OGFOD2

protein-coding

2-oxoglutarate and iron dependent oxygenase domain containing 2

Gene summary

Predicted to enable several functions, including L-ascorbic acid binding activity; dioxygenase activity; and iron ion binding activity. Located in nuclear body. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001304833.2

Inheritance

—

ClinVar variants

U:90B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.21

Max pathogenic AF

—

Genomic locus

chr12:122,974,580-122,980,043

External References & Databases

Ensembl (ENSG00000111325)

Transcript & Mutation Effects

hg38 • Region Span ~5.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OGFOD2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 90

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001304833.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			87 clinvar	2 clinvar		89
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	90	4	0	94

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 51 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001304833.2	RefSeq	NP_001291762.1	7	MANE Select
ENST00000228922.12	Ensembl	ENSP00000228922.7	7	MANE Select
NM_001304834.2	RefSeq	NP_001291763.1	3	Standard
NM_001304835.2	RefSeq	NP_001291764.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

oxidation-reduction process

Molecular Function

iron ion binding
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
L-ascorbic acid binding
dioxygenase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397389
Coding exons: 6
Length: 5464
Individuals with no LoFs: 124714
Homozygous LoFs: 0
Heterozygous LoFs: 77
Defined: 124791
p: 0.000309

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.16	249	203	1.23	0.0000142	1837
Missense (PolyPhen)		74	63.708	1.1615		615
Synonymous	-1.48	111	92.9	1.20	0.00000667	633
Loss of Function	-0.698	16	13.3	1.21	6.54e-7	137

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0012	0.0012	notable
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00034	0.00034	rare
South Asian	0.00029	0.00029	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.331
RVIS EVS: -0.44
RVIS percentile EVS: 24.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.904

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium