulation of cholesterol metabolic process;regulation of synaptic vesicle endocytosis;regulation of TORC1 signaling;regulation of cortisol biosynthetic process;regulation of progesterone biosynthetic process
• Cellular component: nucleus;cytoplasm;endosome;cytosol;cytoskeleton;plasma membrane;vesicle membrane;nuclear matrix;nuclear speck;presynapse;postsynapse;glutamatergic synapse
• Molecular function: NAD+ kinase activity;diacylglycerol kinase activity;protein binding;ATP binding;kinase binding;transmembrane receptor protein tyrosine kinase activator activity;activating transcription factor binding;phospholipase binding;metal ion binding