NQO2

N-ribosyldihydronicotinamide:quinone reductase 2

Basic information

Region (hg38): 6:2987986-3019755

Previous symbols: [ "NMOR2" ]

Links

ENSG00000124588 ∙ NCBI:4835 ∙ OMIM:160998 ∙ HGNC:7856 ∙ Uniprot:P16083 ∙ 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 NQO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NQO2 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						0
missense			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	15	1	1

Variants in NQO2

This is a list of pathogenic ClinVar variants found in the NQO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-3010037-T-C		not specified	Uncertain significance (May 23, 2023)
6-3010046-A-G		not specified	Uncertain significance (Dec 21, 2022)
6-3010064-A-G		Ovarian cancer	Benign (Jan 01, 2022)
6-3010073-A-T		not specified	Uncertain significance (Aug 12, 2021)
6-3010075-G-A		not specified	Uncertain significance (May 14, 2024)
6-3012539-G-A			Benign (Jun 25, 2018)
6-3012555-A-G		not specified	Uncertain significance (Apr 26, 2023)
6-3012591-G-A		not specified	Uncertain significance (Sep 01, 2021)
6-3012601-A-T		not specified	Uncertain significance (Apr 19, 2024)
6-3012621-G-T		not specified	Uncertain significance (Mar 30, 2024)
6-3012648-C-T		not specified	Uncertain significance (Mar 28, 2022)
6-3015626-G-A		not specified	Uncertain significance (Jun 28, 2023)
6-3015632-G-A		not specified	Uncertain significance (Feb 28, 2024)
6-3016885-G-A		not specified	Uncertain significance (May 09, 2022)
6-3016905-G-A		not specified	Uncertain significance (Dec 21, 2022)
6-3016950-A-G		not specified	Uncertain significance (May 05, 2023)
6-3016969-T-G		not specified	Uncertain significance (Jan 26, 2023)
6-3019528-G-A		not specified	Likely benign (Dec 28, 2022)
6-3019605-T-G		not specified	Uncertain significance (Apr 22, 2024)
6-3019637-C-A		not specified	Uncertain significance (Feb 27, 2024)
6-3019642-A-G		not specified	Uncertain significance (Feb 27, 2024)
6-3019647-G-A		not specified	Uncertain significance (Feb 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NQO2	protein_coding	protein_coding	ENST00000338130	6	31776

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.76e-7	0.320	125703	1	44	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.475	118	133	0.884	0.00000741	1508
Missense in Polyphen		52	55.572	0.93572		669
Synonymous	-0.580	62	56.5	1.10	0.00000380	441
Loss of Function	0.384	10	11.4	0.877	5.49e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000297	0.000297
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000291	0.000281
Middle Eastern	0.0000548	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The enzyme apparently serves as a quinone reductase in connection with conjugation reactions of hydroquinones involved in detoxification pathways as well as in biosynthetic processes such as the vitamin K-dependent gamma-carboxylation of glutamate residues in prothrombin synthesis. {ECO:0000269|PubMed:18254726}.
• Pathway: Photodynamic therapy-induced NFE2L2 (NRF2) survival signaling;Phase I - Functionalization of compounds;Biological oxidations;Metabolism (Consensus)

Recessive Scores

• pRec: 0.229

Intolerance Scores

• loftool: 0.817
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.59

Haploinsufficiency Scores

• pHI: 0.0939
• hipred: N
• hipred_score: 0.144
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.890

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nqo2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm; hematopoietic system phenotype; immune system phenotype; homeostasis/metabolism 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: xenobiotic metabolic process;electron transport chain;oxidation-reduction process
• Cellular component: nucleoplasm;cytosol;extracellular exosome
• Molecular function: dihydronicotinamide riboside quinone reductase activity;NAD(P)H dehydrogenase (quinone) activity;protein binding;zinc ion binding;electron transfer activity;oxidoreductase activity;oxidoreductase activity, acting on other nitrogenous compounds as donors;chloride ion binding;protein homodimerization activity;FAD binding;melatonin binding;resveratrol binding