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 (63 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	3	4
missense			66	3	1	70
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)			4			4
Total	0	0	71	4	4

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOAT1	protein_coding	protein_coding	ENST00000367619	15	64891

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125649	0	98	125747	0.000390

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.980	256	304	0.842	0.0000167	3622
Missense in Polyphen		90	121.02	0.74367		1429
Synonymous	0.279	99	103	0.965	0.00000530	1007
Loss of Function	1.78	19	29.4	0.645	0.00000131	376

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000390	0.000389
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.000188	0.000185
European (Non-Finnish)	0.000623	0.000615
Middle Eastern	0.000164	0.000163
South Asian	0.000328	0.000327
Other	0.000166	0.000163

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

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

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

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