NUDT22

Summary

NUDT22 (nudix hydrolase 22, HGNC:28189) is a protein-coding gene on chromosome 11q13.1, encoding Uridine diphosphate glucose pyrophosphatase NUDT22 (Q9BRQ3). Hydrolyzes UDP-glucose to glucose 1-phosphate and UMP and UDP-galactose to galactose 1-phosphate and UMP.

Enables UDP-sugar diphosphatase activity and metal ion binding activity. Located in nucleoplasm.

Source: NCBI Gene 84304 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 54 total
• MANE Select transcript: NM_032344

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28189
Approved symbol	NUDT22
Name	nudix hydrolase 22
Location	11q13.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC13045
Ensembl gene	ENSG00000149761
Ensembl biotype	protein_coding
Entrez	84304

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 6 protein_coding, 5 retained_intron, 3 nonsense_mediated_decay

ENST00000279206, ENST00000422364, ENST00000428347, ENST00000441250, ENST00000534929, ENST00000535000, ENST00000537094, ENST00000537707, ENST00000539325, ENST00000543358, ENST00000543501, ENST00000545184, ENST00000934227, ENST00000934228

RefSeq mRNA: 4 — MANE Select: NM_032344 NM_001128612, NM_001128613, NM_001271831, NM_032344

CCDS: CCDS44640, CCDS8061

Canonical transcript exons

ENST00000279206 — 6 exons

Exon	Start	End
ENSE00000728414	64229247	64229344
ENSE00001139190	64226635	64227132
ENSE00001196025	64227568	64227666
ENSE00003463819	64229478	64229571
ENSE00003682817	64229850	64230016
ENSE00003888806	64226274	64226427

Expression profiles

Bgee: expression breadth ubiquitous, 237 present calls, max score 97.69.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.7047 / max 342.1206, expressed in 1814 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
114873	17.2682	1807
114874	3.0216	1587
114875	1.7258	617
114872	0.5695	302
114876	0.1195	31

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	97.69	gold quality
apex of heart	UBERON:0002098	97.55	gold quality
granulocyte	CL:0000094	96.50	gold quality
metanephros cortex	UBERON:0010533	96.00	gold quality
lower esophagus mucosa	UBERON:0035834	95.96	gold quality
transverse colon	UBERON:0001157	95.44	gold quality
spleen	UBERON:0002106	95.16	gold quality
right lobe of thyroid gland	UBERON:0001119	95.11	gold quality
small intestine Peyer’s patch	UBERON:0003454	95.01	gold quality
body of stomach	UBERON:0001161	94.99	gold quality
right atrium auricular region	UBERON:0006631	94.91	gold quality
body of pancreas	UBERON:0001150	94.87	gold quality
heart left ventricle	UBERON:0002084	94.81	gold quality
right lobe of liver	UBERON:0001114	94.60	gold quality
cardiac ventricle	UBERON:0002082	94.58	gold quality
left lobe of thyroid gland	UBERON:0001120	94.55	gold quality
cardiac atrium	UBERON:0002081	94.45	gold quality
right adrenal gland	UBERON:0001233	94.40	gold quality
left adrenal gland cortex	UBERON:0035825	94.23	gold quality
small intestine	UBERON:0002108	94.18	gold quality
right adrenal gland cortex	UBERON:0035827	94.07	gold quality
left adrenal gland	UBERON:0001234	93.93	gold quality
adenohypophysis	UBERON:0002196	93.84	gold quality
cortex of kidney	UBERON:0001225	93.73	gold quality
adrenal cortex	UBERON:0001235	93.67	gold quality
heart	UBERON:0000948	93.58	gold quality
minor salivary gland	UBERON:0001830	93.58	gold quality
thyroid gland	UBERON:0002046	93.54	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.29	gold quality
esophagus mucosa	UBERON:0002469	93.26	gold quality

Single-cell (SCXA)

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

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

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• NUDT22 promotes cancer growth through pyrimidine salvage. (PMID:36871087)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	nudt22	ENSDARG00000071671
mus_musculus	Nudt22	ENSMUSG00000037349
rattus_norvegicus	Nudt22	ENSRNOG00000021158

Protein

Protein identifiers

Uridine diphosphate glucose pyrophosphatase NUDT22 — Q9BRQ3 (reviewed: Q9BRQ3)

Alternative names: Nucleoside diphosphate-linked moiety X motif 22

All UniProt accessions (5): Q9BRQ3, F5H1N0, G3V1M6, H0YGG2, J3KQJ3

UniProt curated annotations — full annotation on UniProt →

Function. Hydrolyzes UDP-glucose to glucose 1-phosphate and UMP and UDP-galactose to galactose 1-phosphate and UMP. Preferred substrate is UDP-glucose.

Similarity. Belongs to the Nudix hydrolase family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9BRQ3-1	1	yes
Q9BRQ3-2	2
Q9BRQ3-3	3

RefSeq proteins (4): NP_001122084, NP_001122085, NP_001258760, NP_115720* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000086	NUDIX_hydrolase_dom	Domain
IPR055295	NUDT22/NUDT9-like	Family

UniProt features (56 total): helix 15, strand 12, binding site 10, turn 5, sequence variant 4, mutagenesis site 3, splice variant 2, chain 1, domain 1, region of interest 1, sequence conflict 1, short sequence motif 1

Structure

Experimental structures (PDB)

33 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
5RKZ	X-RAY DIFFRACTION	1.38
5R53	X-RAY DIFFRACTION	1.4
5R57	X-RAY DIFFRACTION	1.44
5R5A	X-RAY DIFFRACTION	1.44
5LF9	X-RAY DIFFRACTION	1.45
5R52	X-RAY DIFFRACTION	1.48
5R55	X-RAY DIFFRACTION	1.48
5R5S	X-RAY DIFFRACTION	1.5
5R56	X-RAY DIFFRACTION	1.51
5R5B	X-RAY DIFFRACTION	1.53
5R5P	X-RAY DIFFRACTION	1.53
5R5E	X-RAY DIFFRACTION	1.58
5R5K	X-RAY DIFFRACTION	1.6
5R5M	X-RAY DIFFRACTION	1.6
5R5F	X-RAY DIFFRACTION	1.63
5R5L	X-RAY DIFFRACTION	1.63
5R51	X-RAY DIFFRACTION	1.65
5R5D	X-RAY DIFFRACTION	1.65
5R5R	X-RAY DIFFRACTION	1.65
5R5C	X-RAY DIFFRACTION	1.68
5R5I	X-RAY DIFFRACTION	1.7
5R5Q	X-RAY DIFFRACTION	1.71
5R5G	X-RAY DIFFRACTION	1.77
5R54	X-RAY DIFFRACTION	1.79
5R5H	X-RAY DIFFRACTION	1.79
5R5O	X-RAY DIFFRACTION	1.79
5LOU	X-RAY DIFFRACTION	1.8
5R50	X-RAY DIFFRACTION	1.87
5R5N	X-RAY DIFFRACTION	1.87
5R58	X-RAY DIFFRACTION	1.98

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BRQ3-F1	93.28	0.83

Functional residue map

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

Ligand- & substrate-binding residues (10): 158; 189; 193; 274; 56; 87; 139; 144; 151; 156

Mutagenesis-validated functional residues (3):

Position	Phenotype
156	abolishes enzyme activity with udp-galactose.
189	abolishes enzyme activity with udp-galactose.
193	abolishes enzyme activity with udp-galactose.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 61 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, chr11q13, CAGCTG_AP4_Q5, MODULE_313, HNF4_DR1_Q3, PPAR_DR1_Q2, ELK1_01, ACTTTAT_MIR1425P, NUYTTEN_EZH2_TARGETS_DN, SCGGAAGY_ELK1_02, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3, FORTSCHEGGER_PHF8_TARGETS_DN

GO Biological Process (0):

GO Molecular Function (5): UDP-sugar diphosphatase activity (GO:0008768), metal ion binding (GO:0046872), GDP-mannose hydrolase activity (GO:0052751), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (1): nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
pyrophosphatase activity	2
cation binding	1
binding	1
catalytic activity	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

740 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NUDT22	NUDT14	O95848	774
NUDT22	NUDT17	P0C025	745
NUDT22	NUDT12	Q9BQG2	724
NUDT22	NUDT5	Q9UKK9	718
NUDT22	NUDT18	Q6ZVK8	703
NUDT22	NUDT2	P50583	676
NUDT22	NUDT1	P36639	641
NUDT22	PPP1R14B	Q96C90	609
NUDT22	NUDT3	O95989	592
NUDT22	NUDT6	P53370	591
NUDT22	NUDT15	Q9NV35	586
NUDT22	NUDT4B	A0A024RBG1	580
NUDT22	NUDT9	Q9BW91	579
NUDT22	NUDT21	O43809	572
NUDT22	NUDT7	P0C024	544

IntAct

82 interactions, top by confidence:

A	B	Type	Score
NUDT22	TLE5	psi-mi:“MI:0915”(physical association)	0.670
TLE5	NUDT22	psi-mi:“MI:0915”(physical association)	0.670
NUDT22	RUSC1	psi-mi:“MI:0915”(physical association)	0.600
NUDT22	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
ZNF648	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
ZBTB33	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
TCF4	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
DNAL4	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
ZNF143	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
INCA1	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
ZNF398	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
USP54	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
NUDT22	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
SAXO1	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
DDIT4L	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
KLHL26	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
NUDT22	LHX3	psi-mi:“MI:0915”(physical association)	0.560
ZNF343	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
NUDT22	WDR54	psi-mi:“MI:0915”(physical association)	0.560
NUDT22	ZNF581	psi-mi:“MI:0915”(physical association)	0.560
ARID5A	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
ZNF655	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
ZNF19	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
TLE5	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
SPATA7	NUDT22	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (28): NUDT22 (Two-hybrid), NUDT22 (Affinity Capture-MS), NUDT22 (Affinity Capture-MS), NUDT22 (Two-hybrid), NUDT22 (Two-hybrid), NUDT22 (Two-hybrid), NUDT22 (Two-hybrid), NUDT22 (Two-hybrid), NUDT22 (Two-hybrid), NUDT22 (Two-hybrid), NUDT22 (Two-hybrid), FAM154A (Two-hybrid), ZNF19 (Two-hybrid), RUSC1 (Two-hybrid), USP54 (Two-hybrid)

ESM2 similar proteins: A2AA28, A4FV42, A4FV98, A6NDG6, D3YWP0, D3ZVU9, O15315, O35719, O70277, O75382, O94759, P21964, P57775, P81799, Q2TBS1, Q3UGX3, Q4R3I0, Q5E9V4, Q5H879, Q5RJL2, Q5SUV1, Q6DC64, Q7Z624, Q86WI3, Q86XA0, Q8BNV1, Q8C436, Q8CIW5, Q8IZ69, Q8N8L6, Q8N9F0, Q8VCX6, Q8WXB1, Q96AZ1, Q96FB5, Q96RR1, Q9BQD7, Q9BRQ3, Q9BUU2, Q9CQL0

Diamond homologs: Q2TBI8, Q6P9U1, Q8VYR2, Q9BRQ3, Q9DD16

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	47
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1376 predictions. Top by Δscore:

Variant	Effect	Δscore
11:64229240:A:AG	acceptor_gain	1.0000
11:64229242:C:A	acceptor_gain	1.0000
11:64229340:GTCCA:G	donor_gain	1.0000
11:64229341:TCCA:T	donor_gain	1.0000
11:64229345:G:GG	donor_gain	1.0000
11:64229349:G:GG	donor_gain	1.0000
11:64226005:C:A	donor_gain	0.9900
11:64226028:AGGC:A	donor_gain	0.9900
11:64227579:T:TA	acceptor_gain	0.9900
11:64229240:ACC:A	acceptor_gain	0.9900
11:64229242:CGCA:C	acceptor_loss	0.9900
11:64229243:GCAG:G	acceptor_loss	0.9900
11:64229244:CAGGT:C	acceptor_loss	0.9900
11:64229245:A:AG	acceptor_gain	0.9900
11:64229245:A:C	acceptor_loss	0.9900
11:64229245:AGGT:A	acceptor_gain	0.9900
11:64229246:G:A	acceptor_loss	0.9900
11:64229246:G:GG	acceptor_gain	0.9900
11:64229246:GGT:G	acceptor_gain	0.9900
11:64229246:GGTG:G	acceptor_gain	0.9900
11:64229342:CCA:C	donor_gain	0.9900
11:64229343:CA:C	donor_gain	0.9900
11:64229346:T:G	donor_loss	0.9900
11:64229348:A:AC	donor_loss	0.9900
11:64229473:TCCA:T	acceptor_loss	0.9900
11:64229475:CAGGT:C	acceptor_loss	0.9900
11:64229476:A:AT	acceptor_loss	0.9900
11:64229549:G:GT	donor_gain	0.9900
11:64229848:A:AG	acceptor_gain	0.9900
11:64229849:G:GG	acceptor_gain	0.9900

AlphaMissense

1918 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:64229334:T:C	F223L	0.996
11:64229336:C:A	F223L	0.996
11:64229336:C:G	F223L	0.996
11:64226834:T:C	F61S	0.993
11:64226833:T:C	F61L	0.991
11:64226835:C:A	F61L	0.991
11:64226835:C:G	F61L	0.991
11:64226934:C:A	N94K	0.989
11:64226934:C:G	N94K	0.989
11:64227120:C:A	H156Q	0.989
11:64227120:C:G	H156Q	0.989
11:64229329:C:A	A221D	0.988
11:64229335:T:C	F223S	0.988
11:64229906:A:C	K276N	0.988
11:64229906:A:T	K276N	0.988
11:64226836:C:A	R62S	0.987
11:64227056:T:A	V135D	0.987
11:64229325:A:C	S220R	0.987
11:64229327:T:A	S220R	0.987
11:64229327:T:G	S220R	0.987
11:64229341:T:A	V225D	0.987
11:64226832:G:C	K60N	0.985
11:64226832:G:T	K60N	0.985
11:64229289:G:C	G208R	0.985
11:64229894:C:G	C272W	0.984
11:64229902:C:A	A275D	0.984
11:64227110:C:A	P153H	0.983
11:64226818:T:C	F56L	0.982
11:64226820:C:A	F56L	0.982
11:64226820:C:G	F56L	0.982

dbSNP variants (sampled 300 via entrez): RS1000136739 (11:64228904 A>G,T), RS1000299009 (11:64228632 T>A,C,G), RS1000445974 (11:64226339 G>A), RS1000774539 (11:64226560 A>C,G), RS1002629045 (11:64230473 G>C), RS1002884392 (11:64228554 C>T), RS1002898986 (11:64224472 T>G), RS1002932120 (11:64230670 C>A,G,T), RS1003263805 (11:64228908 G>A,T), RS1003822218 (11:64230471 G>A,C), RS1004128134 (11:64227785 G>A), RS1004349649 (11:64228965 C>G), RS1004479954 (11:64228416 G>C), RS1005284811 (11:64230754 G>A), RS1005355150 (11:64230525 C>A,T)

Disease associations

OMIM: gene `` | 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
GCST004132_98	Crohn’s disease	5.000000e-06
GCST010136_47	Fruit consumption	9.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008111	diet measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	decreases expression	2
Valproic Acid	increases expression, increases methylation	2
GSK-J4	decreases expression	1
arsenite	affects binding, increases reaction	1
sodium arsenite	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
bisphenol S	decreases methylation	1
jinfukang	affects cotreatment, increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Diazinon	increases methylation	1
Doxorubicin	increases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Antirheumatic Agents	decreases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1
Vitamin K 3	affects expression	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E2EZ	HAP1 NUDT22 (-) 1	Cancer cell line	Male
CVCL_E2F0	HAP1 NUDT22 (-) 2	Cancer cell line	Male
CVCL_E2F1	HAP1 NUDT22 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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