OGFOD3

Summary

OGFOD3 (2-oxoglutarate and iron dependent oxygenase domain containing 3, HGNC:26174) is a protein-coding gene on chromosome 17q25.3, encoding 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 3 (Q6PK18).

Predicted to enable several functions, including L-ascorbic acid binding activity; dioxygenase activity; and iron ion binding activity. Located in membrane.

Source: NCBI Gene 79701 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 91 total
• MANE Select transcript: NM_024648

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26174
Approved symbol	OGFOD3
Name	2-oxoglutarate and iron dependent oxygenase domain containing 3
Location	17q25.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22222
Ensembl gene	ENSG00000181396
Ensembl biotype	protein_coding
Entrez	79701

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 11 protein_coding, 3 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000313056, ENST00000329197, ENST00000577495, ENST00000577606, ENST00000578287, ENST00000578586, ENST00000579407, ENST00000580445, ENST00000582146, ENST00000582593, ENST00000583445, ENST00000583897, ENST00000851497, ENST00000851498, ENST00000851499, ENST00000851500, ENST00000949676

RefSeq mRNA: 2 — MANE Select: NM_024648 NM_024648, NM_175902

CCDS: CCDS11811, CCDS11812

Canonical transcript exons

ENST00000313056 — 9 exons

Exon	Start	End
ENSE00002712832	82389210	82392534
ENSE00003477667	82415398	82415627
ENSE00003555376	82409368	82409410
ENSE00003576576	82403937	82404090
ENSE00003602511	82411455	82411530
ENSE00003671626	82405324	82405380
ENSE00003672909	82398196	82398319
ENSE00003677505	82406418	82406482
ENSE00003846456	82418412	82418586

Expression profiles

Bgee: expression breadth ubiquitous, 274 present calls, max score 95.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.6494 / max 132.9220, expressed in 1810 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
168986	20.7894	1810
168985	0.8600	560

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	95.92	gold quality
parotid gland	UBERON:0001831	91.32	gold quality
cervix squamous epithelium	UBERON:0006922	90.69	gold quality
apex of heart	UBERON:0002098	90.53	gold quality
right lobe of thyroid gland	UBERON:0001119	89.64	gold quality
left lobe of thyroid gland	UBERON:0001120	89.39	gold quality
hindlimb stylopod muscle	UBERON:0004252	89.13	gold quality
thyroid gland	UBERON:0002046	88.96	gold quality
stromal cell of endometrium	CL:0002255	88.92	gold quality
body of pancreas	UBERON:0001150	88.84	gold quality
gastrocnemius	UBERON:0001388	88.58	gold quality
adenohypophysis	UBERON:0002196	88.49	gold quality
right adrenal gland	UBERON:0001233	88.45	gold quality
left adrenal gland	UBERON:0001234	88.45	gold quality
left adrenal gland cortex	UBERON:0035825	88.44	gold quality
muscle of leg	UBERON:0001383	88.39	gold quality
heart left ventricle	UBERON:0002084	88.12	gold quality
pituitary gland	UBERON:0000007	88.07	gold quality
right atrium auricular region	UBERON:0006631	88.05	gold quality
cardiac ventricle	UBERON:0002082	87.87	gold quality
right coronary artery	UBERON:0001625	87.79	gold quality
right adrenal gland cortex	UBERON:0035827	87.73	gold quality
adrenal gland	UBERON:0002369	87.64	gold quality
adrenal cortex	UBERON:0001235	87.62	gold quality
palpebral conjunctiva	UBERON:0001812	87.47	gold quality
saliva-secreting gland	UBERON:0001044	87.37	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	87.24	gold quality
body of stomach	UBERON:0001161	87.19	gold quality
left coronary artery	UBERON:0001626	87.12	gold quality
mucosa of transverse colon	UBERON:0004991	87.12	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.19
E-GEOD-99795	no	83.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

85 targeting OGFOD3, 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-3613-3P	100.00	76.36	7965
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-3156-3P	99.76	66.72	939
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-3714	99.71	70.74	2671
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-4516	99.61	67.78	3390

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ogfod3	ENSDARG00000078481
mus_musculus	Ogfod3	ENSMUSG00000025169
rattus_norvegicus	Ogfod3	ENSRNOG00000036668

Protein

Protein identifiers

2-oxoglutarate and iron-dependent oxygenase domain-containing protein 3 — Q6PK18 (reviewed: Q6PK18)

All UniProt accessions (6): Q6PK18, J3QLI8, J3QRG1, K7ELK1, K7ELR2, K7ENS7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Cofactor. Binds 1 Fe(2+) ion per subunit.

Similarity. Belongs to the OGFOD3 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6PK18-1	1	yes
Q6PK18-2	2

RefSeq proteins (2): NP_078924, NP_787098 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005123	Oxoglu/Fe-dep_dioxygenase_dom	Domain
IPR006620	Pro_4_hyd_alph	Domain
IPR039210	OGFOD3	Family
IPR044862	Pro_4_hyd_alph_FE2OG_OXY	Domain

Pfam: PF13640

UniProt features (17 total): binding site 4, topological domain 2, sequence variant 2, chain 1, glycosylation site 1, splice variant 1, sequence conflict 1, transmembrane region 1, domain 1, region of interest 1, compositionally biased region 1, active site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6PK18-F1	85.74	0.75

Functional residue map

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

Catalytic / active sites (1): 298

Ligand- & substrate-binding residues (4): 288; 298; 230; 232

Glycosylation sites (1): 215

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

GO Molecular Function (6): iron ion binding (GO:0005506), oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705), L-ascorbic acid binding (GO:0031418), dioxygenase activity (GO:0051213), oxidoreductase activity (GO:0016491), metal ion binding (GO:0046872)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
oxidoreductase activity	2
transition metal ion binding	1
vitamin binding	1
carboxylic acid binding	1
monosaccharide binding	1
heterocyclic compound binding	1
catalytic activity	1
cation binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

416 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OGFOD3	RAPGEFL1	Q9UHV5	560
OGFOD3	OXLD1	Q5BKU9	504
OGFOD3	LIN52	Q52LA3	488
OGFOD3	TDRKH	Q9Y2W6	384
OGFOD3	UTS2R	Q9UKP6	383
OGFOD3	KIAA0930	Q6ICG6	373
OGFOD3	LRRC17	Q8N6Y2	373
OGFOD3	CEP44	Q9C0F1	373
OGFOD3	QSOX2	Q6ZRP7	348
OGFOD3	GNPNAT1	Q96EK6	343
OGFOD3	GLYR1	Q49A26	334
OGFOD3	MANBA	O00462	319
OGFOD3	PDPR	Q8NCN5	318
OGFOD3	GIGYF2	Q6Y7W6	306
OGFOD3	HSD17B12	Q53GQ0	304

IntAct

17 interactions, top by confidence:

A	B	Type	Score
TRDN	TMEM223	psi-mi:“MI:0914”(association)	0.640
CANX	PGRMC1	psi-mi:“MI:0914”(association)	0.570
TMEM9	ESYT2	psi-mi:“MI:0914”(association)	0.530
OGFOD3	CLGN	psi-mi:“MI:0914”(association)	0.530
GALNS	CLGN	psi-mi:“MI:0914”(association)	0.530
SPCS3	ENTPD6	psi-mi:“MI:0914”(association)	0.530
HSCB	RBP5	psi-mi:“MI:0914”(association)	0.350
OGFOD3	MPC2	psi-mi:“MI:0914”(association)	0.350
HLA-C	HLA-H	psi-mi:“MI:0914”(association)	0.350
ENTPD2	CLGN	psi-mi:“MI:0914”(association)	0.350
BPIFB1	OGFOD3	psi-mi:“MI:0914”(association)	0.350
C1QC	VWA8	psi-mi:“MI:0914”(association)	0.350
CLGN	TMEM131L	psi-mi:“MI:0914”(association)	0.350
SLC37A3	PLXNB2	psi-mi:“MI:0914”(association)	0.350
SLC39A7	ESYT2	psi-mi:“MI:0914”(association)	0.350
SLC39A9	TRAFD1	psi-mi:“MI:0914”(association)	0.350

BioGRID (50): ATP2C1 (Affinity Capture-MS), CLGN (Affinity Capture-MS), CANX (Affinity Capture-MS), C1GALT1C1 (Affinity Capture-MS), DNAJB9 (Affinity Capture-MS), NHLRC3 (Affinity Capture-MS), GPC6 (Affinity Capture-MS), LMF1 (Affinity Capture-MS), EIF2AK3 (Affinity Capture-MS), TRIP6 (Affinity Capture-MS), DNAJB9 (Affinity Capture-MS), CANX (Affinity Capture-MS), EIF2AK3 (Affinity Capture-MS), ATP2C1 (Affinity Capture-MS), TRIP6 (Affinity Capture-MS)

ESM2 similar proteins: A2RSX7, A2RUC4, D4PHA7, O95461, P33488, P33490, P59723, Q1JP61, Q2TBF2, Q3TA59, Q3TCT4, Q3TDN0, Q497B8, Q5BKC6, Q5M843, Q5M900, Q5NDE3, Q5NDE8, Q5NDE9, Q5NDF0, Q5NDF1, Q5NDF2, Q5REF6, Q5U367, Q5XGE0, Q66PG3, Q66PG4, Q6AY40, Q6NRQ1, Q6PK18, Q7LFX5, Q812F8, Q8BG58, Q8BJQ9, Q8BLR9, Q8BW41, Q8N371, Q8NAT1, Q8TDX6, Q91XQ5

Diamond homologs: O75718, Q32P28, Q3V1T4, Q4KLM6, Q64375, Q6JHU7, Q6JHU8, Q6PK18, Q8CG70, Q8CG71, Q8IVL5, Q8IVL6, Q8K2B0, Q90830, Q92791, Q9CYD3, Q9R1J8, Q5M843, Q5XGE0, Q9D136

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	7
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2132 predictions. Top by Δscore:

Variant	Effect	Δscore
17:82392531:CGAC:C	acceptor_gain	1.0000
17:82392532:GACCT:G	acceptor_loss	1.0000
17:82392533:ACCTG:A	acceptor_loss	1.0000
17:82392534:CCT:C	acceptor_loss	1.0000
17:82392535:C:CC	acceptor_gain	1.0000
17:82392535:C:CG	acceptor_loss	1.0000
17:82392536:T:G	acceptor_loss	1.0000
17:82404087:CTCC:C	acceptor_gain	1.0000
17:82404088:TCC:T	acceptor_gain	1.0000
17:82404089:CC:C	acceptor_gain	1.0000
17:82404089:CCC:C	acceptor_gain	1.0000
17:82404089:CCCT:C	acceptor_loss	1.0000
17:82404090:CC:C	acceptor_gain	1.0000
17:82404090:CCT:C	acceptor_loss	1.0000
17:82404091:C:CC	acceptor_gain	1.0000
17:82404092:T:A	acceptor_loss	1.0000
17:82405318:CCTTA:C	donor_loss	1.0000
17:82405319:CTTA:C	donor_loss	1.0000
17:82405320:TTACC:T	donor_loss	1.0000
17:82405321:TACCG:T	donor_loss	1.0000
17:82405322:A:AC	donor_gain	1.0000
17:82405322:ACCGG:A	donor_loss	1.0000
17:82405323:C:CA	donor_gain	1.0000
17:82405323:CCG:C	donor_gain	1.0000
17:82405378:TATC:T	acceptor_loss	1.0000
17:82405380:TC:T	acceptor_loss	1.0000
17:82405381:C:CC	acceptor_gain	1.0000
17:82405381:CTGTG:C	acceptor_loss	1.0000
17:82405383:G:C	acceptor_gain	1.0000
17:82415387:T:A	donor_gain	1.0000

AlphaMissense

2066 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:82392500:G:C	N286K	0.997
17:82392500:G:T	N286K	0.997
17:82392518:G:C	F280L	0.997
17:82392518:G:T	F280L	0.997
17:82392520:A:G	F280L	0.997
17:82398257:G:C	F254L	0.997
17:82398257:G:T	F254L	0.997
17:82398259:A:G	F254L	0.997
17:82398302:G:C	F239L	0.997
17:82398302:G:T	F239L	0.997
17:82398304:A:G	F239L	0.997
17:82404006:G:C	F210L	0.997
17:82404006:G:T	F210L	0.997
17:82404008:A:G	F210L	0.997
17:82406472:A:G	L145P	0.997
17:82392438:C:T	C307Y	0.996
17:82392496:G:C	H288D	0.996
17:82398237:A:C	F261C	0.996
17:82403960:A:G	Y226H	0.996
17:82406451:A:G	L152P	0.996
17:82392513:G:C	S282W	0.995
17:82392531:C:G	R276P	0.995
17:82398298:A:C	Y241D	0.995
17:82403998:C:G	R213P	0.995
17:82406432:A:C	F158L	0.995
17:82406432:A:T	F158L	0.995
17:82406434:A:G	F158L	0.995
17:82409405:G:T	A129D	0.995
17:82392443:G:C	F305L	0.994
17:82392443:G:T	F305L	0.994

dbSNP variants (sampled 300 via entrez): RS1000238115 (17:82408143 A>G), RS1000242740 (17:82402655 G>C), RS1000268363 (17:82396762 C>A,G), RS1000437433 (17:82418905 G>A,C), RS1000575133 (17:82401144 C>A,G,T), RS1000588582 (17:82407826 G>A,T), RS1000691202 (17:82401389 G>A), RS1000862756 (17:82418035 C>T), RS1000893041 (17:82417636 T>A,C), RS1000976182 (17:82406821 C>A,T), RS1001005017 (17:82412350 G>A), RS1001114741 (17:82404824 T>TCCA), RS1001190957 (17:82401848 T>A), RS1001289405 (17:82417856 A>C), RS1001335539 (17:82418228 G>C,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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases methylation	2
aristolochic acid I	decreases expression	1
sodium arsenite	decreases expression	1
benzo(e)pyrene	decreases methylation	1
di-n-butylphosphoric acid	affects expression	1
abrine	decreases expression	1
Ethanol	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation	1
Ethyl Methanesulfonate	decreases expression	1
Formaldehyde	decreases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Methapyrilene	decreases methylation	1
Methyl Methanesulfonate	decreases expression	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, increases abundance, increases expression	1
Smoke	decreases expression	1
Antirheumatic Agents	decreases expression	1
Cadmium Chloride	increases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	decreases expression	1
tert-Butylhydroperoxide	decreases expression	1
Vitamin K 3	affects expression	1
Particulate Matter	increases abundance, increases expression, affects cotreatment	1

Clinical trials (associated diseases)

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