SQLE
squalene epoxidase
Basic information
Region (hg38): 8:124998497-125022283
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (50 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SQLE gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003129.4. 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 | |||||
| missense | 45 | 49 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 45 | 6 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SQLE | protein_coding | protein_coding | ENST00000265896 | 11 | 23787 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.976 | 0.0241 | 124599 | 0 | 5 | 124604 | 0.0000201 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.14 | 227 | 281 | 0.808 | 0.0000134 | 3685 |
| Missense in Polyphen | 61 | 95.994 | 0.63546 | 1247 | ||
| Synonymous | 0.144 | 104 | 106 | 0.982 | 0.00000548 | 1136 |
| Loss of Function | 4.04 | 3 | 24.7 | 0.122 | 0.00000126 | 330 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000186 | 0.0000177 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000337 | 0.0000327 |
| Other | 0.000354 | 0.000331 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the first oxygenation step in sterol biosynthesis and is suggested to be one of the rate-limiting enzymes in this pathway.;
- Pathway
- Steroid biosynthesis - Homo sapiens (human);Bisphosphonate Pathway, Pharmacodynamics;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;Cholesterol Biosynthesis;Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Activation of gene expression by SREBF (SREBP);Demo complete;Statin Pathway;Metabolism of lipids;Regulation of cholesterol biosynthesis by SREBP (SREBF);Squalene and cholesterol biosynthesis;Metabolism;cholesterol biosynthesis III (via desmosterol);cholesterol biosynthesis II (via 24,25-dihydrolanosterol);superpathway of cholesterol biosynthesis;Metabolism of steroids;epoxysqualene biosynthesis;cholesterol biosynthesis I;Steroids metabolism;Cholesterol biosynthesis;Activation of gene expression by SREBF (SREBP)
(Consensus)
Recessive Scores
- pRec
- 0.329
Intolerance Scores
- loftool
- 0.303
- rvis_EVS
- -0.09
- rvis_percentile_EVS
- 46.99
Haploinsufficiency Scores
- pHI
- 0.355
- hipred
- Y
- hipred_score
- 0.699
- ghis
- 0.515
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.979
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sqle
- Phenotype
- skeleton phenotype; immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; craniofacial phenotype; growth/size/body region 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);
Gene ontology
- Biological process
- cholesterol biosynthetic process;cellular aromatic compound metabolic process;cholesterol metabolic process;response to organic substance;sterol biosynthetic process;regulation of cholesterol biosynthetic process;oxidation-reduction process
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;organelle membrane
- Molecular function
- squalene monooxygenase activity;flavin adenine dinucleotide binding