QSOX1

protein-coding

quiescin sulfhydryl oxidase 1

Gene summary

This gene encodes a protein that contains domains of thioredoxin and ERV1, members of two long-standing gene families. The gene expression is induced as fibroblasts begin to exit the proliferative cycle and enter quiescence, suggesting that this gene plays an important role in growth regulation. Two transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Previous symbols:

QSCN6

MANE transcript

NM_002826.5

Inheritance

—

ClinVar variants

U:152B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr1:180,154,869-180,204,030

External References & Databases

Ensembl (ENSG00000116260)

Transcript & Mutation Effects

hg38 • Region Span ~49.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to QSOX1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 145

not providedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002826.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	3 clinvar	2 clinvar	7
missense			145 clinvar	6 clinvar	3 clinvar	154
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	152	9	5	166

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002826.5	RefSeq	NP_002817.2	12	MANE Select
ENST00000367602.8	Ensembl	ENSP00000356574.3	12	MANE Select
NM_001004128.3	RefSeq	NP_001004128.1	13	Standard
ENST00000367600.5	Ensembl	ENSP00000356572.5	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neutrophil degranulation
Post-translational protein phosphorylation
Post-translational protein modification
Metabolism of proteins
Innate Immune System

Biological Process

platelet degranulation
negative regulation of macroautophagy
neutrophil degranulation
post-translational protein modification
cellular protein metabolic process

Molecular Function

protein disulfide isomerase activity
flavin-linked sulfhydryl oxidase activity

Cellular Component

extracellular region
extracellular space
endoplasmic reticulum lumen
Golgi apparatus
integral component of Golgi membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367602
Coding exons: 12
Length: 49197
Individuals with no LoFs: 125569
Homozygous LoFs: 0
Heterozygous LoFs: 179
Defined: 125748
p: 0.000712

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.342	410	430	0.954	0.0000251	4784
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0080	0.0077	notable
Latino/Admixed American	0.00048	0.00046	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00022	0.00021	rare
South Asian	0.00010	0.000098	rare
Other	0.00087	0.00081	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.131

Intolerance Scores

LoFtool: 0.814
RVIS EVS: -0.08
RVIS percentile EVS: 47.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0512

Gene Damage Prediction

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