NUDT17

Summary

NUDT17 (nudix hydrolase 17, HGNC:26618) is a protein-coding gene on chromosome 1q21.1, encoding m7GpppN-mRNA hydrolase NUDT17 (P0C025). Acts as a decapping enzyme capable of hydrolyzing monomethylated capped RNAs (in vitro).

Predicted to enable NADH pyrophosphatase activity. Predicted to be involved in NAD catabolic process; NADH metabolic process; and NADP catabolic process. Predicted to be active in peroxisome.

Source: NCBI Gene 200035 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 42 total
• MANE Select transcript: NM_001012758

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26618
Approved symbol	NUDT17
Name	nudix hydrolase 17
Location	1q21.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ34433
Ensembl gene	ENSG00000186364
Ensembl biotype	protein_coding
Entrez	200035

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000334513, ENST00000444015, ENST00000460879, ENST00000477878, ENST00000498192, ENST00000867824, ENST00000867825, ENST00000949037, ENST00000949038

RefSeq mRNA: 1 — MANE Select: NM_001012758 NM_001012758

CCDS: CCDS72865

Canonical transcript exons

ENST00000334513 — 8 exons

Exon	Start	End
ENSE00001340185	145846598	145846690
ENSE00001340187	145846433	145846458
ENSE00001423846	145848377	145848954
ENSE00001905197	145845630	145845832
ENSE00003484283	145848112	145848264
ENSE00003511336	145847583	145847719
ENSE00003595919	145846013	145846196
ENSE00003707658	145847250	145847348

Expression profiles

Bgee: expression breadth ubiquitous, 182 present calls, max score 97.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.2485 / max 39.1722, expressed in 1483 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
4952	3.1569	1471
4953	0.0916	23

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oviduct epithelium	UBERON:0004804	97.29	gold quality
tendon of biceps brachii	UBERON:0008188	88.31	gold quality
pancreatic ductal cell	CL:0002079	85.87	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.93	gold quality
buccal mucosa cell	CL:0002336	82.27	silver quality
cerebellar hemisphere	UBERON:0002245	80.76	gold quality
right hemisphere of cerebellum	UBERON:0014890	80.51	gold quality
granulocyte	CL:0000094	80.47	gold quality
cerebellar cortex	UBERON:0002129	80.46	gold quality
upper arm skin	UBERON:0004263	80.40	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.13	gold quality
cerebellum	UBERON:0002037	78.69	gold quality
fallopian tube	UBERON:0003889	78.12	gold quality
apex of heart	UBERON:0002098	77.52	gold quality
ventricular zone	UBERON:0003053	77.52	gold quality
nucleus accumbens	UBERON:0001882	77.28	gold quality
anterior cingulate cortex	UBERON:0009835	77.06	gold quality
tendon	UBERON:0000043	76.53	gold quality
right frontal lobe	UBERON:0002810	76.43	gold quality
caudate nucleus	UBERON:0001873	75.98	gold quality
lower esophagus mucosa	UBERON:0035834	75.70	gold quality
spleen	UBERON:0002106	75.51	gold quality
prefrontal cortex	UBERON:0000451	75.28	gold quality
hindlimb stylopod muscle	UBERON:0004252	75.24	gold quality
monocyte	CL:0000576	75.19	gold quality
leukocyte	CL:0000738	75.15	gold quality
right uterine tube	UBERON:0001302	74.97	gold quality
Brodmann (1909) area 9	UBERON:0013540	74.81	gold quality
hypothalamus	UBERON:0001898	74.52	gold quality
tibialis anterior	UBERON:0001385	74.42	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.73

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Association between NUDT17 polymorphisms and breast cancer risk. (PMID:38756100)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	nudt17	ENSDARG00000008014
mus_musculus	Nudt17	ENSMUSG00000028100
rattus_norvegicus	Nudt17	ENSRNOG00000037217

Paralogs (3): NUDT1 (ENSG00000106268), NUDT12 (ENSG00000112874), NUDT18 (ENSG00000275074)

Protein

Protein identifiers

m7GpppN-mRNA hydrolase NUDT17 — P0C025 (reviewed: P0C025)

Alternative names: Nucleoside diphosphate-linked moiety X motif 17

All UniProt accessions (1): P0C025

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a decapping enzyme capable of hydrolyzing monomethylated capped RNAs (in vitro). Hydrolyzes monomethylated capped RNA after alpha and beta phosphates to form N(7)-methyl-GDP. Shows low activity towards unmethylated capped RNA.

Similarity. Belongs to the Nudix hydrolase family.

RefSeq proteins (1): NP_001012776* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000086	NUDIX_hydrolase_dom	Domain
IPR015797	NUDIX_hydrolase-like_dom_sf	Homologous_superfamily
IPR033716	Nudt17_dom	Domain
IPR050241	NAD-cap_RNA_hydrolase_NudC	Family

Pfam: PF00293

Catalyzed reactions (Rhea), 1 shown:

• a 5’-end (N(7)-methyl 5’-triphosphoguanosine)-ribonucleoside in mRNA + H2O = N(7)-methyl-GDP + a 5’-end phospho-ribonucleoside in mRNA + 2 H(+) (RHEA:67484)

UniProt features (30 total): strand 15, helix 8, binding site 2, chain 1, domain 1, region of interest 1, turn 1, short sequence motif 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
5LF8	X-RAY DIFFRACTION	2.56

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0C025-F1	85.64	0.68

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 (2): 142; 146

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 70 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, GOBP_NADPPLUS_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_NADPLUS_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, GOBP_ORGANOPHOSPHATE_CATABOLIC_PROCESS, GOBP_NUCLEOSIDE_PHOSPHATE_CATABOLIC_PROCESS, GOBP_PURINE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOBP_PURINE_CONTAINING_COMPOUND_CATABOLIC_PROCESS, chr1q21, GOCC_MICROBODY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, GOBP_PYRIDINE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOMF_DINUCLEOTIDE_PHOSPHATASE_ACTIVITY

GO Biological Process (4): NADP+ catabolic process (GO:0006742), NAD+ catabolic process (GO:0019677), RNA decapping (GO:0110154), obsolete NADH metabolic process (GO:0006734)

GO Molecular Function (4): NADH pyrophosphatase activity (GO:0035529), metal ion binding (GO:0046872), 5’-(N(7)-methylguanosine 5’-triphospho)-[mRNA] hydrolase activity (GO:0140933), hydrolase activity (GO:0016787)

GO Cellular Component (1): peroxisome (GO:0005777)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
purine nucleotide catabolic process	2
pyridine nucleotide catabolic process	2
NADP+ metabolic process	1
NAD+ metabolic process	1
RNA metabolic process	1
dinucleotide phosphatase activity	1
cation binding	1
pyrophosphatase activity	1
catalytic activity	1
microbody	1

Protein interactions and networks

STRING

306 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NUDT17	NUDT12	Q9BQG2	762
NUDT17	NUDT22	Q9BRQ3	745
NUDT17	NUDT19	A8MXV4	740
NUDT17	NUDT18	Q6ZVK8	736
NUDT17	NUDT2	P50583	726
NUDT17	NUDT14	O95848	718
NUDT17	NUDT5	Q9UKK9	710
NUDT17	NUDT15	Q9NV35	693
NUDT17	NUDT3	O95989	657
NUDT17	TMEM225	Q6GV28	596
NUDT17	NUDT1	P36639	587
NUDT17	NUDT4B	A0A024RBG1	580
NUDT17	NUDT6	P53370	572
NUDT17	DHRS12	A0PJE2	543
NUDT17	NUDT21	O43809	541

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A4FU01, A4FUG7, A6NE52, D2HS90, D4A929, O15287, O94761, O95382, P0C025, P29473, P29474, P51617, P70313, P97270, Q05932, Q14296, Q15477, Q1JPD6, Q2LGB3, Q3MHT4, Q3U5Q7, Q3V1L6, Q562E7, Q5M8V2, Q5ND34, Q5PQ04, Q5RA67, Q5RAJ5, Q5XIS1, Q62406, Q69ZM6, Q6ZS72, Q6ZVH7, Q6ZVK8, Q75NR7, Q76MJ5, Q7M733, Q80UU1, Q8BLY7, Q8BTN6

Diamond homologs: A1AA28, A4FUG7, A7ZKS4, A7ZZ89, B1IUD3, B1LI09, B1XA44, P0AEI6, P0AEI7, P0AEI8, P0AEI9, P0C025, P50584, Q0T5N8, Q0TIT9, Q1RD19, Q31ZL0, Q32EZ2, Q3Z2Y5, Q4V8V2, Q5M8V2, Q5PQ04, Q6PEC0, Q75UV1, Q8NFP7, Q9CWD3, Q9KK75, A1ADA3, A4WDK7, A6TBV3, A7ZP69, A8A2B8, A9MJC8, A9N5B7, B1IXT6, B1LLK5, B1X8W4, B4SYW7, B4TBG2, B4TPH8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1018 predictions. Top by Δscore:

Variant	Effect	Δscore
1:145845773:T:TA	donor_gain	0.9900
1:145846034:C:CT	acceptor_gain	0.9900
1:145847247:C:CC	acceptor_gain	0.9900
1:145847251:CAGA:C	acceptor_gain	0.9900
1:145848109:C:CC	acceptor_gain	0.9900
1:145848114:CTGCA:C	acceptor_gain	0.9900
1:145846195:CC:C	donor_gain	0.9800
1:145846196:AC:A	donor_gain	0.9800
1:145847992:T:C	acceptor_gain	0.9800
1:145847718:C:CC	donor_gain	0.9700
1:145847719:A:AC	donor_gain	0.9700
1:145846195:C:CG	donor_loss	0.9600
1:145846196:A:C	donor_loss	0.9600
1:145846197:CA:C	donor_loss	0.9600
1:145846198:TCACC:T	donor_loss	0.9600
1:145846199:CTC:C	donor_loss	0.9600
1:145846200:ACT:A	donor_loss	0.9600
1:145846202:ATACT:A	donor_loss	0.9600
1:145847718:CAGGA:C	donor_gain	0.9600
1:145846203:AATAC:A	donor_loss	0.9500
1:145846630:T:A	donor_gain	0.9500
1:145847249:GA:G	acceptor_gain	0.9500
1:145848111:CA:C	acceptor_gain	0.9500
1:145846034:C:T	acceptor_gain	0.9400
1:145846201:TACT:T	donor_loss	0.9400
1:145847250:AGA:A	acceptor_gain	0.9400
1:145847499:A:C	acceptor_gain	0.9400
1:145847579:T:G	acceptor_loss	0.9400
1:145847581:CCTG:C	acceptor_loss	0.9400
1:145848069:T:C	acceptor_gain	0.9400

AlphaMissense

2068 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:145847625:T:A	W213R	0.982
1:145847625:T:C	W213R	0.982
1:145846184:T:A	W122R	0.976
1:145846184:T:C	W122R	0.976
1:145848230:T:C	F284L	0.972
1:145848232:T:A	F284L	0.972
1:145848232:T:G	F284L	0.972
1:145848234:C:A	A285D	0.963
1:145847627:G:C	W213C	0.960
1:145847627:G:T	W213C	0.960
1:145848215:A:C	S279R	0.958
1:145848217:C:A	S279R	0.958
1:145848217:C:G	S279R	0.958
1:145848245:T:A	W289R	0.957
1:145848245:T:C	W289R	0.957
1:145846186:G:C	W122C	0.954
1:145846186:G:T	W122C	0.954
1:145846137:T:A	V106D	0.951
1:145845695:T:C	F19L	0.948
1:145845697:C:A	F19L	0.948
1:145845697:C:G	F19L	0.948
1:145846685:T:A	W164R	0.948
1:145846685:T:C	W164R	0.948
1:145846140:T:C	L107S	0.943
1:145846687:G:C	W164C	0.938
1:145846687:G:T	W164C	0.938
1:145846149:G:C	R110P	0.929
1:145846690:G:C	E165D	0.926
1:145846690:G:T	E165D	0.926
1:145846031:T:C	F71L	0.924

dbSNP variants (sampled 300 via entrez): RS1000597933 (1:145846665 C>T), RS1001718595 (1:145847361 G>A,C), RS1003820509 (1:145845110 G>T), RS1005167671 (1:145847066 C>T), RS1005469989 (1:145845941 C>A,T), RS1007593303 (1:145845644 G>A), RS1007622661 (1:145845435 G>T), RS1007955823 (1:145844090 G>A,T), RS1007968662 (1:145844359 G>T), RS1009826216 (1:145846624 T>A,C), RS1011039064 (1:145845372 G>A,T), RS1011370705 (1:145844021 T>C), RS1011826081 (1:145849194 T>C), RS1012628509 (1:145848814 G>A), RS1013594972 (1:145843670 A>C)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	increases abundance, increases expression	2
Smoke	increases abundance, increases expression, decreases expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
triphenyl phosphate	affects expression	1
abrine	increases expression	1
jinfukang	increases expression	1
Sunitinib	decreases expression	1
Atrazine	increases expression	1
Cisplatin	decreases expression	1
Coal	increases abundance, increases expression	1
Doxorubicin	decreases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Cadmium Chloride	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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