DGAT2

diacylglycerol O-acyltransferase 2, the group of Diacylglycerol O-acyltransferase 2 family

Basic information

Region (hg38): 11:75759511-75801535

Links

ENSG00000062282 ∙ NCBI:84649 ∙ OMIM:606983 ∙ HGNC:16940 ∙ Uniprot:Q96PD7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Charcot-Marie-Tooth disease (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DGAT2 gene.

• Inborn genetic diseases (12 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DGAT2 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	2
missense			12	3		15
nonsense			1		1	2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	4	2

Variants in DGAT2

This is a list of pathogenic ClinVar variants found in the DGAT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-75769088-T-C		not specified	Uncertain significance (Jun 24, 2022)
11-75784741-T-C		Charcot-Marie-Tooth disease type 2A1	Uncertain significance (-)
11-75790290-A-C		not specified	Uncertain significance (Oct 26, 2022)
11-75790710-T-C			Benign (Mar 29, 2018)
11-75797190-T-C			Uncertain significance (Apr 21, 2016)
11-75797213-T-C			Benign/Likely benign (Apr 01, 2024)
11-75797228-C-G		not specified	Uncertain significance (Apr 12, 2022)
11-75797272-G-A			Benign (Feb 01, 2024)
11-75797325-C-T		not specified	Uncertain significance (Jun 28, 2022)
11-75798246-T-C		not specified	Uncertain significance (Aug 02, 2022)
11-75798272-C-A			Benign (Jul 01, 2022)
11-75798306-C-T			Uncertain significance (Jun 01, 2022)
11-75798307-G-A			Likely benign (Oct 01, 2023)
11-75798318-A-G		not specified	Uncertain significance (Oct 05, 2023)
11-75798319-A-G		not specified	Uncertain significance (Jun 18, 2021)
11-75798354-A-G		not specified	Uncertain significance (Nov 21, 2022)
11-75798369-G-A			Likely benign (Oct 01, 2023)
11-75798374-C-T			Likely benign (Apr 01, 2024)
11-75800375-C-T		not specified	Uncertain significance (Jul 10, 2023)
11-75800406-C-G		not specified	Uncertain significance (Aug 08, 2023)
11-75800428-A-C		not specified	Uncertain significance (Jun 09, 2022)
11-75800480-C-A		not specified	Uncertain significance (Jul 14, 2022)
11-75800498-A-C		not specified	Uncertain significance (Jun 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DGAT2	protein_coding	protein_coding	ENST00000228027	8	42023

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.36e-12	0.142	125565	0	183	125748	0.000728

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.823	180	214	0.842	0.0000112	2490
Missense in Polyphen		44	59.739	0.73653		719
Synonymous	-0.663	94	86.2	1.09	0.00000464	782
Loss of Function	0.658	19	22.4	0.850	0.00000136	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00129	0.00129
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000489	0.000489
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00104	0.00104
Middle Eastern	0.000489	0.000489
South Asian	0.000392	0.000392
Other	0.000978	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential acyltransferase that catalyzes the terminal and only committed step in triacylglycerol synthesis by using diacylglycerol and fatty acyl CoA as substrates. Required for synthesis and storage of intracellular triglycerides. Probably plays a central role in cytosolic lipid accumulation. In liver, is primarily responsible for incorporating endogenously synthesized fatty acids into triglycerides (By similarity). Functions also as an acyl-CoA retinol acyltransferase (ARAT). {ECO:0000250}.
• Pathway: Glycerolipid metabolism - Homo sapiens (human);Fat digestion and absorption - Homo sapiens (human);Triacylglyceride Synthesis;Metabolism of lipids;Acyl chain remodeling of DAG and TAG;Metabolism;Glycerophospholipid metabolism;Triglyceride biosynthesis;Triglyceride metabolism;triacylglycerol biosynthesis;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.851
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.388
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.902

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dgat2
• Phenotype: limbs/digits/tail 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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)

Zebrafish Information Network

• Gene name: dgat2
• Affected structure: liver
• Phenotype tag: abnormal
• Phenotype quality: fatty

Gene ontology

• Biological process: glycerol metabolic process;positive regulation of triglyceride biosynthetic process;triglyceride biosynthetic process;lipid storage;low-density lipoprotein particle clearance;long-chain fatty-acyl-CoA metabolic process;cellular triglyceride homeostasis;acylglycerol acyl-chain remodeling;retinol metabolic process;cholesterol homeostasis;positive regulation of gluconeogenesis;negative regulation of fatty acid oxidation;diacylglycerol metabolic process;regulation of lipoprotein metabolic process;fatty acid homeostasis;fat pad development;cellular response to oleic acid;regulation of cholesterol metabolic process;regulation of plasma lipoprotein particle levels
• Cellular component: mitochondrion;endoplasmic reticulum;endoplasmic reticulum membrane;lipid droplet;integral component of membrane;integral component of endoplasmic reticulum membrane;perinuclear region of cytoplasm;perinuclear endoplasmic reticulum membrane
• Molecular function: 2-acylglycerol O-acyltransferase activity;diacylglycerol O-acyltransferase activity;protein homodimerization activity;retinol O-fatty-acyltransferase activity