SQOR

sulfide quinone oxidoreductase

Basic information

Region (hg38): 15:45631147-45691281

Previous symbols: [ "SQRDL" ]

Links

ENSG00000137767 ∙ NCBI:58472 ∙ OMIM:617658 ∙ HGNC:20390 ∙ Uniprot:Q9Y6N5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• sulfide quinone oxidoreductase deficiency (Strong), mode of inheritance: AR
• Leigh syndrome (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Sulfide:quinone oxidoreductase deficiency	AR	Biochemical	The condition can involve neurometabolic sequelae, and adequate caloric intake with fasting avoidance has been recommended; Medical management. (eg, with hydroxycobalamin and methylene blue) has been suggested as potentially beneficial	Biochemical; Neurologic	32160317

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SQOR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SQOR 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						0
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in SQOR

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

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

Position	Type	Phenotype	Significance	ClinVar
15-45658982-T-G		not specified	Uncertain significance (Apr 19, 2024)
15-45659006-G-A		not specified	Uncertain significance (Mar 02, 2023)
15-45659087-G-T		not specified	Uncertain significance (Jan 19, 2024)
15-45659104-C-T		not specified	Uncertain significance (Nov 03, 2023)
15-45659105-G-A		not specified	Uncertain significance (May 23, 2023)
15-45659107-A-G		not specified	Uncertain significance (Mar 18, 2024)
15-45659144-T-C		not specified	Uncertain significance (Jan 16, 2024)
15-45661956-G-A		not specified	Uncertain significance (Feb 23, 2023)
15-45661963-C-A		not specified	Uncertain significance (Jan 26, 2023)
15-45662021-C-T		not specified	Uncertain significance (Dec 11, 2023)
15-45662088-C-G		not specified	Uncertain significance (Apr 01, 2024)
15-45662117-G-A		not specified	Uncertain significance (Jan 03, 2024)
15-45669952-G-A		not specified	Uncertain significance (May 21, 2024)
15-45669967-CT-C		Sulfide quinone oxidoreductase deficiency	Pathogenic (Mar 05, 2021)
15-45673631-G-A		not specified	Uncertain significance (Jun 19, 2024)
15-45673650-C-G		not specified	Uncertain significance (May 31, 2023)
15-45673773-T-C		not specified	Uncertain significance (Feb 07, 2023)
15-45673784-G-A		Sulfide quinone oxidoreductase deficiency	Pathogenic (Mar 05, 2021)
15-45676158-G-A		not specified	Uncertain significance (Sep 28, 2022)
15-45676215-G-A		not specified	Uncertain significance (May 18, 2023)
15-45676266-G-A		not specified	Uncertain significance (Nov 08, 2022)
15-45676282-A-G		not specified	Uncertain significance (Feb 15, 2023)
15-45682517-G-C		not specified	Uncertain significance (May 30, 2024)
15-45682520-G-A		not specified	Uncertain significance (Feb 06, 2023)
15-45682565-G-A		SQOR-related disorder	Likely benign (May 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SQOR	protein_coding	protein_coding	ENST00000260324	9	60147

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.13e-10	0.341	125669	0	79	125748	0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.532	225	249	0.905	0.0000131	2906
Missense in Polyphen		99	106.64	0.92838		1199
Synonymous	-0.557	102	95.1	1.07	0.00000540	898
Loss of Function	0.920	17	21.6	0.786	0.00000117	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00154	0.00151
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000272	0.000272
Finnish	0.0000535	0.0000462
European (Non-Finnish)	0.000172	0.000167
Middle Eastern	0.000272	0.000272
South Asian	0.000403	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the oxidation of hydrogen sulfide with the help of a quinone, such as ubiquinone, giving rise to thiosulfate and ultimately to sulfane (molecular sulfur) atoms. Requires an additional electron acceptor; can use sulfite, sulfide or cyanide (in vitro). {ECO:0000269|PubMed:22852582}.
• Pathway: Sulfur metabolism - Homo sapiens (human);Sulfide oxidation to sulfate;Degradation of cysteine and homocysteine;Metabolism of amino acids and derivatives;Metabolism;Sulfur amino acid metabolism (Consensus)

Recessive Scores

• pRec: 0.253

Intolerance Scores

• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.85

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.112
• ghis: 0.443

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Sqor

Gene ontology

• Biological process: sulfide oxidation, using sulfide:quinone oxidoreductase;hydrogen sulfide metabolic process
• Cellular component: mitochondrial inner membrane
• Molecular function: quinone binding;sulfide:quinone oxidoreductase activity;FAD binding