SOAT1

sterol O-acyltransferase 1

Basic information

Region (hg38): 1:179293713-179358680

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.

• Inborn genetic diseases (17 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.

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				1	3	4
missense			16		1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	17	1	4

Variants in SOAT1

This is a list of pathogenic ClinVar variants found in the SOAT1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-179302702-G-T		not specified	Uncertain significance (May 30, 2022)
1-179302709-C-G		not specified	Uncertain significance (Aug 09, 2021)
1-179302769-C-T		not specified	Uncertain significance (Dec 20, 2021)
1-179302781-T-A		not specified	Uncertain significance (Oct 27, 2023)
1-179302789-G-A			Likely benign (Mar 31, 2018)
1-179323473-T-C		not specified	Uncertain significance (Jan 04, 2024)
1-179335639-A-G		not specified	Uncertain significance (Dec 28, 2023)
1-179337859-C-A		not specified	Uncertain significance (Aug 16, 2021)
1-179339527-A-G		not specified	Uncertain significance (Jan 24, 2023)
1-179341080-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-179341086-T-G		not specified	Uncertain significance (Oct 26, 2022)
1-179341109-G-A			Benign (Jul 31, 2018)
1-179341111-C-G		not specified	Uncertain significance (Oct 12, 2022)
1-179341140-C-G			Benign (Jun 26, 2018)
1-179341178-G-A			Benign (Jul 31, 2018)
1-179341185-C-T		not specified	Uncertain significance (Jan 07, 2022)
1-179342127-T-C		not specified	Uncertain significance (Feb 14, 2023)
1-179342169-T-C		not specified	Uncertain significance (Dec 26, 2023)
1-179342188-A-G			Benign (May 26, 2018)
1-179342190-C-T		not specified	Uncertain significance (Sep 09, 2021)
1-179342879-A-G		not specified	Uncertain significance (Mar 07, 2023)
1-179343621-A-G		not specified	Uncertain significance (Aug 02, 2021)
1-179344988-G-C		not specified	Uncertain significance (Mar 29, 2023)
1-179347606-T-C		not specified	Uncertain significance (Jan 04, 2024)
1-179347663-A-T		not specified	Uncertain significance (Sep 14, 2022)

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
7.36e-10	0.881	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

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

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

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