SQLE

squalene epoxidase

Basic information

Region (hg38): 8:124998497-125022283

Links

ENSG00000104549 ∙ NCBI:6713 ∙ OMIM:602019 ∙ HGNC:11279 ∙ Uniprot:Q14534 ∙ 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 SQLE gene.

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.

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		1
missense			26	4		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	5	0

Variants in SQLE

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

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

Position	Type	Phenotype	Significance	ClinVar
8-124999473-G-T		not specified	Uncertain significance (Jan 20, 2025)
8-124999479-A-G		not specified	Uncertain significance (May 31, 2023)
8-124999542-C-T		not specified	Uncertain significance (Oct 06, 2023)
8-124999557-G-T		not specified	Uncertain significance (Feb 28, 2025)
8-124999644-G-A		not specified	Uncertain significance (Jun 17, 2024)
8-124999651-C-T		not specified	Uncertain significance (Nov 15, 2024)
8-125003212-A-G		not specified	Uncertain significance (Nov 27, 2024)
8-125003228-G-C		not specified	Likely benign (Jun 24, 2022)
8-125003231-C-G		not specified	Uncertain significance (Dec 12, 2024)
8-125003426-G-A		not specified	Likely benign (Oct 03, 2022)
8-125005680-C-T		not specified	Uncertain significance (Feb 07, 2025)
8-125007407-G-A		not specified	Uncertain significance (Jun 24, 2022)
8-125007431-G-A		not specified	Uncertain significance (Dec 02, 2022)
8-125007432-A-G		not specified	Uncertain significance (Nov 10, 2024)
8-125007441-T-A		not specified	Uncertain significance (Sep 06, 2022)
8-125007483-T-C		not specified	Uncertain significance (Mar 04, 2024)
8-125008987-T-G		not specified	Uncertain significance (Jul 26, 2022)
8-125009043-A-G		not specified	Uncertain significance (Jul 17, 2024)
8-125009182-A-T		not specified	Uncertain significance (Oct 06, 2022)
8-125009220-C-T		not specified	Uncertain significance (Jun 02, 2023)
8-125009221-C-T		not specified	Uncertain significance (Jan 23, 2023)
8-125009309-A-G			Likely benign (Oct 01, 2022)
8-125009320-A-G		not specified	Uncertain significance (Jan 27, 2025)
8-125011558-T-C		not specified	Uncertain significance (Nov 13, 2024)
8-125011629-C-G		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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