DGKZ

diacylglycerol kinase zeta, the group of Diacylglycerol kinases|Ankyrin repeat domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 11:46332905-46380554

Links

ENSG00000149091 ∙ NCBI:8525 ∙ OMIM:601441 ∙ HGNC:2857 ∙ Uniprot:Q13574 ∙ 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 DGKZ gene.

• atypical cerebral palsy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DGKZ 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			3	73	10	86
missense			166	13	9	188
nonsense			1			1
start loss						0
frameshift	1		2			3
inframe indel			2	1		3
splice donor/acceptor (+/-2bp)						0
splice region			12	19	2	33
non coding			2	42	12	56
Total	1	0	176	129	31

Highest pathogenic variant AF is 0.000408

Variants in DGKZ

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

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

Position	Type	Phenotype	Significance	ClinVar
11-46333355-G-A		not specified	Uncertain significance (Oct 18, 2021)
11-46333364-G-C		not specified	Uncertain significance (Oct 16, 2024)
11-46333375-G-A		not specified	Uncertain significance (Feb 05, 2024)
11-46333376-A-T		not specified	Uncertain significance (Dec 12, 2023)
11-46333441-G-A		not specified	Uncertain significance (May 31, 2023)
11-46333453-C-G		not specified	Uncertain significance (Feb 14, 2023)
11-46333457-A-G		not specified	Uncertain significance (Aug 30, 2021)
11-46347674-C-T			Likely benign (Dec 01, 2022)
11-46347746-C-T			Likely benign (Nov 01, 2022)
11-46366263-ACTTT-A			Uncertain significance (Jun 03, 2023)
11-46366284-C-T		not specified	Uncertain significance (Feb 07, 2023)
11-46366285-G-A			Benign (Nov 24, 2023)
11-46366288-G-A		not specified	Uncertain significance (Jan 26, 2022)
11-46366293-G-A			Uncertain significance (Dec 11, 2023)
11-46366302-C-G			Benign (Jan 25, 2024)
11-46366310-G-A			Likely benign (Jan 09, 2024)
11-46366314-C-T			Uncertain significance (Feb 06, 2023)
11-46366318-A-G			Benign (Jan 29, 2024)
11-46366320-C-T		not specified	Uncertain significance (Jan 09, 2024)
11-46366321-G-A			Uncertain significance (Jun 28, 2022)
11-46366327-G-A		not specified	Uncertain significance (Dec 05, 2024)
11-46366333-T-C			Benign (Jan 22, 2024)
11-46366356-C-T			Likely benign (May 17, 2023)
11-46366357-G-A		not specified	Uncertain significance (Aug 04, 2023)
11-46366359-C-A		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DGKZ	protein_coding	protein_coding	ENST00000454345	31	47650

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0395	0.960	125698	1	23	125722	0.0000955

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.76	493	698	0.706	0.0000460	7089
Missense in Polyphen		120	276.48	0.43403		2913
Synonymous	-0.0469	288	287	1.00	0.0000192	2261
Loss of Function	5.73	17	68.0	0.250	0.00000404	679

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000186	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000282	0.000231
European (Non-Finnish)	0.0000940	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000103	0.0000980
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Displays a strong preference for 1,2-diacylglycerols over 1,3-diacylglycerols, but lacks substrate specificity among molecular species of long chain diacylglycerols. Isoform 2 but not isoform 1 regulates RASGRP1 activity (PubMed:11257115). Positively regulates insulin-induced translocation of SLC2A4 to the cell membrane in adipocytes (By similarity). Activates PIP5K1A activity via generation of phosphatidic acid (PubMed:15157668). {ECO:0000250|UniProtKB:Q80UP3, ECO:0000269|PubMed:11257115, ECO:0000269|PubMed:15157668}.
• 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);Myometrial Relaxation and Contraction Pathways;Leptin Insulin Overlap;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: 0.238

Intolerance Scores

• loftool: 0.606
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.69

Haploinsufficiency Scores

• pHI: 0.130
• hipred: Y
• hipred_score: 0.790
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dgkz
• Phenotype: immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: phosphatidic acid biosynthetic process;protein kinase C-activating G protein-coupled receptor signaling pathway;cell migration;platelet activation;intracellular signal transduction;diacylglycerol metabolic process;glycerolipid metabolic process;lipid phosphorylation;positive regulation of 1-phosphatidylinositol-4-phosphate 5-kinase activity
• Cellular component: nucleus;cytoplasm;plasma membrane;postsynaptic density;nuclear speck;lamellipodium;glutamatergic synapse
• Molecular function: NAD+ kinase activity;diacylglycerol kinase activity;protein binding;ATP binding;kinase activity;metal ion binding