SOAT1

protein-coding

sterol O-acyltransferase 1

Gene summary

The protein encoded by this gene belongs to the acyltransferase family. It is located in the endoplasmic reticulum, and catalyzes the formation of fatty acid-cholesterol esters. This gene has been implicated in the formation of beta-amyloid and atherosclerotic plaques by controlling the equilibrium between free cholesterol and cytoplasmic cholesteryl esters. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2011]

Previous symbols:

SOAT
STAT

MANE transcript

NM_003101.6

Inheritance

—

ClinVar variants

U:73B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr1:179,293,714-179,358,680

External References & Databases

Ensembl (ENSG00000057252)

Transcript & Mutation Effects

hg38 • Region Span ~65.0 kb

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GenCC 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 SOAT1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 64

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003101.6. 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				1 clinvar	3 clinvar	4
missense			67 clinvar	3 clinvar	1 clinvar	71
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	73	4	4	81

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003101.6	RefSeq	NP_003092.4	15	MANE Select
ENST00000367619.8	Ensembl	ENSP00000356591.3	15	MANE Select
NM_001252511.2	RefSeq	NP_001239440.1	14	Standard
NM_001252512.2	RefSeq	NP_001239441.1	13	Standard

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)
Statin Pathway, Pharmacodynamics
Simvastatin Action Pathway
Pravastatin Action Pathway

Biological Process

cholesterol metabolic process
macrophage derived foam cell differentiation
cholesterol storage
cholesterol efflux
very-low-density lipoprotein particle assembly

Molecular Function

fatty-acyl-CoA binding
sterol O-acyltransferase activity
protein binding
cholesterol binding
cholesterol O-acyltransferase activity

Cellular Component

endoplasmic reticulum
endoplasmic reticulum membrane
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367619
Coding exons: 15
Length: 64891
Individuals with no LoFs: 125649
Homozygous LoFs: 0
Heterozygous LoFs: 98
Defined: 125747
p: 0.000390

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.980	256	304	0.842	0.0000167	3622
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00062	0.00062	rare
South Asian	0.00033	0.00033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.501

Intolerance Scores

LoFtool: 0.886
RVIS EVS: -0.29
RVIS percentile EVS: 33.47

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.900

Gene Damage Prediction

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