DGKA

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

Basic information

Region (hg38): 12:55927319-55954027

Previous symbols: [ "DAGK", "DAGK1" ]

Links

ENSG00000065357 ∙ NCBI:1606 ∙ OMIM:125855 ∙ HGNC:2849 ∙ Uniprot:P23743 ∙ 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 DGKA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DGKA 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	3	5
missense			29	3	2	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding						0
Total	0	0	29	5	5

Variants in DGKA

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

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

Position	Type	Phenotype	Significance	ClinVar
12-55936553-A-G		not specified	Uncertain significance (Jun 17, 2024)
12-55937048-G-T		not specified	Uncertain significance (Aug 30, 2022)
12-55937415-G-C		not specified	Uncertain significance (Dec 04, 2024)
12-55937420-G-A		not specified	Uncertain significance (Oct 13, 2023)
12-55937511-G-A		not specified	Likely benign (Oct 06, 2022)
12-55937993-A-G		not specified	Likely benign (Apr 12, 2024)
12-55938532-C-T		not specified	Uncertain significance (Dec 15, 2023)
12-55938555-A-T		not specified	Uncertain significance (Sep 26, 2024)
12-55938925-A-G		DGKA-related disorder	Likely benign (Feb 22, 2022)
12-55938948-G-A		not specified	Uncertain significance (Oct 26, 2022)
12-55938971-T-A		not specified	Uncertain significance (Oct 29, 2024)
12-55939195-G-A		not specified	Uncertain significance (Nov 08, 2022)
12-55939426-C-T		DGKA-related disorder	Benign (Feb 09, 2018)
12-55939429-C-T		DGKA-related disorder	Benign (Jan 06, 2020)
12-55939439-A-C		not specified	Uncertain significance (May 27, 2022)
12-55939459-C-A		not specified	Uncertain significance (Aug 01, 2024)
12-55940094-C-T		not specified	Uncertain significance (Jun 24, 2022)
12-55940101-C-G		not specified	Uncertain significance (Oct 09, 2024)
12-55940383-C-G		not specified	Uncertain significance (Aug 08, 2023)
12-55940401-A-G		DGKA-related disorder	Benign (Nov 07, 2019)
12-55940651-G-A		not specified	Uncertain significance (Dec 09, 2024)
12-55940655-A-G		not specified	Uncertain significance (Oct 29, 2024)
12-55940907-C-T		not specified	Uncertain significance (Jan 11, 2023)
12-55940908-G-A		DGKA-related disorder	Likely benign (Mar 27, 2019)
12-55940920-T-G			Benign (Feb 09, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DGKA	protein_coding	protein_coding	ENST00000331886	23	26709

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.461	0.539	125665	0	83	125748	0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.50	270	413	0.654	0.0000221	4843
Missense in Polyphen		71	176.33	0.40266		2129
Synonymous	1.83	126	155	0.813	0.00000869	1384
Loss of Function	5.08	11	49.6	0.222	0.00000274	531

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000604	0.000601
European (Non-Finnish)	0.000527	0.000519
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.000816	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Upon cell stimulation converts the second messenger diacylglycerol into phosphatidate, initiating the resynthesis of phosphatidylinositols and attenuating protein kinase C activity.
• 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);Familial lipoprotein lipase deficiency;Glycerolipid Metabolism;Glycerol Kinase Deficiency;Phospholipid Biosynthesis;D-glyceric acidura;Signaling by GPCR;Signal Transduction;TCR;Effects of PIP2 hydrolysis;Platelet activation, signaling and aggregation;Glycerophospholipid metabolism;Hemostasis;G alpha (q) signalling events;GPCR downstream signalling;Calcineurin-regulated NFAT-dependent transcription in lymphocytes (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.253
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.74

Haploinsufficiency Scores

• pHI: 0.345
• hipred: Y
• hipred_score: 0.774
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.923

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dgka
• Phenotype: immune system phenotype; reproductive system phenotype; hematopoietic system phenotype; endocrine/exocrine gland phenotype

Gene ontology

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