SOAT2
protein-codingsterol O-acyltransferase 2
Gene summary
Summary:This gene is a member of a small family of acyl coenzyme A:cholesterol acyltransferases. The gene encodes a membrane-bound enzyme localized in the endoplasmic reticulum that produces intracellular cholesterol esters from long-chain fatty acyl CoA and cholesterol. The cholesterol esters are then stored as cytoplasmic lipid droplets inside the cell. The enzyme is implicated in cholesterol absorption in the intestine and in the assembly and secretion of apolipoprotein B-containing lipoproteins such as very low density lipoprotein (VLDL). Several alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SOAT2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003578.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 78 | 10 | 1 | 89 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 79 | 10 | 3 | 92 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003569.1 | 15 | MANE Select | |
| Ensembl | ENSP00000301466.3 | 15 | MANE Select | |
| Ensembl | ENSP00000442234.1 | 9 | Standard | |
| Ensembl | ENSP00000450120.1 | 5 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| soat2 | Danio rerio | Structure: yolk Quality: increased size abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Steroid biosynthesis - Homo sapiens (human)
- Cholesterol metabolism - Homo sapiens (human)
- LDL clearance
- Plasma lipoprotein clearance
- Transport of small molecules
Biological Process
- cholesterol metabolic process
- macrophage derived foam cell differentiation
- intestinal cholesterol absorption
- cholesterol efflux
- very-low-density lipoprotein particle assembly
Molecular Function
- fatty-acyl-CoA binding
- cholesterol binding
- transferase activity, transferring acyl groups
- cholesterol O-acyltransferase activity
Cellular Component
- endoplasmic reticulum
- endoplasmic reticulum membrane
- brush border
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000301466
- Coding exons
- 15
- Length
- 21021
- Individuals with no LoFs
- 125318
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 429
- Defined
- 125748
- p
- 0.00171
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.622 | 289 | 320 | 0.902 | 0.0000198 | 3331 |
| Missense (PolyPhen) | 104 | 124.18 | 0.83748 | 1457 | ||
| Synonymous | 0.337 | 129 | 134 | 0.963 | 0.00000869 | 1051 |
| Loss of Function | -0.725 | 39 | 34.4 | 1.13 | 0.00000193 | 333 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0012 | 0.0012 | notable |
| Latino/Admixed American | 0.0016 | 0.0016 | notable |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.0043 | 0.0042 | notable |
| Finnish | 0.00066 | 0.00060 | rare |
| European (Non-Finnish) | 0.0011 | 0.0010 | notable |
| South Asian | 0.0045 | 0.0045 | notable |
| Other | 0.0013 | 0.0013 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in lipoprotein assembly and dietary cholesterol absorption. In addition to its acyltransferase activity, it may act as a ligase. May provide cholesteryl esters for lipoprotein secretion from hepatocytes and intestinal mucosa.;
Recessive Scores
- pRec
- 0.210
Intolerance Scores
- LoFtool
- 0.900
- RVIS EVS
- 0.18
- RVIS percentile EVS
- 66.17
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.947
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |