SOAT1
Basic information
Region (hg38): 1:179293714-179358680
Previous symbols: [ "SOAT", "STAT" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (59 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 4 | |||||
missense | 56 | 60 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 56 | 4 | 4 |
GnomAD
Source:
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:
- 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