NQO1

NAD(P)H quinone dehydrogenase 1

Basic information

Region (hg38): 16:69706996-69726668

Previous symbols: [ "NMOR1", "DIA4" ]

Links

ENSG00000181019 ∙ NCBI:1728 ∙ OMIM:125860 ∙ HGNC:2874 ∙ Uniprot:P15559 ∙ 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 NQO1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NQO1 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				107	1	108
missense		1	109	5	1	116
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding			1	3		4
Total	0	2	110	115	2

Variants in NQO1

This is a list of pathogenic ClinVar variants found in the NQO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-69710977-C-T		not specified	Likely benign (Apr 07, 2022)
16-69710984-T-C		not specified	Uncertain significance (May 05, 2023)
16-69710985-A-T		not specified	Likely benign (Mar 01, 2024)
16-69710986-G-T		not specified	Uncertain significance (Apr 07, 2024)
16-69710992-A-T		not specified	Uncertain significance (Jun 08, 2023)
16-69710994-C-G		not specified	Benign/Likely benign (Sep 20, 2022)
16-69711000-G-A		not specified	Likely benign (Mar 29, 2022)
16-69711001-T-A		not specified	Uncertain significance (Mar 30, 2022)
16-69711002-C-T		not specified	Uncertain significance (Jun 23, 2022)
16-69711003-A-G		not specified	Likely benign (Mar 04, 2021)
16-69711006-T-G		not specified	Likely benign (Apr 15, 2021)
16-69711009-G-A		not specified	Likely benign (Jan 04, 2023)
16-69711012-G-A		not specified	Likely benign (May 03, 2021)
16-69711012-G-T		not specified	Likely benign (Sep 03, 2022)
16-69711013-G-C		not specified	Uncertain significance (Mar 07, 2022)
16-69711014-A-T		not specified	Uncertain significance (Jun 23, 2022)
16-69711016-T-C		not specified	Uncertain significance (Sep 12, 2023)
16-69711018-G-C		not specified	Likely benign (Dec 23, 2022)
16-69711021-C-A		not specified	Uncertain significance (Nov 02, 2023)
16-69711024-G-A		NQO1-related disorder • not specified	Likely benign (Feb 23, 2022)
16-69711026-G-A		not specified	Uncertain significance (Jul 31, 2021)
16-69711027-A-G		not specified	Likely benign (Jun 30, 2019)
16-69711028-T-C		not specified	Uncertain significance (Oct 20, 2022)
16-69711029-G-A		not specified	Uncertain significance (May 10, 2024)
16-69711032-C-T		not specified	Uncertain significance (May 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NQO1	protein_coding	protein_coding	ENST00000320623	6	19956

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-9	0.101	124869	12	866	125747	0.00350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	106	150	0.705	0.00000768	1803
Missense in Polyphen		35	58.312	0.60022		687
Synonymous	-0.0322	58	57.7	1.01	0.00000338	516
Loss of Function	0.113	14	14.5	0.968	7.88e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0414	0.0412
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000326	0.000326
Finnish	0.000739	0.000739
European (Non-Finnish)	0.000810	0.000809
Middle Eastern	0.000326	0.000326
South Asian	0.000261	0.000261
Other	0.00310	0.00310

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The enzyme apparently serves as a quinone reductase in connection with conjugation reactions of hydroquinons involved in detoxification pathways as well as in biosynthetic processes such as the vitamin K-dependent gamma-carboxylation of glutamate residues in prothrombin synthesis.
• Pathway: Ubiquinone and other terpenoid-quinone biosynthesis - Homo sapiens (human);Doxorubicin Pathway (Cancer Cell), Pharmacodynamics;Hepatocellular carcinoma - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Doxorubicin Pathway, Pharmacokinetics;Pathways in cancer - Homo sapiens (human);Phenytoin Pathway, Pharmacokinetics;Platinum Pathway, Pharmacokinetics/Pharmacodynamics;Phenytoin (Antiarrhythmic) Action Pathway;Doxorubicin Metabolism Pathway;Vitamin K Metabolism;Dopamine metabolism;Aryl Hydrocarbon Receptor;Apoptosis-related network due to altered Notch3 in ovarian cancer;Aryl Hydrocarbon Receptor Pathway;Nuclear Receptors Meta-Pathway;NRF2 pathway;Transcriptional activation by NRF2;Photodynamic therapy-induced NFE2L2 (NRF2) survival signaling;Simplified Interaction Map Between LOXL4 and Oxidative Stress Pathway;Benzene metabolism;Oxidative Stress;Estrogen metabolism;Regulation of ornithine decarboxylase (ODC);Metabolism of polyamines;Metabolism of amino acids and derivatives;Metabolism;Validated transcriptional targets of TAp63 isoforms (Consensus)

Recessive Scores

• pRec: 0.755

Intolerance Scores

• loftool: 0.989
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.38

Haploinsufficiency Scores

• pHI: 0.130
• hipred: Y
• hipred_score: 0.575
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nqo1
• Phenotype: neoplasm; homeostasis/metabolism phenotype; cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of cellular amino acid metabolic process;xenobiotic metabolic process;nitric oxide biosynthetic process;synaptic transmission, cholinergic;aging;response to nutrient;response to toxic substance;removal of superoxide radicals;electron transport chain;response to estradiol;negative regulation of apoptotic process;negative regulation of catalytic activity;positive regulation of neuron apoptotic process;response to ethanol;response to electrical stimulus;cellular response to hydrogen peroxide;cellular response to metal ion;response to nitrogen compound;response to hydrogen sulfide
• Cellular component: cytoplasm;cytosol;dendrite;neuronal cell body
• Molecular function: RNA binding;NAD(P)H dehydrogenase (quinone) activity;cytochrome-b5 reductase activity, acting on NAD(P)H;superoxide dismutase activity;protein binding;electron transfer activity;oxidoreductase activity;identical protein binding