DGKG

diacylglycerol kinase gamma, the group of Diacylglycerol kinases|EF-hand domain containing

Basic information

Region (hg38): 3:186105667-186362234

Previous symbols: [ "DAGK3" ]

Links

ENSG00000058866 ∙ NCBI:1608 ∙ OMIM:601854 ∙ HGNC:2853 ∙ Uniprot:P49619 ∙ 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 DGKG gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DGKG 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					1	1
missense			52	1		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	52	1	1

Variants in DGKG

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

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

Position	Type	Phenotype	Significance	ClinVar
3-186105685-G-A		not specified	Uncertain significance (Oct 25, 2022)
3-186105833-C-T		not specified	Uncertain significance (Sep 17, 2021)
3-186105863-G-A		ETV5-related disorder	Likely benign (Aug 28, 2019)
3-186106153-C-T			Benign (Nov 10, 2018)
3-186106184-T-C			Benign (Jun 21, 2021)
3-186106215-T-C			Benign (Jun 18, 2021)
3-186150103-C-T		not specified	Uncertain significance (Apr 25, 2022)
3-186150133-C-G		not specified	Uncertain significance (Sep 06, 2022)
3-186150163-G-A		not specified	Uncertain significance (Jun 24, 2022)
3-186164992-C-T		not specified	Uncertain significance (Feb 06, 2024)
3-186188208-C-T		not specified	Likely benign (Feb 06, 2023)
3-186188331-C-A		not specified	Uncertain significance (May 02, 2024)
3-186211795-C-T			Benign (Feb 25, 2018)
3-186211806-T-C		not specified	Uncertain significance (Nov 09, 2022)
3-186211829-G-T		not specified	Uncertain significance (Mar 30, 2024)
3-186242532-C-G		not specified	Uncertain significance (Feb 28, 2023)
3-186242565-C-T		not specified	Uncertain significance (Mar 07, 2024)
3-186251868-G-C		not specified	Uncertain significance (May 04, 2022)
3-186251869-G-A		not specified	Uncertain significance (Aug 17, 2022)
3-186251910-C-G		not specified	Uncertain significance (Jan 26, 2022)
3-186253105-G-A		not specified	Uncertain significance (Dec 06, 2022)
3-186253181-A-G			Likely benign (Aug 01, 2022)
3-186257857-T-C		not specified	Uncertain significance (Mar 13, 2023)
3-186257859-C-T		not specified	Uncertain significance (Jan 29, 2024)
3-186257908-G-C		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DGKG	protein_coding	protein_coding	ENST00000265022	24	256570

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.02e-13	0.988	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.125	464	472	0.984	0.0000273	5249
Missense in Polyphen		165	202.5	0.81483		2403
Synonymous	-0.462	187	179	1.04	0.0000112	1444
Loss of Function	2.53	27	45.4	0.595	0.00000193	556

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00121	0.00121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000232	0.000220
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Reverses the normal flow of glycerolipid biosynthesis by phosphorylating diacylglycerol back to phosphatidic acid.
• 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: 0.190

Intolerance Scores

• loftool: 0.130
• rvis_EVS: -1.52
• rvis_percentile_EVS: 3.42

Haploinsufficiency Scores

• pHI: 0.452
• hipred: N
• hipred_score: 0.372
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dgkg

Gene ontology

• Biological process: signal transduction;protein kinase C-activating G protein-coupled receptor signaling pathway;platelet activation;intracellular signal transduction;diacylglycerol metabolic process;glycerolipid metabolic process;lipid phosphorylation;neuron development
• Cellular component: cytoplasm;plasma membrane
• Molecular function: NAD+ kinase activity;diacylglycerol kinase activity;calcium ion binding;ATP binding