OGFOD1

protein-coding

2-oxoglutarate and iron dependent oxygenase domain containing 1

Gene summary

Enables peptidyl-proline 3-dioxygenase activity. Involved in several processes, including peptidyl-proline hydroxylation; regulation of translational termination; and stress granule assembly. Located in cytoplasmic stress granule; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_018233.4

Inheritance

—

ClinVar variants

U:76B:5

Top phenotype

Retinitis pigmentosa 74

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr16:56,451,521-56,479,104

External References & Databases

Ensembl (ENSG00000087263)

Transcript & Mutation Effects

hg38 • Region Span ~27.6 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 OGFOD1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 74

not providedTotal: 4

Retinitis pigmentosa 74Total: 1

Bardet-Biedl syndrome 2Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018233.4. 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				2 clinvar	1 clinvar	3
missense			74 clinvar	2 clinvar		76
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	76	4	1	81

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018233.4	RefSeq	NP_060703.3	13	MANE Select
ENST00000566157.6	Ensembl	ENSP00000457258.1	13	MANE Select
NM_001324357.2	RefSeq	NP_001311286.1	13	Standard
NM_001324358.2	RefSeq	NP_001311287.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of translational termination
cell population proliferation
protein hydroxylation
peptidyl-proline hydroxylation
stress granule assembly

Molecular Function

iron ion binding
L-ascorbic acid binding
peptidyl-proline dioxygenase activity
peptidyl-proline 3-dioxygenase activity

Cellular Component

nucleus
cytoplasm
cytosol
cytoplasmic stress granule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000566157
Coding exons: 13
Length: 27611
Individuals with no LoFs: 125660
Homozygous LoFs: 0
Heterozygous LoFs: 88
Defined: 125748
p: 0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.613	258	287	0.898	0.0000140	3631
Missense (PolyPhen)		81	90.017	0.89983		1109
Synonymous	0.851	93	104	0.894	0.00000496	941
Loss of Function	0.475	27	29.8	0.906	0.00000143	368

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00049	0.00049	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00066	0.00065	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00028	0.00028	rare
South Asian	0.00063	0.00062	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Prolyl 3-hydroxylase that catalyzes 3-hydroxylation of 'Pro-62' of small ribosomal subunit uS12 (RPS23), thereby regulating protein translation termination efficiency. Involved in stress granule formation. {ECO:0000269|PubMed:20154146, ECO:0000269|PubMed:24550447, ECO:0000269|PubMed:24550462}.;

Recessive Scores

pRec: 0.0898

Intolerance Scores

LoFtool: 0.955
RVIS EVS: -0.75
RVIS percentile EVS: 13.58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0959

Gene Damage Prediction

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