NOX5

NADPH oxidase 5, the group of EF-hand domain containing

Basic information

Region (hg38): 15:69014694-69062762

Links

ENSG00000255346 ∙ NCBI:79400 ∙ OMIM:606572 ∙ HGNC:14874 ∙ Uniprot:Q96PH1 ∙ 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 NOX5 gene.

• Inborn genetic diseases (33 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOX5 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			32	2	3	37
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	32	3	4

Variants in NOX5

This is a list of pathogenic ClinVar variants found in the NOX5 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-69026541-G-A		not specified	Uncertain significance (Jul 13, 2022)
15-69026557-G-C		not specified	Uncertain significance (Jun 13, 2022)
15-69026563-G-A		not specified	Likely benign (May 05, 2023)
15-69026607-G-A			Likely benign (Aug 29, 2018)
15-69026616-C-G		not specified	Uncertain significance (Oct 25, 2022)
15-69028254-G-A		not specified	Uncertain significance (Aug 16, 2021)
15-69028261-G-A		not specified	Uncertain significance (Jan 19, 2024)
15-69028321-C-T		not specified	Uncertain significance (Jul 12, 2022)
15-69028330-A-T			Benign (Jun 26, 2018)
15-69028332-C-T		not specified	Uncertain significance (Mar 24, 2023)
15-69031629-T-C		not specified	Uncertain significance (Aug 01, 2022)
15-69031634-A-G		not specified	Uncertain significance (Jun 03, 2022)
15-69031745-A-G		not specified	Uncertain significance (Feb 02, 2024)
15-69033137-C-A		not specified	Uncertain significance (Dec 02, 2022)
15-69033189-C-T		not specified	Uncertain significance (Dec 14, 2021)
15-69033208-C-G		not specified	Uncertain significance (May 17, 2023)
15-69033236-G-C		not specified	Uncertain significance (May 26, 2022)
15-69035363-C-T		not specified	Uncertain significance (Feb 27, 2024)
15-69035369-C-T		not specified	Uncertain significance (Nov 19, 2022)
15-69035394-C-T			Benign (Dec 31, 2019)
15-69035397-G-A			Benign (Dec 31, 2019)
15-69035845-C-T		not specified	Uncertain significance (Dec 18, 2023)
15-69035882-C-A			Likely benign (Mar 01, 2023)
15-69035889-A-G		not specified	Uncertain significance (Dec 05, 2022)
15-69037061-G-A		not specified	Likely benign (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOX5	protein_coding	protein_coding	ENST00000388866	16	132220

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.05e-28	0.0000296	124088	57	1603	125748	0.00662

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.838	406	456	0.890	0.0000263	4983
Missense in Polyphen		120	135.23	0.88735		1652
Synonymous	0.396	182	189	0.963	0.0000112	1523
Loss of Function	-0.552	40	36.4	1.10	0.00000163	391

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0921	0.0919
Ashkenazi Jewish	0.00	0.00
East Asian	0.000552	0.000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000867	0.000862
Middle Eastern	0.000552	0.000544
South Asian	0.000953	0.000915
Other	0.00312	0.00310

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent NADPH oxidase that generates superoxide. Also functions as a calcium-dependent proton channel and may regulate redox-dependent processes in lymphocytes and spermatozoa. May play a role in cell growth and apoptosis. Isoform v2 and isoform v5 are involved in endothelial generation of reactive oxygen species (ROS), proliferation and angiogenesis and contribute to endothelial response to thrombin. {ECO:0000269|PubMed:11483596, ECO:0000269|PubMed:12686516, ECO:0000269|PubMed:17275676}.
• Pathway: Detoxification of Reactive Oxygen Species;Cellular responses to stress;Cellular responses to external stimuli (Consensus)

Recessive Scores

• pRec: 0.766

Intolerance Scores

• loftool: 0.113
• rvis_EVS: 1.58
• rvis_percentile_EVS: 95.79

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.207
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.311

Gene Damage Prediction

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

Gene ontology

• Biological process: angiogenesis;endothelial cell proliferation;apoptotic process;defense response;cell population proliferation;regulation of proton transport;cellular response to oxidative stress;superoxide anion generation;regulation of fusion of sperm to egg plasma membrane;cytokine secretion;oxidation-reduction process;cytoskeleton-dependent cytokinesis;proton transmembrane transport
• Cellular component: endoplasmic reticulum membrane;plasma membrane;integral component of membrane;NADPH oxidase complex
• Molecular function: calcium ion binding;proton channel activity;superoxide-generating NADPH oxidase activity;heme binding;flavin adenine dinucleotide binding;NADP binding