DGKD

diacylglycerol kinase delta, the group of Diacylglycerol kinases|Pleckstrin homology domain containing|Sterile alpha motif domain containing

Basic information

Region (hg38): 2:233354494-233472104

Links

ENSG00000077044 ∙ NCBI:8527 ∙ OMIM:601826 ∙ HGNC:2851 ∙ Uniprot:Q16760 ∙ 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 DGKD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DGKD 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				16	5	21
missense			56	2	1	59
nonsense			1			1
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					2	2
Total	0	0	57	18	9

Variants in DGKD

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

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

Position	Type	Phenotype	Significance	ClinVar
2-233354541-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-233354542-T-A			Likely benign (Jul 17, 2018)
2-233354543-C-G		not specified	Uncertain significance (Dec 06, 2022)
2-233354546-C-G		not specified	Uncertain significance (Jan 02, 2024)
2-233354552-C-A		not specified	Conflicting classifications of pathogenicity (Jan 23, 2024)
2-233354562-C-G		not specified	Uncertain significance (Aug 08, 2023)
2-233354567-C-A		not specified	Uncertain significance (Jan 11, 2023)
2-233354567-C-G		not specified	Uncertain significance (Feb 01, 2023)
2-233354569-G-A			Likely benign (May 21, 2018)
2-233354615-C-T		not specified	Uncertain significance (Aug 14, 2024)
2-233354616-C-T		not specified	Uncertain significance (Mar 02, 2023)
2-233388264-T-C		not specified	Uncertain significance (Oct 09, 2024)
2-233388294-A-G		not specified	Uncertain significance (Apr 13, 2022)
2-233390406-A-G		not specified	Uncertain significance (Dec 17, 2023)
2-233434380-G-A		not specified	Uncertain significance (Aug 01, 2024)
2-233434477-A-C		not specified	Uncertain significance (Jun 29, 2022)
2-233434777-G-C		not specified	Uncertain significance (Aug 02, 2021)
2-233434787-G-A			Uncertain significance (-)
2-233434804-G-A		not specified	Uncertain significance (Feb 13, 2023)
2-233434848-A-G		not specified	Uncertain significance (Oct 05, 2021)
2-233434856-C-T		Primary dilated cardiomyopathy	Uncertain significance (Jun 01, 2023)
2-233434863-C-T		not specified	Uncertain significance (Jul 02, 2024)
2-233435819-G-A		DGKD-related disorder	Likely benign (Jun 05, 2018)
2-233435853-C-T		not specified	Uncertain significance (Oct 07, 2024)
2-233435880-A-G		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DGKD	protein_coding	protein_coding	ENST00000264057	30	117598

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0722	0.928	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.96	507	732	0.692	0.0000455	7908
Missense in Polyphen		117	266.64	0.4388		2926
Synonymous	-1.31	344	314	1.09	0.0000221	2371
Loss of Function	5.85	17	69.7	0.244	0.00000367	766

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000300	0.000297
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000982	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as signaling molecule. {ECO:0000269|PubMed:17880279}.
• 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: 0.137

Intolerance Scores

• loftool: 0.202
• rvis_EVS: -2.34
• rvis_percentile_EVS: 1.16

Haploinsufficiency Scores

• pHI: 0.131
• hipred: Y
• hipred_score: 0.685
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dgkd
• Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: endocytosis;signal transduction;epidermal growth factor receptor signaling pathway;protein kinase C-activating G protein-coupled receptor signaling pathway;multicellular organism development;response to organic substance;protein transport;second-messenger-mediated signaling;platelet activation;intracellular signal transduction;diacylglycerol metabolic process;glycerolipid metabolic process;lipid phosphorylation;protein homooligomerization
• Cellular component: nucleus;cytoplasm;cytosol;plasma membrane
• Molecular function: NAD+ kinase activity;diacylglycerol kinase activity;protein binding;ATP binding;diacylglycerol binding;protein homodimerization activity;metal ion binding;protein heterodimerization activity