NUDT13

Summary

NUDT13 (nudix hydrolase 13, HGNC:18827) is a protein-coding gene on chromosome 10q22.2, encoding NAD(P)H pyrophosphatase NUDT13, mitochondrial (Q86X67). NAD(P)H pyrophosphatase that hydrolyzes NADH into NMNH and AMP, and NADPH into NMNH and 2’,5’-ADP.

Predicted to enable NADH pyrophosphatase activity. Predicted to be involved in NADH metabolic process and NADP catabolic process. Located in mitochondrion.

Source: NCBI Gene 25961 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 61 total
• Dosage sensitivity (ClinGen): haploinsufficiency dosage sensitivity unlikely, triplosensitivity no evidence
• MANE Select transcript: NM_015901

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18827
Approved symbol	NUDT13
Name	nudix hydrolase 13
Location	10q22.2
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp586P2219
Ensembl gene	ENSG00000166321
Ensembl biotype	protein_coding
OMIM	609233
Entrez	25961

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 7 protein_coding, 2 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000349051, ENST00000357321, ENST00000372997, ENST00000469925, ENST00000488223, ENST00000537969, ENST00000544879, ENST00000617744, ENST00000850962, ENST00000898515, ENST00000972079

RefSeq mRNA: 6 — MANE Select: NM_015901 NM_001283014, NM_001283015, NM_001283016, NM_001283017, NM_001283019, NM_015901

CCDS: CCDS31220, CCDS60551, CCDS60552

Canonical transcript exons

ENST00000357321 — 9 exons

Exon	Start	End
ENSE00003587729	73120018	73120157
ENSE00003591011	73125118	73125243
ENSE00003614272	73124214	73124320
ENSE00003620015	73122175	73122309
ENSE00003687878	73114357	73114448
ENSE00003753438	73125398	73125509
ENSE00003842617	73130703	73131823
ENSE00003843407	73110455	73110567
ENSE00004283007	73126673	73126827

Expression profiles

Bgee: expression breadth ubiquitous, 192 present calls, max score 85.43.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.8097 / max 32.8607, expressed in 1390 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
105521	2.4727	1308
105520	0.3369	164

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.43	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.09	gold quality
right lobe of liver	UBERON:0001114	80.58	gold quality
apex of heart	UBERON:0002098	80.03	gold quality
mucosa of transverse colon	UBERON:0004991	78.85	gold quality
gastrocnemius	UBERON:0001388	78.63	gold quality
muscle of leg	UBERON:0001383	78.29	gold quality
hindlimb stylopod muscle	UBERON:0004252	77.07	gold quality
body of pancreas	UBERON:0001150	75.98	gold quality
left adrenal gland cortex	UBERON:0035825	75.83	gold quality
monocyte	CL:0000576	75.77	gold quality
granulocyte	CL:0000094	75.59	gold quality
metanephros cortex	UBERON:0010533	75.55	gold quality
mononuclear cell	CL:0000842	75.53	gold quality
left adrenal gland	UBERON:0001234	75.49	gold quality
heart left ventricle	UBERON:0002084	75.46	gold quality
right adrenal gland	UBERON:0001233	75.40	gold quality
leukocyte	CL:0000738	75.18	gold quality
right adrenal gland cortex	UBERON:0035827	75.17	gold quality
transverse colon	UBERON:0001157	75.10	gold quality
lower esophagus mucosa	UBERON:0035834	74.91	gold quality
adrenal tissue	UBERON:0018303	74.84	gold quality
body of stomach	UBERON:0001161	74.77	gold quality
cardiac ventricle	UBERON:0002082	74.69	gold quality
right uterine tube	UBERON:0001302	74.39	gold quality
muscle layer of sigmoid colon	UBERON:0035805	73.90	gold quality
small intestine Peyer’s patch	UBERON:0003454	73.59	gold quality
right atrium auricular region	UBERON:0006631	73.59	gold quality
right ovary	UBERON:0002118	73.43	gold quality
skin of leg	UBERON:0001511	73.41	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

48 targeting NUDT13, 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-1184	99.99	68.19	1458
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-8084	99.73	69.57	1760
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-548AU-3P	99.70	68.22	1373
HSA-MIR-452-5P	99.65	69.63	1762
HSA-MIR-6516-3P	99.65	68.57	1238
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-486-5P	99.51	70.39	707
HSA-MIR-5009-3P	99.45	69.43	1341
HSA-MIR-542-3P	99.34	67.58	1270
HSA-MIR-1206	99.30	69.32	1016
HSA-MIR-29A-5P	99.08	68.59	1813
HSA-MIR-3164	99.02	68.39	1071
HSA-MIR-6820-3P	99.02	68.50	1035
HSA-MIR-6737-3P	98.95	68.56	1577
HSA-MIR-7157-3P	98.95	68.70	1582
HSA-MIR-1245B-5P	98.88	66.55	576

Functional genomics

ClinGen dosage: haploinsufficiency 40 (dosage sensitivity unlikely), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	nudt13	ENSDARG00000057417
mus_musculus	Nudt13	ENSMUSG00000021809
rattus_norvegicus	Nudt13	ENSRNOG00000048195

Protein

Protein identifiers

NAD(P)H pyrophosphatase NUDT13, mitochondrial — Q86X67 (reviewed: Q86X67)

Alternative names: Nucleoside diphosphate-linked moiety X motif 13, Protein KiSS-16

All UniProt accessions (3): A0A087X1G4, B4E059, Q86X67

UniProt curated annotations — full annotation on UniProt →

Function. NAD(P)H pyrophosphatase that hydrolyzes NADH into NMNH and AMP, and NADPH into NMNH and 2’,5’-ADP. Has a marked preference for the reduced pyridine nucleotides. Does not show activity toward NAD-capped RNAs; the NAD-cap is an atypical cap present at the 5’-end of some RNAs.

Subcellular location. Mitochondrion.

Tissue specificity. Highly expressed in metastasis-suppressed chromosome 6 melanoma hybrids.

Cofactor. Divalent metal cations. Mg(2+) or Mn(2+).

Similarity. Belongs to the Nudix hydrolase family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q86X67-1	1	yes
Q86X67-2	2
Q86X67-3	3
Q86X67-4	4

RefSeq proteins (6): NP_001269943, NP_001269944, NP_001269945, NP_001269946, NP_001269948, NP_056985* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000086	NUDIX_hydrolase_dom	Domain
IPR015375	NADH_PPase-like_N	Domain
IPR015376	Znr_NADH_PPase	Domain
IPR015797	NUDIX_hydrolase-like_dom_sf	Homologous_superfamily
IPR020084	NUDIX_hydrolase_CS	Conserved_site
IPR049734	NudC-like_C	Domain

Pfam: PF00293, PF09296, PF09297

Catalyzed reactions (Rhea), 3 shown:

• NAD(+) + H2O = beta-nicotinamide D-ribonucleotide + AMP + 2 H(+) (RHEA:11800)
• NADH + H2O = reduced beta-nicotinamide D-ribonucleotide + AMP + 2 H(+) (RHEA:48868)
• NADPH + H2O = reduced beta-nicotinamide D-ribonucleotide + adenosine 2’,5’-bisphosphate + 2 H(+) (RHEA:60820)

UniProt features (10 total): splice variant 4, sequence variant 2, transit peptide 1, chain 1, domain 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86X67-F1	88.46	0.75

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-499943	Interconversion of nucleotide di- and triphosphates

MSigDB gene sets: 139 (showing top): CAR_TNFRSF25, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, AACYNNNNTTCCS_UNKNOWN, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_INTERCONVERSION, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, TCCCRNNRTGC_UNKNOWN, GOCC_MITOCHONDRIAL_MATRIX, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, MORF_CCNF, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, MORF_RFC5, MORF_EIF4E, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3

GO Biological Process (2): nucleobase-containing small molecule interconversion (GO:0015949), nucleobase-containing small molecule metabolic process (GO:0055086)

GO Molecular Function (6): NAD+ diphosphatase activity (GO:0000210), NADPH pyrophosphatase activity (GO:0010943), pyrophosphatase activity (GO:0016462), NADH pyrophosphatase activity (GO:0035529), metal ion binding (GO:0046872), hydrolase activity (GO:0016787)

GO Cellular Component (2): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Metabolism of nucleotides	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
dinucleotide phosphatase activity	3
nucleobase-containing small molecule metabolic process	1
nucleobase-containing compound metabolic process	1
small molecule metabolic process	1
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	1
cation binding	1
catalytic activity	1
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrion	1
intracellular organelle lumen	1

Protein interactions and networks

STRING

702 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NUDT13	NUDT7	P0C024	611
NUDT13	NUDT1	P36639	587
NUDT13	NUDT8	Q8WV74	579
NUDT13	NUDT2	P50583	572
NUDT13	NUDT15	Q9NV35	566
NUDT13	RSPRY1	Q96DX4	557
NUDT13	NUDT5	Q9UKK9	541
NUDT13	CCDC106	Q9BWC9	540
NUDT13	NUDT19	A8MXV4	504
NUDT13	ZC3H15	Q8WU90	497
NUDT13	FIZ1	Q96SL8	494
NUDT13	DTWD2	Q8NBA8	492
NUDT13	MRPS34	P82930	472
NUDT13	RCBTB1	Q8NDN9	470
NUDT13	TPRA1	Q86W33	464

IntAct

3 interactions, top by confidence:

A	B	Type	Score
NUDT13	ICAM1	psi-mi:“MI:0914”(association)	0.350
NUDT13	PLPBP	psi-mi:“MI:0914”(association)	0.350

BioGRID (21): IVD (Affinity Capture-MS), NUDT13 (Co-fractionation), PDCD6 (Co-fractionation), ICAM1 (Affinity Capture-MS), NUDT13 (Synthetic Lethality), NUDT13 (Affinity Capture-MS), IVD (Affinity Capture-MS), ICAM1 (Affinity Capture-MS), RPL36AL (Affinity Capture-MS), PROSC (Affinity Capture-MS), HARS2 (Affinity Capture-MS), MRRF (Affinity Capture-MS), OXSM (Affinity Capture-MS), SPRYD4 (Affinity Capture-MS), MCCC1 (Affinity Capture-MS)

ESM2 similar proteins: A5DLC6, A8X493, B0WSW8, B0WSX1, B0X4N1, B3MF31, B3MZN7, B3NP10, B3NY19, B4GA28, B4H0S8, B4JXP7, B4KSL6, B4L340, B4MNL1, B4N1V2, B4P925, B4PYH5, B5DZN7, F4IE66, G5EDZ2, M1W859, O14353, P41888, P56523, P78963, Q03319, Q16GH0, Q16P87, Q16P90, Q21657, Q29GM0, Q5R864, Q5XI69, Q655R6, Q6PE54, Q756G8, Q7QFL7, Q86X67, Q8IU29

Diamond homologs: A1AIG7, A1JIJ0, A4TS22, A4VLQ5, A4W5B9, A5F3M9, A5UA57, A5UGU3, A5W1F2, A6TGQ3, A6V6Z8, A6VQT1, A7FNH4, A7MJ81, A7ZUL1, A8A796, A8AKS7, A9N0K8, A9R8D3, B0KMR5, B1IUQ1, B1J6H6, B1JJK8, B1LNU8, B1XBZ9, B2K122, B2TWI3, B2VG76, B4T0Z8, B4TCT5, B4TQK6, B5BJR5, B5F1H9, B5FQL1, B5QYF1, B5RFI8, B5XYE2, B5Z092, B6I5K7, B7LA85

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1960 predictions. Top by Δscore:

Variant	Effect	Δscore
10:73110568:G:GG	donor_gain	1.0000
10:73122258:G:GT	donor_gain	1.0000
10:73122307:GTG:G	donor_gain	1.0000
10:73110566:GA:G	donor_gain	0.9900
10:73114355:A:G	acceptor_gain	0.9900
10:73118469:TAGGG:T	acceptor_gain	0.9900
10:73120013:TACA:T	acceptor_loss	0.9900
10:73120015:CA:C	acceptor_loss	0.9900
10:73120016:A:AC	acceptor_loss	0.9900
10:73120016:A:AG	acceptor_gain	0.9900
10:73120017:G:GG	acceptor_gain	0.9900
10:73120017:GGT:G	acceptor_gain	0.9900
10:73120017:GGTAT:G	acceptor_gain	0.9900
10:73120153:GTTAG:G	donor_gain	0.9900
10:73120154:TTAGG:T	donor_loss	0.9900
10:73120155:TAGGT:T	donor_loss	0.9900
10:73120156:AGGT:A	donor_loss	0.9900
10:73120157:GGTA:G	donor_loss	0.9900
10:73120158:G:GG	donor_gain	0.9900
10:73120158:GTA:G	donor_loss	0.9900
10:73120159:T:G	donor_loss	0.9900
10:73121403:GCAC:G	donor_gain	0.9900
10:73121404:C:T	donor_gain	0.9900
10:73122173:A:AG	acceptor_gain	0.9900
10:73122174:G:GG	acceptor_gain	0.9900
10:73122174:GA:G	acceptor_gain	0.9900
10:73122276:GATC:G	donor_gain	0.9900
10:73122303:A:AG	donor_gain	0.9900
10:73122303:A:G	donor_gain	0.9900
10:73125204:GC:G	donor_gain	0.9900

AlphaMissense

2288 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:73125497:T:C	F231L	0.994
10:73125499:T:A	F231L	0.994
10:73125499:T:G	F231L	0.994
10:73130739:T:A	W299R	0.990
10:73130739:T:C	W299R	0.990
10:73126700:G:C	R244P	0.988
10:73125136:T:A	W162R	0.986
10:73125136:T:C	W162R	0.986
10:73125206:G:C	R185P	0.985
10:73122267:T:C	F106L	0.976
10:73122269:T:A	F106L	0.976
10:73122269:T:G	F106L	0.976
10:73125440:T:C	C212R	0.974
10:73130741:G:C	W299C	0.973
10:73130741:G:T	W299C	0.973
10:73125453:G:C	R216P	0.972
10:73125138:G:C	W162C	0.971
10:73125138:G:T	W162C	0.971
10:73125154:T:C	F168L	0.968
10:73125156:C:A	F168L	0.968
10:73125156:C:G	F168L	0.968
10:73125423:T:A	V206E	0.966
10:73125447:T:A	L214H	0.966
10:73130865:T:A	W341R	0.965
10:73130865:T:C	W341R	0.965
10:73125444:T:C	L213P	0.964
10:73126708:G:C	A247P	0.963
10:73126762:T:A	W265R	0.959
10:73126762:T:C	W265R	0.959
10:73125420:T:C	L205P	0.958

dbSNP variants (sampled 300 via entrez): RS1000134771 (10:73110118 G>A), RS1000240189 (10:73116308 C>T), RS1000244191 (10:73126478 C>A), RS1000383926 (10:73130717 G>A,C), RS1000384922 (10:73111286 G>C,T), RS1000417542 (10:73111055 C>G), RS1000742864 (10:73109774 C>T), RS1000842343 (10:73118228 T>TA), RS1000851674 (10:73125656 T>TAC), RS1001014552 (10:73111143 CT>C,CTT), RS1001026622 (10:73124819 T>C), RS1001133403 (10:73131813 A>C,G), RS1001463932 (10:73130143 T>C), RS1001575139 (10:73131235 G>A,T), RS1001651448 (10:73110655 G>A)

Disease associations

OMIM: gene MIM:609233 | 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
GCST006414_1	Atrial fibrillation	9.000000e-35
GCST008891_12	Cognitive performance (processing speed)	8.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004363	information processing speed

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases methylation, decreases expression	2
Tobacco Smoke Pollution	decreases expression, increases methylation	2
Cyclosporine	decreases expression	2
Aflatoxin B1	decreases expression, increases expression	2
lasiocarpine	increases expression	1
chlortoluron	decreases expression	1
trichostatin A	increases expression	1
cobaltous chloride	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Gold	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Plant Extracts	increases expression, affects cotreatment	1
Thiram	decreases expression	1
Tretinoin	affects expression	1
Tunicamycin	increases expression	1
Urethane	decreases expression	1
Okadaic Acid	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D1I4	HAP1 NUDT13 (-) 1	Cancer cell line	Male
CVCL_D1I5	HAP1 NUDT13 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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