DGKH

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

Basic information

Region (hg38): 13:42040036-42256578

Links

ENSG00000102780 ∙ NCBI:160851 ∙ OMIM:604071 ∙ HGNC:2854 ∙ Uniprot:Q86XP1 ∙ 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 DGKH gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DGKH 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
missense			45	2		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				8		8
splice region						0
non coding						0
Total	0	0	45	12	0

Variants in DGKH

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

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

Position	Type	Phenotype	Significance	ClinVar
13-42048797-C-G		not specified	Uncertain significance (Jul 05, 2023)
13-42048805-C-T		not specified	Uncertain significance (Jul 31, 2024)
13-42048832-G-C		not specified	Uncertain significance (Oct 07, 2024)
13-42048911-G-C		not specified	Uncertain significance (Jan 30, 2024)
13-42048958-G-A		not specified	Uncertain significance (Dec 01, 2022)
13-42127524-G-C		not specified	Uncertain significance (May 08, 2023)
13-42127524-G-T		not specified	Uncertain significance (Aug 02, 2021)
13-42155370-C-A		not specified	Uncertain significance (Mar 21, 2023)
13-42155373-T-C		not specified	Uncertain significance (Sep 21, 2023)
13-42155390-T-A		not specified	Uncertain significance (Feb 06, 2024)
13-42155675-G-C		not specified	Uncertain significance (May 08, 2024)
13-42155759-G-C		not specified	Uncertain significance (Nov 21, 2024)
13-42159244-C-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT			Likely benign (Mar 01, 2023)
13-42159244-C-CTTTTTTTTTTTTTTTTTTTTTTTTTT			Likely benign (Dec 01, 2022)
13-42159244-C-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT			Likely benign (Dec 01, 2022)
13-42159244-C-CTTTTTTTTTTTTTTT			Likely benign (Jan 01, 2023)
13-42159244-C-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT			Likely benign (Jan 01, 2023)
13-42159244-C-CTTTTTTTTTTTTTTTTTTTT			Likely benign (Nov 01, 2022)
13-42159244-C-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT			Likely benign (Dec 01, 2022)
13-42159244-C-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT			Likely benign (Nov 01, 2022)
13-42159307-A-G		not specified	Uncertain significance (Jun 17, 2024)
13-42159329-C-T		not specified	Uncertain significance (Aug 15, 2024)
13-42165425-A-G		not specified	Uncertain significance (Aug 12, 2021)
13-42166542-G-A		not specified	Uncertain significance (Nov 14, 2024)
13-42166608-G-A		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DGKH	protein_coding	protein_coding	ENST00000337343	30	216539

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0264	0.974	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.00	430	645	0.667	0.0000343	7948
Missense in Polyphen		125	252.43	0.49519		3231
Synonymous	1.40	218	246	0.886	0.0000146	2326
Loss of Function	5.85	18	71.3	0.253	0.00000410	820

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000934	0.0000924
European (Non-Finnish)	0.000239	0.000237
Middle Eastern	0.000163	0.000163
South Asian	0.000197	0.000163
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphorylates diacylglycerol (DAG) to generate phosphatidic acid (PA). Plays a key role in promoting cell growth. Activates the Ras/B-Raf/C-Raf/MEK/ERK signaling pathway induced by EGF. Regulates the recruitment of RAF1 and BRAF from cytoplasm to membranes and their heterodimerization. {ECO:0000269|PubMed:12810723, ECO:0000269|PubMed:19710016}.
• 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: 0.132

Intolerance Scores

• loftool: 0.231
• rvis_EVS: -1.3
• rvis_percentile_EVS: 4.92

Haploinsufficiency Scores

• pHI: 0.203
• hipred: Y
• hipred_score: 0.621
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.938

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dgkh

Gene ontology

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