OGFOD2

Summary

OGFOD2 (2-oxoglutarate and iron dependent oxygenase domain containing 2, HGNC:25823) is a protein-coding gene on chromosome 12q24.31, encoding 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 2 (Q6N063).

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

Source: NCBI Gene 79676 — RefSeq curated summary.

At a glance

• GWAS associations: 12
• Clinical variants (ClinVar): 99 total
• MANE Select transcript: NM_001304833

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25823
Approved symbol	OGFOD2
Name	2-oxoglutarate and iron dependent oxygenase domain containing 2
Location	12q24.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13491, FLJ37501
Ensembl gene	ENSG00000111325
Ensembl biotype	protein_coding
Entrez	79676

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 12 protein_coding, 8 protein_coding_CDS_not_defined, 5 retained_intron, 1 nonsense_mediated_decay

ENST00000228922, ENST00000397389, ENST00000406539, ENST00000420319, ENST00000454694, ENST00000535970, ENST00000536150, ENST00000536439, ENST00000536615, ENST00000537966, ENST00000538628, ENST00000538755, ENST00000540324, ENST00000541360, ENST00000542037, ENST00000542117, ENST00000542940, ENST00000544358, ENST00000544852, ENST00000545033, ENST00000545056, ENST00000545317, ENST00000545396, ENST00000545612, ENST00000545976, ENST00000966950

RefSeq mRNA: 7 — MANE Select: NM_001304833 NM_001304833, NM_001304834, NM_001304835, NM_001304836, NM_001304837, NM_001304838, NM_024623

CCDS: CCDS41855, CCDS76617, CCDS76618

Canonical transcript exons

ENST00000228922 — 7 exons

Exon	Start	End
ENSE00002305412	122979083	122980042
ENSE00003541775	122978442	122978569
ENSE00003575318	122975811	122975867
ENSE00003601323	122976654	122976767
ENSE00003679087	122978753	122979010
ENSE00003786830	122976871	122976970
ENSE00003978219	122975244	122975383

Expression profiles

Bgee: expression breadth ubiquitous, 137 present calls, max score 90.72.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.3448 / max 131.7125, expressed in 1789 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
128549	9.8107	1773
128548	1.5341	1016

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	90.72	gold quality
left testis	UBERON:0004533	89.64	gold quality
right testis	UBERON:0004534	89.54	gold quality
testis	UBERON:0000473	89.22	gold quality
granulocyte	CL:0000094	88.78	gold quality
body of pancreas	UBERON:0001150	88.43	gold quality
duodenum	UBERON:0002114	87.94	gold quality
mucosa of transverse colon	UBERON:0004991	87.01	gold quality
right adrenal gland cortex	UBERON:0035827	86.77	gold quality
right lobe of liver	UBERON:0001114	86.55	gold quality
right adrenal gland	UBERON:0001233	86.39	gold quality
blood	UBERON:0000178	86.33	gold quality
left adrenal gland	UBERON:0001234	86.02	gold quality
left adrenal gland cortex	UBERON:0035825	86.02	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.81	gold quality
pituitary gland	UBERON:0000007	85.63	gold quality
body of stomach	UBERON:0001161	85.41	gold quality
adenohypophysis	UBERON:0002196	85.27	gold quality
stromal cell of endometrium	CL:0002255	85.13	gold quality
apex of heart	UBERON:0002098	84.69	gold quality
right lobe of thyroid gland	UBERON:0001119	84.67	gold quality
adrenal gland	UBERON:0002369	84.67	gold quality
cortex of kidney	UBERON:0001225	84.66	gold quality
adult mammalian kidney	UBERON:0000082	84.36	gold quality
spleen	UBERON:0002106	84.19	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	84.16	gold quality
fundus of stomach	UBERON:0001160	84.13	gold quality
bone marrow cell	CL:0002092	83.92	gold quality
left lobe of thyroid gland	UBERON:0001120	83.92	gold quality
stomach	UBERON:0000945	83.62	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.02
E-GEOD-110499	no	131.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting OGFOD2, 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-124-3P	99.89	73.74	3043
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-593-5P	99.34	69.50	965
HSA-MIR-4254	99.11	65.15	1315
HSA-MIR-485-5P	99.10	64.78	1889
HSA-MIR-6884-5P	99.10	64.50	1987
HSA-MIR-1207-3P	98.99	66.22	1532
HSA-MIR-7157-3P	98.95	68.70	1582
HSA-MIR-4769-3P	97.95	68.17	1002
HSA-MIR-6817-5P	97.95	67.86	1026
HSA-MIR-6807-5P	97.51	64.25	1046
HSA-MIR-4296	96.35	63.55	1233
HSA-MIR-4749-5P	92.16	62.26	179
HSA-MIR-4706	89.76	60.23	156

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ogfod2	ENSDARG00000056211
mus_musculus	Ogfod2	ENSMUSG00000023707
rattus_norvegicus	Ogfod2	ENSRNOG00000001081

Paralogs (1): PTCD1 (ENSG00000106246)

Protein

Protein identifiers

2-oxoglutarate and iron-dependent oxygenase domain-containing protein 2 — Q6N063 (reviewed: Q6N063)

All UniProt accessions (3): Q6N063, F5H145, F5H890

UniProt curated annotations — full annotation on UniProt →

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

Similarity. Belongs to the OGFOD2 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q6N063-1	1	yes
Q6N063-2	2
Q6N063-3	3
Q6N063-4	4

RefSeq proteins (7): NP_001291762, NP_001291763, NP_001291764, NP_001291765, NP_001291766, NP_001291767, NP_078899 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005123	Oxoglu/Fe-dep_dioxygenase_dom	Domain
IPR006620	Pro_4_hyd_alph	Domain

Pfam: PF25238

UniProt features (13 total): splice variant 5, binding site 4, sequence conflict 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6N063-F1	94.11	0.92

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 (4): 235; 237; 290; 300

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 114 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, GCANCTGNY_MYOD_Q6, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_DN, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, CAGCTG_AP4_Q5, GOCC_NUCLEAR_BODY, E2F1_Q3_01, chr12q24, GOMF_L_ASCORBIC_ACID_BINDING, GOMF_DIOXYGENASE_ACTIVITY, GOMF_ORGANIC_ACID_BINDING

GO Biological Process (0):

GO Molecular Function (7): 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), protein binding (GO:0005515), oxidoreductase activity (GO:0016491), metal ion binding (GO:0046872)

GO Cellular Component (0):

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
binding	1
catalytic activity	1
cation binding	1

Protein interactions and networks

STRING

514 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OGFOD2	ABCB9	Q9NP78	635
OGFOD2	OGFOD1	Q8N543	558
OGFOD2	WBP1	Q96G27	553
OGFOD2	PITPNM2	Q9BZ72	510
OGFOD2	TMEM218	A2RU14	509
OGFOD2	WDR83	Q9BRX9	498
OGFOD2	JMJD4	Q9H9V9	460
OGFOD2	ARL6IP4	Q66PJ3	449
OGFOD2	YJEFN3	A6XGL0	433
OGFOD2	HSPBAP1	Q96EW2	428
OGFOD2	SBNO1	A3KN83	419
OGFOD2	MPHOSPH9	Q99550	417
OGFOD2	CTDSPL2	Q05D32	402
OGFOD2	RASSF3	Q86WH2	387
OGFOD2	SNRNP35	Q16560	377

IntAct

4 interactions, top by confidence:

A	B	Type	Score
INSR	RIMOC1	psi-mi:“MI:0914”(association)	0.350
OGFOD2	EEF1G	psi-mi:“MI:0915”(physical association)	0.000
OGFOD2	KAT5	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): OGFOD2 (Affinity Capture-RNA), OGFOD2 (Negative Genetic), EEF1G (Two-hybrid), KAT5 (Two-hybrid), OGFOD2 (Two-hybrid), OGFOD2 (Two-hybrid), OGFOD2 (Co-fractionation)

ESM2 similar proteins: A1L251, A1YVX4, A3KGZ2, A4H7G5, A8QFQ3, C0SUU8, O60066, P0CB42, P0DO23, P34283, P49896, P70551, Q01F03, Q08C92, Q13686, Q28C22, Q2KHP8, Q30DN6, Q3ED68, Q3SWY8, Q4DCH3, Q4QFY1, Q4R4A2, Q57X81, Q5F3R2, Q5REF9, Q5U2S3, Q5XUN4, Q62240, Q6N063, Q6P158, Q6P5D3, Q75E61, Q7YTB0, Q80Y84, Q8BJM7, Q8MNT9, Q8UVX8, Q8VYB9, Q96AP4

Diamond homologs: A3KGZ2, P0DO23, Q28C22, Q3ED68, Q6N063, Q9CQ04, A0JPH3, A5PK45, O00469, O60568, O77588, P24802, Q02809, Q20679, Q5R6K5, Q5R9N3, Q5U309, Q5U367, Q5U483, Q5UQC3, Q63321, Q6NVG7, Q7Q021, Q811A3, Q8IYK4, Q8K297, Q8NBJ5, Q9R0B9, Q9R0E1, Q9R0E2, Q9VTH0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	86
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1446 predictions. Top by Δscore:

Variant	Effect	Δscore
12:122975379:GCCCG:G	donor_gain	1.0000
12:122975384:G:GG	donor_gain	1.0000
12:122975384:GT:G	donor_loss	1.0000
12:122975385:T:A	donor_loss	1.0000
12:122975386:GAGTG:G	donor_loss	1.0000
12:122976869:AG:A	acceptor_gain	1.0000
12:122976870:GG:G	acceptor_gain	1.0000
12:122978440:A:AG	acceptor_gain	1.0000
12:122978441:G:GG	acceptor_gain	1.0000
12:122978441:GA:G	acceptor_gain	1.0000
12:122978541:G:GT	donor_gain	1.0000
12:122978541:G:T	donor_gain	1.0000
12:122978568:GG:G	donor_gain	1.0000
12:122978569:GG:G	donor_gain	1.0000
12:122978749:CCAGG:C	acceptor_loss	1.0000
12:122978751:A:AG	acceptor_gain	1.0000
12:122978751:AG:A	acceptor_gain	1.0000
12:122978752:G:A	acceptor_loss	1.0000
12:122978752:G:GG	acceptor_gain	1.0000
12:122978752:GG:G	acceptor_gain	1.0000
12:122978752:GGT:G	acceptor_gain	1.0000
12:122978752:GGTGC:G	acceptor_gain	1.0000
12:122975380:CCCG:C	donor_gain	0.9900
12:122975382:CG:C	donor_gain	0.9900
12:122975383:GG:G	donor_gain	0.9900
12:122976599:A:AG	acceptor_gain	0.9900
12:122976600:G:GG	acceptor_gain	0.9900
12:122976653:GCTT:G	acceptor_gain	0.9900
12:122976763:TGCAG:T	donor_loss	0.9900
12:122976764:GCAGG:G	donor_loss	0.9900

AlphaMissense

2238 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:122978879:T:C	F220L	0.996
12:122978881:T:A	F220L	0.996
12:122978881:T:G	F220L	0.996
12:122978931:A:T	D237V	0.992
12:122979299:T:C	F336L	0.991
12:122979301:C:A	F336L	0.991
12:122979301:C:G	F336L	0.991
12:122979230:C:A	R313S	0.989
12:122979209:T:A	W306R	0.988
12:122979209:T:C	W306R	0.988
12:122978891:T:C	Y224H	0.986
12:122978931:A:C	D237A	0.986
12:122978932:T:A	D237E	0.985
12:122978932:T:G	D237E	0.985
12:122979300:T:C	F336S	0.985
12:122978936:G:C	A239P	0.984
12:122979143:C:G	H284D	0.984
12:122979199:C:A	N302K	0.983
12:122979199:C:G	N302K	0.983
12:122978924:C:G	H235D	0.982
12:122978930:G:C	D237H	0.982
12:122978551:C:A	N171K	0.981
12:122978551:C:G	N171K	0.981
12:122978886:T:A	V222D	0.980
12:122979161:C:G	H290D	0.980
12:122978953:T:A	N244K	0.979
12:122978953:T:G	N244K	0.979
12:122978560:C:A	N174K	0.978
12:122978560:C:G	N174K	0.978
12:122978972:T:C	F251L	0.978

dbSNP variants (sampled 300 via entrez): RS1000288082 (12:122975098 C>G,T), RS1000623774 (12:122974051 CAAAT>C), RS1001007711 (12:122973489 G>A,C), RS1002014766 (12:122974914 G>A,C,T), RS1002122209 (12:122973717 C>T), RS1002151142 (12:122979743 G>C), RS1002178266 (12:122978285 C>T), RS1002239633 (12:122974155 T>C,G), RS1002250193 (12:122979435 T>C), RS1002666061 (12:122977086 A>G,T), RS1002811820 (12:122977084 G>A,C), RS1003661460 (12:122977556 G>A), RS1005125395 (12:122975671 G>A,T), RS1005949809 (12:122979380 G>C), RS1006163776 (12:122974740 G>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

12 associations (top):

Study	Trait	p-value
GCST002149_20	Schizophrenia	2.000000e-08
GCST002539_19	Schizophrenia	2.000000e-14
GCST004521_72	Autism spectrum disorder or schizophrenia	8.000000e-12
GCST004902_6	Parkinson’s disease	2.000000e-20
GCST004946_85	Schizophrenia	6.000000e-18
GCST006803_10	Schizophrenia	6.000000e-16
GCST007277_17	Tourette syndrome	2.000000e-06
GCST010703_43	Brain morphology (MOSTest)	1.000000e-08
GCST90020024_441	A body shape index	2.000000e-13
GCST90020025_408	Waist-to-hip ratio adjusted for BMI	3.000000e-18
GCST90020027_1260	Waist-hip index	2.000000e-17
GCST90020029_366	Waist circumference adjusted for body mass index	1.000000e-10

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement
EFO:0007789	BMI-adjusted waist circumference
EFO:0007788	BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cisplatin	affects cotreatment, increases expression	2
testosterone enanthate	affects expression	1
bisphenol A	increases expression	1
quercitrin	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
jinfukang	affects cotreatment, increases expression	1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-ol	decreases expression	1
Sunitinib	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Smoke	decreases expression	1
Valproic Acid	increases methylation	1
Copper Sulfate	decreases expression	1
Acrylamide	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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