QSOX1

quiescin sulfhydryl oxidase 1

Basic information

Region (hg38): 1:180154869-180204030

Previous symbols: [ "QSCN6" ]

Links

ENSG00000116260 ∙ NCBI:5768 ∙ OMIM:603120 ∙ HGNC:9756 ∙ Uniprot:O00391 ∙ 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 QSOX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the QSOX1 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				3	2	5
missense			48		3	51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					1	1
Total	0	0	48	3	6

Variants in QSOX1

This is a list of pathogenic ClinVar variants found in the QSOX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-180154915-G-A		not specified	Uncertain significance (May 16, 2023)
1-180154924-G-T		not specified	Uncertain significance (Jun 22, 2024)
1-180154938-C-T		not specified	Uncertain significance (Dec 14, 2021)
1-180154942-C-T		not specified	Uncertain significance (Jan 18, 2022)
1-180154975-C-T		not specified	Uncertain significance (Sep 12, 2023)
1-180154984-G-T		not specified	Uncertain significance (Apr 04, 2024)
1-180154998-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-180155001-C-T		not specified	Uncertain significance (Jan 26, 2023)
1-180155028-C-A		not specified	Uncertain significance (Jun 24, 2022)
1-180155053-C-A		not specified	Uncertain significance (Jun 02, 2023)
1-180155136-G-A		not specified	Uncertain significance (May 14, 2024)
1-180155158-C-A		not specified	Uncertain significance (Dec 20, 2023)
1-180166509-A-G		not specified	Uncertain significance (May 26, 2022)
1-180166517-G-A		not specified	Uncertain significance (Sep 26, 2022)
1-180166537-G-C		not specified	Uncertain significance (Dec 16, 2023)
1-180166548-C-T		not specified	Uncertain significance (Aug 12, 2022)
1-180166566-A-G			Benign (Aug 16, 2018)
1-180175335-T-C			Likely benign (Dec 01, 2022)
1-180175345-G-A		not specified	Uncertain significance (Jan 10, 2023)
1-180175997-C-T		not specified	Uncertain significance (Feb 14, 2023)
1-180176017-C-T		not specified	Uncertain significance (Apr 11, 2023)
1-180178787-C-T			Likely benign (Jul 04, 2018)
1-180178826-A-G		not specified	Uncertain significance (Jan 09, 2024)
1-180178859-A-C		not specified	Uncertain significance (Jul 15, 2021)
1-180182180-C-G		not specified	Uncertain significance (Apr 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
QSOX1	protein_coding	protein_coding	ENST00000367602	12	49197

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000259	1.00	125569	0	179	125748	0.000712

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.342	410	430	0.954	0.0000251	4784
Missense in Polyphen		111	122.06	0.90942		1490
Synonymous	1.13	161	180	0.893	0.0000107	1581
Loss of Function	3.29	14	35.0	0.399	0.00000207	347

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00844	0.00813
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000164	0.000163
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000224	0.000211
Middle Eastern	0.000164	0.000163
South Asian	0.000102	0.0000980
Other	0.000872	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the oxidation of sulfhydryl groups in peptide and protein thiols to disulfides with the reduction of oxygen to hydrogen peroxide. May contribute to disulfide bond formation in a variety of secreted proteins. In fibroblasts, it may have tumor- suppressing capabilities being involved in growth regulation. {ECO:0000269|PubMed:10542195, ECO:0000269|PubMed:10708601, ECO:0000269|PubMed:12176051, ECO:0000269|PubMed:16806532, ECO:0000269|PubMed:17331072, ECO:0000269|PubMed:18393449}.
• Pathway: Neutrophil degranulation;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.814
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.2

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.273
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0512

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Qsox1
• Phenotype: digestive/alimentary phenotype; limbs/digits/tail phenotype; vision/eye phenotype; immune system phenotype; skeleton phenotype; respiratory system phenotype; 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); craniofacial phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: platelet degranulation;negative regulation of macroautophagy;neutrophil degranulation;post-translational protein modification;cellular protein metabolic process;cell redox homeostasis;oxidation-reduction process
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum lumen;Golgi apparatus;integral component of Golgi membrane;platelet alpha granule lumen;specific granule lumen;intracellular membrane-bounded organelle;intercellular bridge;extracellular exosome;tertiary granule lumen
• Molecular function: protein disulfide isomerase activity;flavin-linked sulfhydryl oxidase activity