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.

not_specified (79 variants)
not_provided (3 variants)

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. These statistics are base on transcript: NM_000003578.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					2 clinvar	2
missense			70 clinvar	8 clinvar	1 clinvar	79
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	71	8	3

Loading clinvar variants...

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