NOX3

NADPH oxidase 3

Basic information

Region (hg38): 6:155395367-155455839

Links

ENSG00000074771 ∙ NCBI:50508 ∙ OMIM:607105 ∙ HGNC:7890 ∙ Uniprot:Q9HBY0 ∙ 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 NOX3 gene.

• Inborn genetic diseases (24 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOX3 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
missense			22	2		24
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	2	1

Variants in NOX3

This is a list of pathogenic ClinVar variants found in the NOX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-155396909-T-C		not specified	Uncertain significance (Aug 20, 2023)
6-155396950-G-A			Benign (Apr 10, 2018)
6-155411280-C-T		not specified	Uncertain significance (Aug 17, 2022)
6-155411284-C-T		not specified	Likely benign (Jul 13, 2021)
6-155411285-G-A		not specified	Uncertain significance (Feb 27, 2024)
6-155411291-C-T		not specified	Uncertain significance (Mar 31, 2022)
6-155411330-T-C		not specified	Uncertain significance (Oct 12, 2021)
6-155411343-A-C		not specified	Uncertain significance (Dec 06, 2023)
6-155422783-C-T		not specified	Uncertain significance (May 06, 2022)
6-155422817-A-C		not specified	Uncertain significance (Nov 09, 2023)
6-155422833-C-T		not specified	Uncertain significance (Jul 15, 2021)
6-155428819-G-A		not specified	Uncertain significance (Feb 22, 2023)
6-155428828-C-T		not specified	Uncertain significance (Jul 25, 2023)
6-155428846-C-T		not specified	Likely benign (Oct 26, 2022)
6-155428962-T-C		not specified	Uncertain significance (Nov 17, 2023)
6-155428986-G-A		not specified	Uncertain significance (Jan 26, 2023)
6-155429010-A-C		not specified	Uncertain significance (May 27, 2022)
6-155429038-G-A		not specified	Uncertain significance (Dec 19, 2023)
6-155430856-A-G		not specified	Uncertain significance (Sep 29, 2023)
6-155430896-A-G		not specified	Uncertain significance (Aug 10, 2021)
6-155436419-G-A		not specified	Uncertain significance (Feb 12, 2024)
6-155436441-G-T		not specified	Uncertain significance (Mar 07, 2023)
6-155436476-G-T		not specified	Uncertain significance (Jan 23, 2023)
6-155436483-G-A		not specified	Uncertain significance (Dec 21, 2023)
6-155436545-C-T		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOX3	protein_coding	protein_coding	ENST00000159060	13	60534

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.63e-14	0.321	125471	1	276	125748	0.00110

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.225	336	325	1.04	0.0000182	3702
Missense in Polyphen		134	131.29	1.0207		1505
Synonymous	-1.05	140	125	1.12	0.00000760	1079
Loss of Function	1.32	26	34.4	0.757	0.00000178	372

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00300	0.00300
Ashkenazi Jewish	0.00696	0.00697
East Asian	0.00377	0.00376
Finnish	0.00	0.00
European (Non-Finnish)	0.000481	0.000466
Middle Eastern	0.00377	0.00376
South Asian	0.000605	0.000588
Other	0.00105	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: NADPH oxidase which constitutively produces superoxide upon formation of a complex with CYBA/p22phox. Plays a role in the biogenesis of otoconia/otolith, which are crystalline structures of the inner ear involved in the perception of gravity. {ECO:0000269|PubMed:15824103}.
• Pathway: Thyroid hormone synthesis;Signal Transduction;RHO GTPases Activate NADPH Oxidases;RHO GTPase Effectors;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.288

Intolerance Scores

• loftool: 0.182
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.7

Haploinsufficiency Scores

• pHI: 0.166
• hipred: N
• hipred_score: 0.251
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.143

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nox3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hearing/vestibular/ear phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: temperature homeostasis;defense response;detection of gravity;superoxide anion generation;otolith development;oxidation-reduction process
• Cellular component: cytoplasm;plasma membrane;NADPH oxidase complex;extracellular exosome
• Molecular function: superoxide-generating NADPH oxidase activity