NUDT16

Summary

NUDT16 (nudix hydrolase 16, HGNC:26442) is a protein-coding gene on chromosome 3q22.1, encoding U8 snoRNA-decapping enzyme (Q96DE0). RNA-binding and decapping enzyme that catalyzes the cleavage of the cap structure of snoRNAs and mRNAs in a metal-dependent manner.

Enables several functions, including RNA binding activity; metal ion binding activity; and pyrophosphatase activity. Involved in RNA metabolic process and positive regulation of cell cycle process. Located in cytoplasm; nucleolus; and nucleoplasm.

Source: NCBI Gene 131870 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 49 total
• MANE Select transcript: NM_152395

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26442
Approved symbol	NUDT16
Name	nudix hydrolase 16
Location	3q22.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ31265
Ensembl gene	ENSG00000198585
Ensembl biotype	protein_coding
OMIM	617381
Entrez	131870

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000502852, ENST00000521288, ENST00000537561

RefSeq mRNA: 3 — MANE Select: NM_152395 NM_001171905, NM_001171906, NM_152395

CCDS: CCDS3070, CCDS54640, CCDS54641

Canonical transcript exons

ENST00000521288 — 3 exons

Exon	Start	End
ENSE00001268801	131383162	131388830
ENSE00002134695	131381774	131381942
ENSE00002362221	131382046	131382315

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 98.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.1094 / max 157.8898, expressed in 1807 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
38612	21.1094	1807

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	98.50	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	94.63	gold quality
left ventricle myocardium	UBERON:0006566	93.74	gold quality
monocyte	CL:0000576	93.54	gold quality
spinal cord	UBERON:0002240	93.09	gold quality
leukocyte	CL:0000738	93.01	gold quality
small intestine Peyer’s patch	UBERON:0003454	92.68	gold quality
medial globus pallidus	UBERON:0002477	92.19	gold quality
amygdala	UBERON:0001876	91.13	gold quality
hypothalamus	UBERON:0001898	91.06	gold quality
small intestine	UBERON:0002108	91.03	gold quality
tibial nerve	UBERON:0001323	90.88	gold quality
heart left ventricle	UBERON:0002084	90.62	gold quality
apex of heart	UBERON:0002098	90.43	gold quality
mucosa of stomach	UBERON:0001199	90.33	gold quality
substantia nigra	UBERON:0002038	90.27	gold quality
cardiac ventricle	UBERON:0002082	90.23	gold quality
mucosa of transverse colon	UBERON:0004991	89.86	gold quality
transverse colon	UBERON:0001157	89.82	gold quality
left uterine tube	UBERON:0001303	89.76	gold quality
right lung	UBERON:0002167	89.69	gold quality
adult mammalian kidney	UBERON:0000082	89.41	gold quality
globus pallidus	UBERON:0001875	89.41	gold quality
right lobe of liver	UBERON:0001114	89.33	gold quality
ileal mucosa	UBERON:0000331	89.31	gold quality
spleen	UBERON:0002106	89.30	gold quality
anterior cingulate cortex	UBERON:0009835	89.24	gold quality
granulocyte	CL:0000094	89.17	gold quality
putamen	UBERON:0001874	89.02	gold quality
heart	UBERON:0000948	88.73	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	16.30

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

146 targeting NUDT16, 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-3163	100.00	77.23	8605
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-4496	99.88	68.89	2236

Literature-anchored findings (GeneRIF, showing 14)

• X29/H29K may be the nuclear counterparts of the cytoplasmic decapping machinery, localized in specialized bodies involved in RNA decay (PMID:17567574)
• Recombinant NUDT16, a decapping enzyme, has been crystallized. NUDT16 plays a pivotal role in U8 snoRNA stability. (PMID:18607096)
• NUDT16 is a (deoxy)inosine diphosphatase that may function mainly in the nucleus to protect cells from deleterious effects of (d)ITP. (PMID:20385596)
• Like Dcp2, Nudt16 also regulates the stability of a subset of mRNAs including a member of the motin family of proteins involved in angiogenesis. (PMID:21070968)
• hNUDT16 can also actively cleave the mGDP cap from mRNAs in the presence of Mg(2)(+) or Mn(2)(+). (PMID:21337011)
• The RNA decapping enzyme NUDT16 selectively degrades 5’-TOP mRNAs during Rift Valley fever virus infection and this decay is triggered in response to mTOR attenuation via the translational repressor 4EBP1/2 axis. (PMID:26038567)
• This study details structural and regulatory mechanisms explaining how substrates are selected for hydrolysis by human NUDT16. (PMID:26121039)
• data suggest the existence in T-ALL of a disrupted RNA decapping pathway, mediated by the DNA methylation-associated loss of NUDT16, which contributes to the natural history of the disease by stabilizing transforming factors, such as is the case of the leukemogenic protein C-MYC (PMID:28344317)
• hNudt16 hydrolysis of dinucleotide cap analogs and short capped oligonucleotides displayed a broader spectrum specificity than is currently known. (PMID:29483298)
• Nudix Hydrolase NUDT16 Regulates 53BP1 Protein by Reversing 53BP1 ADP-Ribosylation. (PMID:31911551)
• Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs. (PMID:32432673)
• CAG RNAs induce DNA damage and apoptosis by silencing NUDT16 expression in polyglutamine degeneration. (PMID:33947817)
• Transcriptomic profile investigations highlight a putative role for NUDT16 in sepsis. (PMID:35174610)
• NUDT16 regulates CtIP PARylation to dictate homologous recombination repair. (PMID:38324469)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:103759	ENSDARG00000019503
mus_musculus	Nudt16	ENSMUSG00000032565
mus_musculus	Nudt16l2	ENSMUSG00000032566
rattus_norvegicus	Nudt16	ENSRNOG00000012962
rattus_norvegicus	Nudt16l2	ENSRNOG00000037305

Paralogs (1): NUDT16L1 (ENSG00000168101)

Protein

Protein identifiers

U8 snoRNA-decapping enzyme — Q96DE0 (reviewed: Q96DE0)

Alternative names: IDP phosphatase, Inosine diphosphate phosphatase, Nucleoside diphosphate-linked moiety X motif 16, Nudix hydrolase 16, U8 snoRNA-binding protein H29K, m7GpppN-mRNA hydrolase

All UniProt accessions (1): Q96DE0

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding and decapping enzyme that catalyzes the cleavage of the cap structure of snoRNAs and mRNAs in a metal-dependent manner. Part of the U8 snoRNP complex that is required for the accumulation of mature 5.8S and 28S rRNA. Has diphosphatase activity and removes m7G and/or m227G caps from U8 snoRNA and leaves a 5’monophosphate on the RNA. Also catalyzes the cleavage of the cap structure on mRNAs. Does not hydrolyze cap analog structures like 7-methylguanosine nucleoside triphosphate (m7GpppG). Also hydrolysis m7G- and m227G U3-capped RNAs but with less efficiencies. Has broad substrate specificity with manganese or cobalt as cofactor and can act on various RNA species. Binds to the U8 snoRNA; metal is not required for RNA-binding. May play a role in the regulation of snoRNAs and mRNAs degradation. Also acts as a phosphatase; hydrolyzes the non-canonical purine nucleotides inosine diphosphate (IDP) and deoxyinosine diphosphate (dITP) as well as guanosine diphosphate (GDP), deoxyguanosine diphosphate (dGDP), xanthine diphosphate (XDP), inosine triphosphate (ITP) and deoxyinosine triphosphate (ITP) to their respective monophosphate derivatives and does not distinguish between the deoxy- and ribose forms. The order of activity with different substrates is IDP > dIDP » GDP = dGDP > XDP = ITP = dITP. Binds strongly to GTP, ITP and XTP. Participates in the hydrolysis of dIDP/IDP and probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions. Exhibits decapping activity towards NAD-capped RNAs and FAD-capped RNAs. Exhibits decapping activity towards dpCoA-capped RNAs in vitro.

Subunit / interactions. Homodimer.

Subcellular location. Nucleus. Nucleoplasm. Nucleolus. Cytoplasm.

Tissue specificity. Expressed strongly in lung, kidney, adrenal gland, testis, heart and brain.

Activity regulation. The phosphatase activity is inhibited by the product IMP.

Cofactor. Binds 3 or 4 divalent metal cations. Acts specifically on U8 snoRNA with magnesium as cofactor. Has broad substrate specificity with bound manganese or cobalt (in vitro).

Similarity. Belongs to the Nudix hydrolase family. NUDT16 subfamily.

Isoforms (4)

UniProt ID	Names	Canonical?
Q96DE0-1	1	yes
Q96DE0-2	2
Q96DE0-3	3
Q96DE0-4	4

RefSeq proteins (3): NP_001165376, NP_001165377, NP_689608* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000086	NUDIX_hydrolase_dom	Domain
IPR015797	NUDIX_hydrolase-like_dom_sf	Homologous_superfamily
IPR054754	NudT16	Family

Pfam: PF22327

Enzyme classification (BRENDA):

• EC 3.6.1.62 — 5’-(N7-methylguanosine 5’-triphospho)-[mRNA] hydrolase (BRENDA: 21 organisms, 123 substrates, 18 inhibitors, 4 Km, 3 kcat entries)
• EC 3.6.1.64 — inosine diphosphate phosphatase (BRENDA: 2 organisms, 18 substrates, 6 inhibitors, 10 Km, 10 kcat entries)

Substrate kinetics (BRENDA)

12 substrates with measured Km, best-characterized 12. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
ITP	0.0082–22.1	2
XDP	0.0062–15.7	2
ADP	0.185	1
ITP	0.0082	1
M7G5’PPP5’-MRNA	0.0034	1
XDP	0.0062	1
ADP	0.285	1
DGDP	0.32	1
DIDP	0.088	1
DITP	24.1	1
GDP	0.33	1
IDP	0.062	1

Catalyzed reactions (Rhea), 6 shown:

• IDP + H2O = IMP + phosphate + H(+) (RHEA:35207)
• dIDP + H2O = dIMP + phosphate + H(+) (RHEA:35211)
• a 5’-end NAD(+)-phospho-ribonucleoside in mRNA + H2O = a 5’-end phospho-adenosine-phospho-ribonucleoside in mRNA + beta-nicotinamide D-ribonucleotide + 2 H(+) (RHEA:60876)
• 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)
• a 5’-end FAD-phospho-ribonucleoside in mRNA + H2O = a 5’-end phospho-adenosine-phospho-ribonucleoside in mRNA + FMN + 2 H(+) (RHEA:67588)
• a 5’-end CoA-ribonucleoside in mRNA + H2O = a 5’-end phospho-adenosine-phospho-ribonucleoside in mRNA + (R)-4’-phosphopantetheine + 2 H(+) (RHEA:67592)

UniProt features (40 total): binding site 11, strand 8, helix 8, splice variant 4, turn 4, sequence conflict 2, chain 1, domain 1, short sequence motif 1

Structure

Experimental structures (PDB)

11 structures.

PDB	Method	Resolution (Å)
2XSQ	X-RAY DIFFRACTION	1.72
3COU	X-RAY DIFFRACTION	1.8
3MGM	X-RAY DIFFRACTION	1.8
5W6X	X-RAY DIFFRACTION	2.1
5VY2	X-RAY DIFFRACTION	2.3
5WJI	X-RAY DIFFRACTION	2.3
6X7V	X-RAY DIFFRACTION	2.3
6CO2	X-RAY DIFFRACTION	2.49
5W6Z	X-RAY DIFFRACTION	2.61
6X7U	X-RAY DIFFRACTION	2.7
6B09	X-RAY DIFFRACTION	3.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96DE0-F1	92.61	0.87

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 (11): 80; 99; 170; 173; 24; 50; 57; 59; 76; 76; 80

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-2393930	Phosphate bond hydrolysis by NUDT proteins

MSigDB gene sets: 165 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, GSE45365_NK_CELL_VS_CD8_TCELL_UP, GSE45365_NK_CELL_VS_CD11B_DC_UP, GOBP_RIBOSOME_BIOGENESIS, GOMF_ENDONUCLEASE_ACTIVITY, GOMF_RNA_NUCLEASE_ACTIVITY, GOMF_METALLOPEPTIDASE_ACTIVITY, GOMF_NUCLEASE_ACTIVITY, GOBP_SNO_S_RNA_METABOLIC_PROCESS, GOZGIT_ESR1_TARGETS_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS

GO Biological Process (7): mRNA catabolic process (GO:0006402), sno(s)RNA catabolic process (GO:0016077), dITP catabolic process (GO:0035863), positive regulation of cell cycle process (GO:0090068), NAD-cap decapping (GO:0110155), negative regulation of rRNA processing (GO:2000233), nucleotide metabolic process (GO:0009117)

GO Molecular Function (20): nucleotide binding (GO:0000166), magnesium ion binding (GO:0000287), mRNA binding (GO:0003729), metalloexopeptidase activity (GO:0008235), manganese ion binding (GO:0030145), snoRNA binding (GO:0030515), chloride ion binding (GO:0031404), dITP diphosphatase activity (GO:0035870), identical protein binding (GO:0042802), protein homodimerization activity (GO:0042803), cobalt ion binding (GO:0050897), dIDP phosphatase activity (GO:0097383), RNA NAD-cap (NMN-forming) hydrolase activity (GO:0110153), 5’-(N(7)-methylguanosine 5’-triphospho)-[mRNA] hydrolase activity (GO:0140933), IDP phosphatase activity (GO:1990003), phosphodiesterase decapping endonuclease activity (GO:1990174), RNA binding (GO:0003723), hydrolase activity (GO:0016787), nucleoside diphosphate phosphatase activity (GO:0017110), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Purine catabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
pyrophosphatase activity	3
RNA catabolic process	2
negative regulation of gene expression	2
RNA binding	2
transition metal ion binding	2
nucleoside diphosphate phosphatase activity	2
nuclear lumen	2
cellular anatomical structure	2
mRNA metabolic process	1
sno(s)RNA metabolic process	1
purine deoxyribonucleotide catabolic process	1
deoxyribonucleoside triphosphate catabolic process	1
purine deoxyribonucleoside triphosphate catabolic process	1
regulation of cell cycle process	1
cell cycle process	1
positive regulation of cell cycle	1
RNA decapping	1
rRNA processing	1
negative regulation of RNA metabolic process	1
negative regulation of ribosome biogenesis	1
regulation of rRNA processing	1
nucleoside phosphate metabolic process	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
metal ion binding	1
metallopeptidase activity	1
exopeptidase activity	1
anion binding	1
nucleoside triphosphate diphosphatase activity	1
protein binding	1
identical protein binding	1
protein dimerization activity	1
catalytic activity, acting on RNA	1
RNA endonuclease activity producing 5’-phosphomonoesters, hydrolytic mechanism	1
nucleic acid binding	1
catalytic activity	1
cation binding	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

736 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NUDT16	DCP2	Q8IU60	706
NUDT16	ADPRS	Q9NX46	695
NUDT16	MACROD1	Q9BQ69	690
NUDT16	XRN1	Q8IZH2	679
NUDT16	NUDT12	Q9BQG2	661
NUDT16	NUDT3	O95989	661
NUDT16	PARG	Q86W56	612
NUDT16	MACROD2	A1Z1Q3	610
NUDT16	NUDT2	P50583	580
NUDT16	NUDT5	Q9UKK9	574
NUDT16	NUDT9	Q9BW91	572
NUDT16	ENPP1	P22413	549
NUDT16	OARD1	Q9Y530	544
NUDT16	DXO	O77932	542
NUDT16	NUDT17	P0C025	541

IntAct

14 interactions, top by confidence:

A	B	Type	Score
NUDT16	NUDT16	psi-mi:“MI:0407”(direct interaction)	0.560
IL1R2	EXOC5	psi-mi:“MI:0914”(association)	0.530
JUN		psi-mi:“MI:0914”(association)	0.350
IL1R2	QSOX1	psi-mi:“MI:0914”(association)	0.350
NUDT16L1	TP53BP1	psi-mi:“MI:0914”(association)	0.350
	DDX3X	psi-mi:“MI:0914”(association)	0.350
KCTD12	DUSP11	psi-mi:“MI:0914”(association)	0.350
NUDT16	MTIF2	psi-mi:“MI:0914”(association)	0.350
NUDT16	BCKDK	psi-mi:“MI:0914”(association)	0.350

BioGRID (27): NUDT16 (Affinity Capture-MS), NUDT16 (Affinity Capture-MS), NUDT16 (Affinity Capture-MS), NUDT16 (Affinity Capture-MS), NUDT16 (Affinity Capture-MS), NUDT16 (Affinity Capture-MS), NUDT16 (Affinity Capture-MS), NUDT16 (Affinity Capture-MS), NUDT16 (Affinity Capture-MS), PARP1 (Biochemical Activity), TP53BP1 (Biochemical Activity), NUDT16L1 (Affinity Capture-Western), NUDT16 (Affinity Capture-Western), NUDT16 (Affinity Capture-MS), ATP12A (Affinity Capture-MS)

ESM2 similar proteins: A0A1D5PJB7, A1A4Q9, A5YM72, A6NLP5, D3KCC4, I3L5V6, O43292, P10938, Q00973, Q05B52, Q09200, Q10468, Q14623, Q148G5, Q16586, Q2V8X7, Q3SZV0, Q561R2, Q5E9M9, Q5M868, Q5ZL13, Q66H45, Q69ZF3, Q6P3D0, Q6P7A1, Q6P9Z4, Q6SZW1, Q6TEC1, Q6ZPS2, Q7TMC8, Q864R5, Q86TX2, Q8IXI1, Q8N0W3, Q8N3Y3, Q8N6R0, Q8NF37, Q8NI29, Q8TCD5, Q8VBW8

Diamond homologs: A1A4Q9, P0DKY8, Q2V8X7, Q6P3D0, Q6TEC1, Q8VHN8, Q96DE0, Q9BRJ7, Q9IAY5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	36
Likely benign	5
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

267 predictions. Top by Δscore:

Variant	Effect	Δscore
3:131381939:ACTGG:A	donor_loss	1.0000
3:131381941:TGGTG:T	donor_loss	1.0000
3:131381942:GGT:G	donor_loss	1.0000
3:131381943:G:A	donor_loss	1.0000
3:131381944:T:G	donor_loss	1.0000
3:131382301:G:GT	donor_gain	1.0000
3:131382311:TGGAG:T	donor_loss	1.0000
3:131382312:GGAGG:G	donor_loss	1.0000
3:131382313:G:GT	donor_gain	1.0000
3:131382313:GAGGT:G	donor_loss	1.0000
3:131382314:AG:A	donor_loss	1.0000
3:131382315:GGTGG:G	donor_loss	1.0000
3:131382317:T:G	donor_loss	1.0000
3:131383282:G:GT	donor_gain	1.0000
3:131383316:GCCT:G	donor_gain	1.0000
3:131383374:A:G	donor_gain	1.0000
3:131381943:G:GG	donor_gain	0.9900
3:131382043:CA:C	acceptor_loss	0.9900
3:131382045:GATGC:G	acceptor_gain	0.9900
3:131383264:T:G	donor_gain	0.9900
3:131383344:G:GT	donor_gain	0.9900
3:131383369:C:G	donor_gain	0.9900
3:131383379:GACC:G	donor_gain	0.9900
3:131381945:GA:G	donor_loss	0.9800
3:131381951:G:GT	donor_gain	0.9800
3:131382044:A:AG	acceptor_gain	0.9800
3:131382045:G:GT	acceptor_gain	0.9800
3:131382045:GA:G	acceptor_gain	0.9800
3:131382045:GAT:G	acceptor_gain	0.9800
3:131383315:GGCCT:G	donor_gain	0.9800

AlphaMissense

1223 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:131382058:T:C	F51L	0.994
3:131382060:C:A	F51L	0.994
3:131382060:C:G	F51L	0.994
3:131382076:T:C	F57L	0.992
3:131382078:C:A	F57L	0.992
3:131382078:C:G	F57L	0.992
3:131383240:T:C	F163L	0.987
3:131383242:T:A	F163L	0.987
3:131383242:T:G	F163L	0.987
3:131382077:T:C	F57S	0.985
3:131383225:T:C	F158L	0.979
3:131383227:C:A	F158L	0.979
3:131383227:C:G	F158L	0.979
3:131381938:T:A	I45K	0.978
3:131382131:G:C	R75P	0.977
3:131381910:T:C	F36L	0.974
3:131381912:C:A	F36L	0.974
3:131381912:C:G	F36L	0.974
3:131382234:C:A	H109Q	0.974
3:131382234:C:G	H109Q	0.974
3:131382065:G:T	G53V	0.973
3:131382062:A:T	D52V	0.972
3:131382065:G:A	G53E	0.972
3:131383241:T:C	F163S	0.971
3:131382246:G:C	K113N	0.970
3:131382246:G:T	K113N	0.970
3:131382063:T:A	D52E	0.969
3:131382063:T:G	D52E	0.969
3:131382137:T:C	L77P	0.968
3:131381873:C:G	C23W	0.965

dbSNP variants (sampled 300 via entrez): RS1000018026 (3:131380083 T>C), RS1000149039 (3:131386589 T>C,G), RS1000260423 (3:131381777 C>G,T), RS1000317911 (3:131382069 C>T), RS1000514650 (3:131384415 G>A), RS1000662443 (3:131379901 C>A,G,T), RS1001126402 (3:131387070 G>C), RS1001150608 (3:131388010 A>G), RS1001180239 (3:131387826 A>G,T), RS1001263758 (3:131381072 C>G), RS1002496136 (3:131381287 G>A), RS1002766883 (3:131381341 C>A,G), RS1003343387 (3:131382776 T>A,C), RS1003357858 (3:131382746 C>G,T), RS1003451536 (3:131384345 T>C)

Disease associations

OMIM: gene MIM:617381 | 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

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression, affects cotreatment	3
Cyclosporine	decreases expression	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
sodium arsenate	increases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
tetrabromobisphenol A	increases expression	1
hydroquinone	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	decreases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
bisphenol AF	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	decreases expression	1
Vehicle Emissions	affects expression, increases abundance	1
Benzo(a)pyrene	decreases expression	1
Coumestrol	affects cotreatment, decreases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Methotrexate	decreases expression	1
Smoke	decreases expression	1
Tetrachlorodibenzodioxin	decreases expression	1
Thiram	decreases expression	1
Tretinoin	increases expression	1

Cellosaurus cell lines

7 cell lines: 7 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_E2EQ	HAP1 NUDT16 (-) 3	Cancer cell line	Male
CVCL_E2ER	HAP1 NUDT16 (-) 4	Cancer cell line	Male
CVCL_E2ES	HAP1 NUDT16 (-) 5	Cancer cell line	Male
CVCL_E2ET	HAP1 NUDT16 (-) 6	Cancer cell line	Male
CVCL_E2EU	HAP1 NUDT16 (-) 7	Cancer cell line	Male
CVCL_TB34	HAP1 NUDT16 (-) 1	Cancer cell line	Male
CVCL_TB35	HAP1 NUDT16 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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