OXNAD1

Summary

OXNAD1 (oxidoreductase NAD binding domain containing 1, HGNC:25128) is a protein-coding gene on chromosome 3p25.1-p24.3, encoding Oxidoreductase NAD-binding domain-containing protein 1 (Q96HP4).

Predicted to enable oxidoreductase activity. Located in mitochondrion.

Source: NCBI Gene 92106 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 92 total
• MANE Select transcript: NM_138381

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25128
Approved symbol	OXNAD1
Name	oxidoreductase NAD binding domain containing 1
Location	3p25.1-p24.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC15763
Ensembl gene	ENSG00000154814
Ensembl biotype	protein_coding
OMIM	620581
Entrez	92106

Gene structure

Transcript identifiers

Ensembl transcripts: 39 — 35 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000285083, ENST00000435829, ENST00000442255, ENST00000452581, ENST00000486267, ENST00000605932, ENST00000606098, ENST00000607329, ENST00000627468, ENST00000857165, ENST00000857166, ENST00000857167, ENST00000857168, ENST00000857169, ENST00000857170, ENST00000857171, ENST00000857172, ENST00000857173, ENST00000857174, ENST00000857175, ENST00000857176, ENST00000857177, ENST00000857178, ENST00000857179, ENST00000857180, ENST00000857181, ENST00000857182, ENST00000926134, ENST00000926135, ENST00000926136, ENST00000926137, ENST00000926138, ENST00000926139, ENST00000953381, ENST00000953382, ENST00000953383, ENST00000953384, ENST00000953385, ENST00000953386

RefSeq mRNA: 9 — MANE Select: NM_138381 NM_001330670, NM_001330671, NM_001352977, NM_001352978, NM_001352980, NM_001352981, NM_001352982, NM_001352983, NM_138381

CCDS: CCDS2630, CCDS87053

Canonical transcript exons

ENST00000285083 — 9 exons

Exon	Start	End
ENSE00001017934	16271659	16271722
ENSE00001129739	16270945	16271071
ENSE00001213283	16303408	16306087
ENSE00001864028	16265212	16265505
ENSE00003468662	16294856	16294997
ENSE00003584882	16301626	16301868
ENSE00003691738	16286342	16286448
ENSE00003692062	16302640	16302748
ENSE00003697424	16269126	16269275

Expression profiles

Bgee: expression breadth ubiquitous, 220 present calls, max score 88.45.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.7897 / max 1666.8024, expressed in 1793 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
35553	15.6854	1787
35557	6.1542	154
35559	0.8353	93
35555	0.6944	79
35556	0.5426	79
35558	0.5200	78
35560	0.2308	55
35554	0.1269	39

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ventricle myocardium	UBERON:0006566	88.45	silver quality
ileal mucosa	UBERON:0000331	88.39	silver quality
kidney epithelium	UBERON:0004819	87.81	silver quality
calcaneal tendon	UBERON:0003701	86.89	gold quality
lymph node	UBERON:0000029	86.58	gold quality
medial globus pallidus	UBERON:0002477	86.10	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.70	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.56	gold quality
duodenum	UBERON:0002114	84.91	gold quality
tendon	UBERON:0000043	84.57	gold quality
vermiform appendix	UBERON:0001154	84.24	gold quality
liver	UBERON:0002107	84.24	gold quality
epithelial cell of pancreas	CL:0000083	83.96	silver quality
right lobe of liver	UBERON:0001114	83.93	gold quality
jejunal mucosa	UBERON:0000399	83.91	gold quality
mucosa of transverse colon	UBERON:0004991	83.80	gold quality
blood	UBERON:0000178	83.65	gold quality
thymus	UBERON:0002370	83.64	gold quality
granulocyte	CL:0000094	83.46	gold quality
sperm	CL:0000019	82.99	silver quality
globus pallidus	UBERON:0001875	82.81	gold quality
hindlimb stylopod muscle	UBERON:0004252	82.69	gold quality
bone marrow cell	CL:0002092	82.51	gold quality
tonsil	UBERON:0002372	82.26	gold quality
muscle tissue	UBERON:0002385	82.25	gold quality
small intestine	UBERON:0002108	82.20	gold quality
skeletal muscle tissue	UBERON:0001134	82.11	gold quality
small intestine Peyer’s patch	UBERON:0003454	81.99	gold quality
rectum	UBERON:0001052	81.97	gold quality
skeletal muscle organ	UBERON:0014892	81.71	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.84
E-CURD-112	yes	7.60

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CREB1, NCOR1

miRNA regulators (miRDB)

78 targeting OXNAD1, 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-4673	100.00	66.64	1490
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-5682	99.89	72.56	1005
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-202-5P	99.78	67.65	991
HSA-MIR-3714	99.71	70.74	2671
HSA-MIR-561-3P	99.64	70.90	3647

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	oxnad1	ENSDARG00000062664
mus_musculus	Oxnad1	ENSMUSG00000021906
rattus_norvegicus	Oxnad1	ENSRNOG00000019760

Paralogs (5): CYB5R4 (ENSG00000065615), CYB5R3 (ENSG00000100243), CYB5R1 (ENSG00000159348), CYB5R2 (ENSG00000166394), CYB5RL (ENSG00000215883)

Protein

Protein identifiers

Oxidoreductase NAD-binding domain-containing protein 1 — Q96HP4 (reviewed: Q96HP4)

All UniProt accessions (5): Q96HP4, C9JLB7, F8WB50, F8WBF3, U3KQU8

RefSeq proteins (9): NP_001317599, NP_001317600, NP_001339906, NP_001339907, NP_001339909, NP_001339910, NP_001339911, NP_001339912, NP_612390* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001433	OxRdtase_FAD/NAD-bd	Domain
IPR017927	FAD-bd_FR_type	Domain
IPR017938	Riboflavin_synthase-like_b-brl	Homologous_superfamily
IPR039261	FNR_nucleotide-bd	Homologous_superfamily
IPR052128	Oxidoreductase_NAD-binding	Family

Pfam: PF00175

UniProt features (7 total): sequence variant 3, signal peptide 1, chain 1, domain 1, binding site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96HP4-F1	87.62	0.80

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 (1): 178–183

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 126 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, CREBP1_Q2, CREB_Q4, WEI_MYCN_TARGETS_WITH_E_BOX, CDP_01, WCTCNATGGY_UNKNOWN, E4F1_Q6, DOUGLAS_BMI1_TARGETS_DN, CREB_Q3, FISCHER_DREAM_TARGETS, NOUZOVA_TRETINOIN_AND_H4_ACETYLATION, CREB_Q2, LEE_BMP2_TARGETS_DN, DELACROIX_RARG_BOUND_MEF, DELACROIX_RAR_BOUND_ES

GO Biological Process (0):

GO Molecular Function (2): oxidoreductase activity (GO:0016491), protein binding (GO:0005515)

GO Cellular Component (1): mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
catalytic activity	1
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1154 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OXNAD1	CAPN7	Q9Y6W3	891
OXNAD1	XIRP1	Q702N8	884
OXNAD1	DPH3	Q96FX2	719
OXNAD1	CAV3	P56539	647
OXNAD1	ZNF641	Q96N77	560
OXNAD1	ZSWIM2	Q8NEG5	534
OXNAD1	PLEKHG1	Q9ULL1	472
OXNAD1	RFTN1	Q14699	451
OXNAD1	FAXC	Q5TGI0	447
OXNAD1	BCAS3	Q9H6U6	443
OXNAD1	FREM3	P0C091	434
OXNAD1	GALNT15	Q8N3T1	415
OXNAD1	RHOG	P35238	401
OXNAD1	RPS6KL1	Q9Y6S9	400
OXNAD1	LTBP2	Q14767	398

IntAct

22 interactions, top by confidence:

A	B	Type	Score
IFT20	OXNAD1	psi-mi:“MI:0915”(physical association)	0.560
OXNAD1	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
OXNAD1	CAPNS2	psi-mi:“MI:0915”(physical association)	0.560
FSD2	OXNAD1	psi-mi:“MI:0915”(physical association)	0.560
OXNAD1	HSPD1	psi-mi:“MI:0914”(association)	0.530
YBEY	NUDT19	psi-mi:“MI:0914”(association)	0.350
MRPL12		psi-mi:“MI:0914”(association)	0.350
OXNAD1	DENR	psi-mi:“MI:0914”(association)	0.350
FEM1A	RNF113A	psi-mi:“MI:0914”(association)	0.350
LINC01565	NDUFS6	psi-mi:“MI:0914”(association)	0.350
FEM1A	DHRS3	psi-mi:“MI:0914”(association)	0.350
OXNAD1	FSD2	psi-mi:“MI:0915”(physical association)	0.000
OXNAD1	FKBP7	psi-mi:“MI:0915”(physical association)	0.000
OXNAD1	CAPNS2	psi-mi:“MI:0915”(physical association)	0.000
OXNAD1	IFT20	psi-mi:“MI:0915”(physical association)	0.000
fabV	OXNAD1	psi-mi:“MI:0915”(physical association)	0.000
hmsH	OXNAD1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (25): HSPD1 (Affinity Capture-MS), SRR (Affinity Capture-MS), DENR (Affinity Capture-MS), PROSC (Affinity Capture-MS), OXNAD1 (Affinity Capture-MS), OXNAD1 (Affinity Capture-MS), PROSC (Affinity Capture-MS), HSPD1 (Affinity Capture-MS), SRR (Affinity Capture-MS), MMAB (Affinity Capture-MS), DENR (Affinity Capture-MS), OXNAD1 (Two-hybrid), OXNAD1 (Two-hybrid), FSD2 (Two-hybrid), CAPNS2 (Two-hybrid)

ESM2 similar proteins: A2AV36, A3KP77, A4IHY0, A8E7D2, B1AS42, D3ZG52, P00387, P17571, P20070, P32232, P35520, Q05B89, Q07G10, Q0CT94, Q13057, Q2UM43, Q3UZW7, Q4V7D6, Q4WN24, Q502I6, Q58DM7, Q58E95, Q58H57, Q5B5L3, Q5EB81, Q5R4D2, Q5RCH4, Q5U378, Q60HG4, Q6ING7, Q6IPT4, Q6JQN1, Q6ZQJ5, Q7T0L7, Q7T0X7, Q7T291, Q7ZW24, Q8AWD2, Q8K4Z3, Q8VE38

Diamond homologs: A3KP77, A4IHY0, Q58DM7, Q5R4D2, Q7T0X7, Q8VE38, Q96HP4, Q3KTM0, Q8U2E4, P20070, Q6FUX5, A0A0H2ZJB2, C6LR75, E1F8H4, E1F8Q4, E2RTZ4, O66586, P04252, P07771, P24232, P26353, P39662, P39676, P40609, P49852, P68641, Q03331, Q1QYU6, Q45692, Q47266, Q54D73, Q57LF5, Q59MV9, Q5PIH6, Q6D245, Q6HLA6, Q6LM37, Q73B49, Q7ABK6, Q7C0F9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	78
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2541 predictions. Top by Δscore:

Variant	Effect	Δscore
3:16265254:C:G	donor_gain	1.0000
3:16269273:AAGG:A	donor_loss	1.0000
3:16269276:G:C	donor_loss	1.0000
3:16271926:A:AG	acceptor_gain	1.0000
3:16271928:ACTT:A	acceptor_gain	1.0000
3:16271931:T:TA	acceptor_gain	1.0000
3:16286341:GATT:G	acceptor_gain	1.0000
3:16286446:GTG:G	donor_gain	1.0000
3:16286449:G:GG	donor_gain	1.0000
3:16299020:GA:G	donor_gain	1.0000
3:16301625:GT:G	acceptor_gain	1.0000
3:16317233:C:CC	acceptor_gain	1.0000
3:16265270:A:T	donor_gain	0.9900
3:16269120:TTGCA:T	acceptor_loss	0.9900
3:16269121:TGCAG:T	acceptor_loss	0.9900
3:16269122:GCAGG:G	acceptor_loss	0.9900
3:16269123:CAG:C	acceptor_loss	0.9900
3:16269124:A:AG	acceptor_gain	0.9900
3:16269125:G:GA	acceptor_loss	0.9900
3:16269125:G:GG	acceptor_gain	0.9900
3:16269276:G:GG	donor_gain	0.9900
3:16271658:GC:G	acceptor_gain	0.9900
3:16271658:GCATA:G	acceptor_gain	0.9900
3:16271927:AACTT:A	acceptor_gain	0.9900
3:16271928:A:AG	acceptor_gain	0.9900
3:16271932:G:A	acceptor_gain	0.9900
3:16286340:A:AG	acceptor_gain	0.9900
3:16286341:G:GG	acceptor_gain	0.9900
3:16286445:AGTGG:A	donor_loss	0.9900
3:16286447:TGG:T	donor_loss	0.9900

AlphaMissense

2039 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:16286447:T:A	W97R	0.996
3:16286447:T:C	W97R	0.996
3:16294896:T:C	F111L	0.996
3:16294898:T:A	F111L	0.996
3:16294898:T:G	F111L	0.996
3:16303554:T:A	W311R	0.995
3:16303554:T:C	W311R	0.995
3:16301720:C:A	A176E	0.994
3:16303474:G:A	G284D	0.994
3:16294948:T:C	L128S	0.993
3:16303471:G:A	C283Y	0.993
3:16303556:G:C	W311C	0.993
3:16303556:G:T	W311C	0.993
3:16294897:T:C	F111S	0.992
3:16303472:T:G	C283W	0.992
3:16286442:G:A	G95D	0.991
3:16294858:T:A	V98D	0.991
3:16286432:T:C	F92L	0.990
3:16286434:T:A	F92L	0.990
3:16286434:T:G	F92L	0.990
3:16301732:G:A	G180E	0.990
3:16303470:T:C	C283R	0.990
3:16303557:T:A	W312R	0.990
3:16303557:T:C	W312R	0.990
3:16294903:T:A	I113K	0.989
3:16294954:T:A	V130E	0.989
3:16301836:A:C	S215R	0.989
3:16301838:T:A	S215R	0.989
3:16301838:T:G	S215R	0.989
3:16286442:G:T	G95V	0.988

dbSNP variants (sampled 300 via entrez): RS1000039465 (3:16348614 C>A,T), RS1000040207 (3:16308515 T>A,G), RS1000042990 (3:16339118 G>A), RS1000053416 (3:16307466 A>G), RS1000115835 (3:16338875 C>T), RS1000151271 (3:16265024 C>T), RS1000155944 (3:16308759 T>C), RS1000169541 (3:16312880 G>C), RS1000181364 (3:16309929 T>C), RS1000250047 (3:16302541 C>A,T), RS1000266985 (3:16330329 A>T), RS1000290002 (3:16295978 C>T), RS1000418511 (3:16264897 G>A), RS1000446373 (3:16264396 A>G), RS1000571403 (3:16331788 A>C)

Disease associations

OMIM: gene MIM:620581 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST003542_179	Night sleep phenotypes	2.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs11721010	OXNAD1		0.00	0

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tretinoin	decreases expression	2
aristolochic acid I	increases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases methylation	1
arsenite	affects binding, increases reaction	1
sodium arsenite	decreases expression	1
perfluorooctanoic acid	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	increases expression	1
(+)-JQ1 compound	decreases expression	1
Fulvestrant	decreases methylation, affects cotreatment	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression, increases abundance	1
Doxorubicin	decreases expression	1
Quercetin	decreases expression	1
Valproic Acid	increases expression, decreases methylation	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression, increases abundance	1
Copper Sulfate	decreases 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_TB82	HAP1 OXNAD1 (-) 1	Cancer cell line	Male
CVCL_XR29	HAP1 OXNAD1 (-) 2	Cancer cell line	Male
CVCL_XR30	HAP1 OXNAD1 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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