QSOX2

quiescin sulfhydryl oxidase 2

Basic information

Region (hg38): 9:136206333-136245812

Previous symbols: [ "QSCN6L1" ]

Links

ENSG00000165661 ∙ NCBI:169714 ∙ OMIM:612860 ∙ HGNC:30249 ∙ Uniprot:Q6ZRP7 ∙ 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 QSOX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the QSOX2 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	2
missense			49	4		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	5	1

Variants in QSOX2

This is a list of pathogenic ClinVar variants found in the QSOX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136208756-T-A		not specified	Uncertain significance (Jul 19, 2023)
9-136208779-G-C		not specified	Uncertain significance (Jun 21, 2023)
9-136208783-A-G		not specified	Uncertain significance (Oct 26, 2021)
9-136208820-C-T		not specified	Uncertain significance (Mar 11, 2022)
9-136208879-G-T		not specified	Uncertain significance (Jan 26, 2022)
9-136208880-C-T		not specified	Uncertain significance (Jun 13, 2023)
9-136208887-G-A			Benign (Jan 03, 2018)
9-136208923-C-G		not specified	Uncertain significance (Mar 07, 2024)
9-136208948-T-A		not specified	Uncertain significance (Oct 30, 2023)
9-136208961-G-T		not specified	Uncertain significance (Oct 12, 2021)
9-136209005-T-A		not specified	Uncertain significance (Nov 29, 2021)
9-136209014-C-T		not specified	Likely benign (Jun 26, 2023)
9-136209016-G-C		not specified	Likely benign (May 13, 2024)
9-136209026-G-A		not specified	Uncertain significance (Oct 12, 2024)
9-136209036-G-T		not specified	Uncertain significance (Jan 16, 2024)
9-136209044-A-G		not specified	Uncertain significance (Jul 05, 2022)
9-136209065-C-T		not specified	Uncertain significance (Mar 27, 2023)
9-136209120-C-G		not specified	Uncertain significance (Oct 03, 2022)
9-136209132-C-T		not specified	Uncertain significance (Oct 20, 2023)
9-136209141-A-G		not specified	Uncertain significance (Oct 11, 2024)
9-136211273-G-A		not specified	Uncertain significance (Sep 03, 2024)
9-136211320-T-C		not specified	Uncertain significance (May 21, 2024)
9-136211342-T-C		not specified	Uncertain significance (Aug 20, 2024)
9-136211355-C-T		not specified	Uncertain significance (May 14, 2024)
9-136211374-C-G		not specified	Uncertain significance (Dec 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
QSOX2	protein_coding	protein_coding	ENST00000358701	12	39509

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.85e-8	0.983	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.635	360	396	0.910	0.0000240	4460
Missense in Polyphen		108	136.42	0.7917		1533
Synonymous	-0.0717	172	171	1.01	0.0000111	1438
Loss of Function	2.24	16	29.0	0.552	0.00000157	313

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000202	0.000193
Middle Eastern	0.000164	0.000163
South Asian	0.0000339	0.0000327
Other	0.000163	0.000163

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. Also seems to play a role in regulating the sensitization of neuroblastoma cells for interferon-gamma-induced apoptosis. {ECO:0000269|PubMed:14633699}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.577
• rvis_EVS: -0.06
• rvis_percentile_EVS: 48.89

Haploinsufficiency Scores

• pHI: 0.226
• hipred: N
• hipred_score: 0.398
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.241

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Qsox2

Gene ontology

• Biological process: cell redox homeostasis;oxidation-reduction process
• Cellular component: extracellular space;nucleoplasm;Golgi apparatus;plasma membrane;integral component of Golgi membrane;nuclear membrane
• Molecular function: protein disulfide isomerase activity;flavin-linked sulfhydryl oxidase activity