GeneBe

SOAT1

sterol O-acyltransferase 1

Basic information

Region (hg38): 1:179293714-179358680

Previous symbols: [ "SOAT", "STAT" ]

Links

ENSG00000057252 ∙ NCBI:6646 ∙ OMIM:102642 ∙ HGNC:11177 ∙ Uniprot:P35610 ∙ 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 SOAT1 gene.

  • not_specified (59 variants)
  • not_provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOAT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003101.6. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
3
clinvar
 4
missense
56
clinvar
3
clinvar
1
clinvar
 60
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 56 4 4
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SOAT1protein_codingprotein_codingENST00000367619 1564891
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
7.36e-100.8811256490981257470.000390
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9802563040.8420.00001673622
Missense in Polyphen90121.020.743671429
Synonymous0.279991030.9650.000005301007
Loss of Function1.781929.40.6450.00000131376

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003900.000389
Ashkenazi Jewish0.000.00
East Asian0.0001640.000163
Finnish0.0001880.000185
European (Non-Finnish)0.0006230.000615
Middle Eastern0.0001640.000163
South Asian0.0003280.000327
Other0.0001660.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Catalyzes the formation of fatty acid-cholesterol esters, which are less soluble in membranes than cholesterol. Plays a role in lipoprotein assembly and dietary cholesterol absorption. In addition to its acyltransferase activity, it may act as a ligase.;
Pathway
Steroid biosynthesis - Homo sapiens (human);Cholesterol metabolism - Homo sapiens (human);Statin Pathway, Pharmacodynamics;Simvastatin Action Pathway;Pravastatin Action Pathway;Atorvastatin Action Pathway;Hyper-IgD syndrome;Cholesteryl ester storage disease;Lysosomal Acid Lipase Deficiency (Wolman Disease);Alendronate Action Pathway;Rosuvastatin Action Pathway;Lovastatin Action Pathway;Mevalonic aciduria;Wolman disease;Risedronate Action Pathway;Cerivastatin Action Pathway;Pamidronate Action Pathway;Fluvastatin Action Pathway;Smith-Lemli-Opitz Syndrome (SLOS);Chondrodysplasia Punctata II, X Linked Dominant (CDPX2);CHILD Syndrome;Desmosterolosis;Hypercholesterolemia;Steroid Biosynthesis;Zoledronate Action Pathway;Ibandronate Action Pathway;Demo complete;Statin Pathway;LDL clearance;Plasma lipoprotein clearance;Transport of small molecules;Bile acid biosynthesis;Steroids metabolism;Plasma lipoprotein assembly, remodeling, and clearance (Consensus)

Recessive Scores

pRec
0.501

Intolerance Scores

loftool
0.886
rvis_EVS
-0.29
rvis_percentile_EVS
33.47

Haploinsufficiency Scores

pHI
0.0906
hipred
N
hipred_score
0.322
ghis
0.438

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.900

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Soat1
Phenotype
endocrine/exocrine gland 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; 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); neoplasm; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype; immune system phenotype; vision/eye phenotype;

Gene ontology

Biological process
cholesterol metabolic process;macrophage derived foam cell differentiation;cholesterol storage;cholesterol efflux;very-low-density lipoprotein particle assembly;low-density lipoprotein particle clearance;cholesterol esterification;cholesterol homeostasis;positive regulation of amyloid precursor protein biosynthetic process
Cellular component
endoplasmic reticulum;endoplasmic reticulum membrane;membrane;integral component of membrane
Molecular function
fatty-acyl-CoA binding;sterol O-acyltransferase activity;protein binding;cholesterol binding;cholesterol O-acyltransferase activity