QNG1

Summary

QNG1 (Q-nucleotide N-glycosylase 1, HGNC:28144) is a protein-coding gene on chromosome 9q21.32, encoding Queuosine 5’-phosphate N-glycosylase/hydrolase (Q5T6V5). Catalyzes the hydrolysis of queuosine 5’-phosphate, releasing the nucleobase queuine (q).

Predicted to enable hydrolase activity. Involved in nucleoside salvage.

Source: NCBI Gene 84267 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 11 total
• MANE Select transcript: NM_032307

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28144
Approved symbol	QNG1
Name	Q-nucleotide N-glycosylase 1
Location	9q21.32
Locus type	gene with protein product
Status	Approved
Aliases	MGC10999
Ensembl gene	ENSG00000165118
Ensembl biotype	protein_coding
OMIM	611342
Entrez	84267

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000314700, ENST00000376340, ENST00000376344

RefSeq mRNA: 2 — MANE Select: NM_032307 NM_001317997, NM_032307

CCDS: CCDS6666, CCDS83381

Canonical transcript exons

ENST00000376344 — 4 exons

Exon	Start	End
ENSE00001090495	83944794	83944989
ENSE00001776113	83956164	83956742
ENSE00001832282	83938311	83939743
ENSE00003690257	83955381	83955640

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 99.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.1566 / max 132.9588, expressed in 1674 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
101161	8.5014	1657
101160	0.6154	376
101159	0.4770	262
101157	0.2949	103
101156	0.2271	67
101158	0.0408	7

Top tissues by expression

258 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	99.84	silver quality
buccal mucosa cell	CL:0002336	99.69	gold quality
kidney epithelium	UBERON:0004819	99.53	gold quality
upper arm skin	UBERON:0004263	99.52	gold quality
renal medulla	UBERON:0000362	99.51	gold quality
nipple	UBERON:0002030	99.42	gold quality
pylorus	UBERON:0001166	99.38	gold quality
cardia of stomach	UBERON:0001162	99.37	gold quality
sperm	CL:0000019	99.15	gold quality
trigeminal ganglion	UBERON:0001675	99.15	gold quality
ventral tegmental area	UBERON:0002691	99.15	gold quality
superior surface of tongue	UBERON:0007371	99.12	gold quality
trachea	UBERON:0003126	99.09	gold quality
medulla oblongata	UBERON:0001896	99.08	gold quality
superior vestibular nucleus	UBERON:0007227	99.02	gold quality
tendon of biceps brachii	UBERON:0008188	99.02	gold quality
dorsal root ganglion	UBERON:0000044	98.98	gold quality
inferior vagus X ganglion	UBERON:0005363	98.97	gold quality
visceral pleura	UBERON:0002401	98.91	gold quality
endothelial cell	CL:0000115	98.89	gold quality
thymus	UBERON:0002370	98.81	gold quality
subthalamic nucleus	UBERON:0001906	98.76	gold quality
pericardium	UBERON:0002407	98.76	gold quality
lateral globus pallidus	UBERON:0002476	98.62	gold quality
dorsal plus ventral thalamus	UBERON:0001897	98.60	gold quality
saphenous vein	UBERON:0007318	98.55	gold quality
pharyngeal mucosa	UBERON:0000355	98.47	gold quality
layer of synovial tissue	UBERON:0007616	98.38	gold quality
parietal pleura	UBERON:0002400	98.33	gold quality
tongue	UBERON:0001723	98.32	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-6386	no	25.10
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting QNG1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-373-3P	99.84	70.68	1668
HSA-MIR-520E-3P	99.84	70.55	1698
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-372-3P	99.83	70.58	1691
HSA-MIR-520A-3P	99.83	70.59	1687
HSA-MIR-520B-3P	99.83	70.56	1699
HSA-MIR-520C-3P	99.83	70.56	1699
HSA-MIR-520D-3P	99.83	70.78	1676
HSA-MIR-4420	99.82	70.08	1624
HSA-MIR-181B-2-3P	99.81	70.06	1646
HSA-MIR-181B-3P	99.81	70.06	1646
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-3913-5P	99.78	67.26	968

Literature-anchored findings (GeneRIF, showing 1)

• Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5’-monophosphate as the biological substrate. (PMID:36610787)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	qng1	ENSDARG00000041372
mus_musculus	Qng1	ENSMUSG00000021550
rattus_norvegicus	Qng1	ENSRNOG00000019232
drosophila_melanogaster	CG9752	FBGN0034614
caenorhabditis_elegans		WBGENE00015702

Protein

Protein identifiers

Queuosine 5’-phosphate N-glycosylase/hydrolase — Q5T6V5 (reviewed: Q5T6V5)

Alternative names: Q-nucleotide N-glycosylase 1, Queuine salvage protein QNG1, Queuosine-nucleotide N-glycosylase/hydrolase

All UniProt accessions (3): Q5T6V5, Q5T6V6, Q5T6V7

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the hydrolysis of queuosine 5’-phosphate, releasing the nucleobase queuine (q). Is required for salvage of queuine from exogenous queuosine (Q) that is imported and then converted to queuosine 5’-phosphate intracellularly. In vitro, can also catalyze the release of the q base directly from Q as substrate; however, it was shown that Q is not the biologically relevant substrate. Shows a very low activity on queuosine 3’,5’-diphosphate, and cannot release q from queuosine 3’-phosphate and from the 5’-nucleotides AMP, UMP, CMP or GMP, indicating specificity for the queuine base. Can complement the yeast mutant SPAC589.05c, restoring Q incorporation into tRNA.

Miscellaneous. Eukaryotes lack the canonical genes for de novo biosynthesis of queuosine (Q), present in most bacteria. Therefore, this molecule must be sourced from ingested food and/or the gut microbiota, and metabolized to its corresponding nucleobase, queuine (q), before incorporation into cytoplasmic and mitochondrial tRNAs. Incorporation of q into the anticodon of some tRNAs contributes to translational efficiency and accuracy.

Similarity. Belongs to the QNG1 protein family.

RefSeq proteins (2): NP_001304926, NP_115683* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019438	Q_salvage	Family

Pfam: PF10343

Catalyzed reactions (Rhea), 1 shown:

• queuosine 5’-phosphate + H2O = queuine + D-ribose 5-phosphate (RHEA:75387)

UniProt features (39 total): helix 20, strand 7, binding site 6, turn 2, chain 1, active site 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7UGK	X-RAY DIFFRACTION	1.78
8DL3	X-RAY DIFFRACTION	2.26

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T6V5-F1	96.27	0.93

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 239 (nucleophile or transition state stabilizer)

Ligand- & substrate-binding residues (6): 53; 237; 239; 314; 315; 319

Post-translational modifications (1): 1

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-6782315	tRNA modification in the nucleus and cytosol

MSigDB gene sets: 151 (showing top): YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_10, TSENG_IRS1_TARGETS_UP, GOBP_TRNA_METABOLIC_PROCESS, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, GOBP_PURINE_CONTAINING_COMPOUND_SALVAGE, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, MARTINEZ_RB1_TARGETS_UP, GOBP_RNA_MODIFICATION, GOBP_NUCLEOBASE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_PURINE_NUCLEOBASE_BIOSYNTHETIC_PROCESS, GOBP_NUCLEOSIDE_SALVAGE, PETRETTO_LEFT_VENTRICLE_MASS_QTL_CIS_DN

GO Biological Process (4): tRNA modification (GO:0006400), purine nucleobase salvage (GO:0043096), nucleoside salvage (GO:0043174), tRNA queuosine(34) biosynthetic process from salvaged queuosine or its precursors (GO:0160254)

GO Molecular Function (3): hydrolase activity (GO:0016787), queuosine nucleosidase activity (GO:0106432), protein binding (GO:0005515)

GO Cellular Component (1): cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
tRNA processing	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
tRNA processing	1
RNA modification	1
purine nucleobase biosynthetic process	1
purine-containing compound salvage	1
nucleoside biosynthetic process	1
metabolic compound salvage	1
tRNA queuosine(34) biosynthetic process	1
catalytic activity	1
purine nucleosidase activity	1
binding	1
cytoplasm	1
cellular anatomical structure	1

Protein interactions and networks

STRING

498 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
QNG1	CD34	P28906	549
QNG1	GKAP1	Q5VSY0	526
QNG1	MARVELD1	Q9BSK0	526
QNG1	RPP25	Q9BUL9	493
QNG1	CIAO2A	Q9H5X1	474
QNG1	TMEM151A	Q8N4L1	448
QNG1	KIF27	Q86VH2	445
QNG1	QTRT1	Q9BXR0	395
QNG1	ZBTB11	O95625	395
QNG1	ZSCAN26	Q16670	374
QNG1	TRIM4	Q9C037	367
QNG1	LMAN2L	Q9H0V9	362
QNG1	RNF181	Q9P0P0	357
QNG1	PGP	A6NDG6	343
QNG1	USE1	Q9NZ43	320

IntAct

31 interactions, top by confidence:

A	B	Type	Score
PRKD2	PRKD3	psi-mi:“MI:0914”(association)	0.730
QNG1	MEOX2	psi-mi:“MI:0915”(physical association)	0.560
PRNP	CARNS1	psi-mi:“MI:0914”(association)	0.350
PRNP	WDR91	psi-mi:“MI:0914”(association)	0.350
LRRK2		psi-mi:“MI:0914”(association)	0.350
QNG1	PPIAL4G	psi-mi:“MI:0914”(association)	0.350
POLL	SULT1C2	psi-mi:“MI:0914”(association)	0.350
UBXN7	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
FAM163B	TSPY2	psi-mi:“MI:0914”(association)	0.350
NTSR1	GPR89A	psi-mi:“MI:0914”(association)	0.350
EMX2	LRP4	psi-mi:“MI:0914”(association)	0.350
XKR4	CCNC	psi-mi:“MI:0914”(association)	0.350
SLC16A2	QNG1	psi-mi:“MI:0914”(association)	0.350
AZU1	UBA6	psi-mi:“MI:0914”(association)	0.350
DND1	UBA6	psi-mi:“MI:0914”(association)	0.350
MRPL49	UBA6	psi-mi:“MI:0914”(association)	0.350
PEX7	UBA6	psi-mi:“MI:0914”(association)	0.350
VENTX	UBA6	psi-mi:“MI:0914”(association)	0.350
IMMP1L	NUDT19	psi-mi:“MI:2364”(proximity)	0.270
GABARAPL1	BLTP3B	psi-mi:“MI:2364”(proximity)	0.270
MAP1LC3B	FAM83G	psi-mi:“MI:2364”(proximity)	0.270
DDX55	U2SURP	psi-mi:“MI:2364”(proximity)	0.270
GNL3	VWA8	psi-mi:“MI:2364”(proximity)	0.270
RPS11	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
SBDS	RPSA2	psi-mi:“MI:2364”(proximity)	0.270
SRSF7	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
QNG1	MEOX2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (42): C9orf64 (Affinity Capture-MS), C9orf64 (Co-fractionation), CARKD (Co-fractionation), DPYD (Co-fractionation), ITPA (Co-fractionation), NEDD8 (Co-fractionation), NMRAL1 (Co-fractionation), PKM (Co-fractionation), C9orf64 (Affinity Capture-MS), C9orf64 (Affinity Capture-MS), C9orf64 (Affinity Capture-MS), C9orf64 (Affinity Capture-MS), PPIAL4G (Affinity Capture-MS), NIF3L1 (Affinity Capture-MS), C9orf64 (Affinity Capture-MS)

ESM2 similar proteins: A7SNN9, B3S0D3, B4JUE4, G3X8U3, O13670, O22585, O35156, O64407, O65015, O74927, O81395, P09948, P21900, P25853, P27660, P32861, P34534, P39683, P40566, P45350, P51039, P51041, P51043, P51820, P79303, Q05762, Q08225, Q10258, Q10313, Q11UE6, Q1JP73, Q1MPA7, Q27828, Q2QRX6, Q3ANY4, Q54II8, Q59136, Q59730, Q59741, Q59748

Diamond homologs: A7SNN9, D1C7A6, G3X8U3, Q1JP73, Q54II8, Q5T6V5, Q9HDZ9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

11 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	1
Likely benign	0
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

871 predictions. Top by Δscore:

Variant	Effect	Δscore
9:83944782:A:AC	donor_gain	1.0000
9:83944783:A:C	donor_gain	1.0000
9:83944789:CAAA:C	donor_loss	1.0000
9:83944790:AAACC:A	donor_loss	1.0000
9:83944791:AACC:A	donor_loss	1.0000
9:83944792:A:C	donor_loss	1.0000
9:83944793:CCTTT:C	donor_loss	1.0000
9:83944988:CC:C	acceptor_gain	1.0000
9:83944989:CC:C	acceptor_gain	1.0000
9:83944993:A:C	acceptor_gain	1.0000
9:83955377:TCA:T	donor_loss	1.0000
9:83955378:CAC:C	donor_loss	1.0000
9:83955379:A:AC	donor_gain	1.0000
9:83955379:ACC:A	donor_loss	1.0000
9:83955380:C:CC	donor_gain	1.0000
9:83955380:C:CT	donor_loss	1.0000
9:83955380:CCT:C	donor_gain	1.0000
9:83955417:TTCA:T	donor_gain	1.0000
9:83955545:C:CC	acceptor_gain	1.0000
9:83955639:CCCTT:C	acceptor_gain	1.0000
9:83955640:CCTT:C	acceptor_gain	1.0000
9:83944985:TTCCC:T	acceptor_gain	0.9900
9:83944986:TCCC:T	acceptor_gain	0.9900
9:83944987:CCC:C	acceptor_gain	0.9900
9:83944987:CCCC:C	acceptor_gain	0.9900
9:83944988:CCC:C	acceptor_gain	0.9900
9:83944990:C:CC	acceptor_gain	0.9900
9:83944990:C:G	acceptor_loss	0.9900
9:83944990:C:T	acceptor_gain	0.9900
9:83944993:A:AC	acceptor_gain	0.9900

AlphaMissense

2234 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:83944967:T:A	K207I	0.990
9:83956273:G:C	F76L	0.986
9:83956273:G:T	F76L	0.986
9:83956275:A:G	F76L	0.986
9:83944966:T:A	K207N	0.977
9:83944966:T:G	K207N	0.977
9:83955534:C:A	R148S	0.974
9:83955534:C:G	R148S	0.974
9:83955466:A:T	V171D	0.973
9:83955512:C:A	G156W	0.971
9:83939700:T:A	R279S	0.969
9:83939700:T:G	R279S	0.969
9:83956276:G:C	N75K	0.969
9:83956276:G:T	N75K	0.969
9:83944904:A:G	F228S	0.966
9:83955398:C:G	D194H	0.966
9:83939698:C:T	G280E	0.965
9:83955523:A:G	L152P	0.965
9:83939699:C:A	G280W	0.964
9:83955477:A:C	F167L	0.963
9:83955477:A:T	F167L	0.963
9:83955479:A:G	F167L	0.963
9:83944876:A:C	F237L	0.962
9:83944876:A:T	F237L	0.962
9:83944878:A:G	F237L	0.962
9:83956267:A:C	F78L	0.960
9:83956267:A:T	F78L	0.960
9:83956269:A:G	F78L	0.960
9:83955489:A:C	F163L	0.959
9:83955489:A:T	F163L	0.959

dbSNP variants (sampled 300 via entrez): RS1000016348 (9:83952840 T>G), RS1000016976 (9:83946110 G>A), RS1000036387 (9:83946941 C>A,T), RS1000088640 (9:83946612 T>C), RS1000175044 (9:83941902 G>A), RS1000507710 (9:83940480 A>G), RS1000618437 (9:83950805 T>C), RS1000777385 (9:83956575 A>T), RS1000838476 (9:83952014 A>G), RS1001036266 (9:83945319 T>A,C,G), RS1001315400 (9:83938015 G>A), RS1001351249 (9:83952653 C>T), RS1001415525 (9:83946234 G>A), RS1001686962 (9:83947686 G>A,C,T), RS1001701921 (9:83953090 G>A,T)

Disease associations

OMIM: gene MIM:611342 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST000817_15	Height	5.000000e-08
GCST006979_357	Heel bone mineral density	1.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009270	heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

38 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation, affects expression	2
Valproic Acid	affects expression, increases expression	2
Particulate Matter	increases expression, decreases expression, increases abundance	2
GSK-J4	decreases expression	1
dicrotophos	decreases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
salinomycin	decreases expression	1
decabromobiphenyl ether	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
tetrabromobisphenol A	increases expression	1
perfluorooctanoic acid	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
entinostat	increases expression	1
K 7174	decreases expression	1
perfluorohexanesulfonic acid	increases expression	1
ICG 001	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
(+)-JQ1 compound	decreases expression	1
bisphenol AF	increases expression	1
Temozolomide	decreases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Leflunomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Air Pollutants, Occupational	decreases expression	1
Vehicle Emissions	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Drugs, Chinese Herbal	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.