SOAT2

sterol O-acyltransferase 2

Basic information

Region (hg38): 12:53103486-53124535

Links

ENSG00000167780 ∙ NCBI:8435 ∙ OMIM:601311 ∙ HGNC:11178 ∙ Uniprot:O75908 ∙ 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 SOAT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOAT2 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					2	2
missense			34	4	1	39
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	4	3

Variants in SOAT2

This is a list of pathogenic ClinVar variants found in the SOAT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-53103590-G-A		not specified	Uncertain significance (Dec 07, 2023)
12-53103626-G-A		not specified	Likely benign (Dec 20, 2022)
12-53103638-G-A		not specified	Uncertain significance (May 29, 2024)
12-53103642-G-A		not specified	Likely benign (Apr 08, 2024)
12-53103650-T-C		not specified	Uncertain significance (Aug 12, 2021)
12-53103654-G-A		not specified	Uncertain significance (Jan 20, 2023)
12-53104175-C-T		not specified	Uncertain significance (Dec 18, 2023)
12-53104203-G-A		not specified	Uncertain significance (Jun 07, 2024)
12-53104205-A-C		not specified	Uncertain significance (Dec 06, 2021)
12-53105135-C-T		not specified	Likely benign (Mar 28, 2023)
12-53105141-G-C		not specified	Uncertain significance (Apr 11, 2023)
12-53105165-G-A		not specified	Likely benign (Jun 12, 2023)
12-53105165-G-C		not specified	Uncertain significance (Oct 09, 2024)
12-53105169-C-T			Benign (Jun 29, 2018)
12-53105173-C-G		not specified	Uncertain significance (Jul 23, 2024)
12-53105186-A-C		not specified	Uncertain significance (Sep 07, 2022)
12-53105566-A-T		not specified	Uncertain significance (Mar 17, 2023)
12-53105920-G-A		not specified	Uncertain significance (Mar 14, 2023)
12-53105932-C-T		not specified	Uncertain significance (Feb 02, 2022)
12-53105935-A-G		not specified	Uncertain significance (Dec 15, 2023)
12-53115400-G-A		not specified	Uncertain significance (Jan 24, 2023)
12-53115427-G-A		not specified	Uncertain significance (Oct 08, 2024)
12-53115427-G-C		not specified	Uncertain significance (Dec 28, 2022)
12-53115473-C-G		not specified	Uncertain significance (Oct 04, 2024)
12-53115503-G-A		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOAT2	protein_coding	protein_coding	ENST00000301466	15	21021

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.58e-28	0.0000219	125318	1	429	125748	0.00171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.622	289	320	0.902	0.0000198	3331
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00281	0.00279
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00432	0.00419
Finnish	0.000660	0.000601
European (Non-Finnish)	0.00106	0.00105
Middle Eastern	0.00432	0.00419
South Asian	0.00451	0.00448
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• 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.
• Pathway: Steroid biosynthesis - Homo sapiens (human);Cholesterol metabolism - Homo sapiens (human);LDL clearance;Plasma lipoprotein clearance;Transport of small molecules;Bile acid biosynthesis;Steroids metabolism;Plasma lipoprotein assembly, remodeling, and clearance (Consensus)

Recessive Scores

• pRec: 0.210

Intolerance Scores

• loftool: 0.900
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.17

Haploinsufficiency Scores

• pHI: 0.393
• hipred: N
• hipred_score: 0.197
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.947

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Soat2
• Phenotype: homeostasis/metabolism 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; digestive/alimentary phenotype

Zebrafish Information Network

• Gene name: soat2
• Affected structure: yolk
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

• Biological process: cholesterol metabolic process;macrophage derived foam cell differentiation;intestinal cholesterol absorption;cholesterol efflux;very-low-density lipoprotein particle assembly;low-density lipoprotein particle clearance;cholesterol esterification;cholesterol homeostasis
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;brush border;integral component of membrane
• Molecular function: fatty-acyl-CoA binding;cholesterol binding;transferase activity, transferring acyl groups;cholesterol O-acyltransferase activity