OGFOD1

2-oxoglutarate and iron dependent oxygenase domain containing 1

Basic information

Region (hg38): 16:56451521-56479104

Links

ENSG00000087263

∙ NCBI:55239 ∙ OMIM:615857 ∙ HGNC:25585 ∙ Uniprot:Q8N543 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OGFOD1 gene.

not_specified (65 variants)
not_provided (2 variants)
Retinitis_pigmentosa_74 (1 variants)
Bardet-Biedl_syndrome_2 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OGFOD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018233.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			64 clinvar	1 clinvar		65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	64	1	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OGFOD1	protein_coding	protein_coding	ENST00000566157	13	27611

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.31e-17	0.0186	125660	0	88	125748	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.613	258	287	0.898	0.0000140	3631
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000800	0.000800
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000656	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.000282	0.000281
Middle Eastern	0.000656	0.000653
South Asian	0.000626	0.000621
Other	0.000327	0.000326

dbNSFP

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

Haploinsufficiency Scores

pHI: 0.0525
hipred: N
hipred_score: 0.216
ghis: 0.598

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0959

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ogfod1
Phenotype: normal phenotype; limbs/digits/tail phenotype; homeostasis/metabolism phenotype; skeleton phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);

Gene ontology

Biological process: regulation of translational termination;cell population proliferation;protein hydroxylation;peptidyl-proline hydroxylation;stress granule assembly;oxidation-reduction process
Cellular component: nucleus;cytoplasm;cytosol;cytoplasmic stress granule
Molecular function: iron ion binding;L-ascorbic acid binding;peptidyl-proline dioxygenase activity;peptidyl-proline 3-dioxygenase activity