DGAT2
Basic information
Region (hg38): 11:75759512-75801535
Links
Phenotypes
GenCC
Source:
- Charcot-Marie-Tooth disease (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
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 | 3 | |||||
missense | 13 | 16 | ||||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 14 | 4 | 3 |
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 (-) | ||
11-75790205-A-G | not specified | Uncertain significance (Oct 08, 2024) | ||
11-75790290-A-C | not specified | Uncertain significance (Oct 26, 2022) | ||
11-75790703-G-A | not specified | Uncertain significance (Oct 12, 2024) | ||
11-75790710-T-C | Benign (Mar 29, 2018) | |||
11-75796329-T-C | not specified | Uncertain significance (Dec 10, 2024) | ||
11-75796353-C-T | not specified | Uncertain significance (Aug 28, 2024) | ||
11-75796495-C-A | not specified | Uncertain significance (Jun 26, 2024) | ||
11-75797175-C-T | Uncertain significance (Mar 18, 2024) | |||
11-75797190-T-C | Uncertain significance (Apr 21, 2016) | |||
11-75797213-T-C | Benign/Likely benign (Jun 01, 2024) | |||
11-75797228-C-G | not specified | Uncertain significance (Apr 12, 2022) | ||
11-75797232-G-A | not specified | Uncertain significance (Nov 26, 2024) | ||
11-75797242-G-A | not specified | Uncertain significance (Sep 10, 2024) | ||
11-75797266-T-G | not specified | Uncertain significance (Apr 08, 2024) | ||
11-75797272-G-A | Benign (Feb 01, 2024) | |||
11-75797298-C-T | Uncertain significance (May 27, 2022) | |||
11-75797302-A-G | not specified | Uncertain significance (Nov 14, 2024) | ||
11-75797325-C-T | not specified | Uncertain significance (Nov 09, 2024) | ||
11-75798246-T-C | not specified | Uncertain significance (Aug 02, 2022) | ||
11-75798272-C-A | Benign (Jul 01, 2022) | |||
11-75798300-T-C | not specified | Uncertain significance (May 13, 2024) | ||
11-75798306-C-T | Uncertain significance (Jun 01, 2022) | |||
11-75798307-G-A | Likely benign (May 01, 2024) |
GnomAD
Source:
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:
- 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