QSOX1
Basic information
Region (hg38): 1:180154869-180204030
Previous symbols: [ "QSCN6" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (126 variants)
- not_provided (11 variants)
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. These statistics are base on transcript: NM_000002826.5. 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 | 5 | |||||
| missense | 121 | 129 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 121 | 8 | 5 |
GnomAD
Source:
| 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:
- 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