OGFOD2

2-oxoglutarate and iron dependent oxygenase domain containing 2

Basic information

Region (hg38): 12:122974580-122980043

Links

ENSG00000111325 ∙ NCBI:79676 ∙ ∙ HGNC:25823 ∙ Uniprot:Q6N063 ∙ 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 OGFOD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OGFOD2 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	32	1	0

Variants in OGFOD2

This is a list of pathogenic ClinVar variants found in the OGFOD2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-122976673-G-A		not specified	Uncertain significance (Feb 15, 2023)
12-122976675-C-T		not specified	Uncertain significance (Dec 15, 2022)
12-122976702-G-A		not specified	Uncertain significance (Oct 13, 2023)
12-122976736-C-T		not specified	Uncertain significance (May 09, 2023)
12-122976952-C-T		not specified	Uncertain significance (Jul 19, 2023)
12-122978444-G-A		not specified	Uncertain significance (Jul 31, 2024)
12-122978484-T-C		not specified	Uncertain significance (Sep 17, 2021)
12-122978487-G-A		not specified	Uncertain significance (Nov 06, 2023)
12-122978493-C-T		not specified	Uncertain significance (Jul 31, 2024)
12-122978518-C-G		not specified	Uncertain significance (Apr 27, 2024)
12-122978526-C-T		not specified	Uncertain significance (Sep 20, 2024)
12-122978528-G-C		not specified	Uncertain significance (Jul 19, 2023)
12-122978550-A-G		not specified	Uncertain significance (Aug 20, 2023)
12-122978771-G-A		not specified	Uncertain significance (Jan 29, 2024)
12-122978780-G-A		not specified	Uncertain significance (May 18, 2022)
12-122978807-C-T		not specified	Uncertain significance (Sep 16, 2021)
12-122978808-G-A		not specified	Uncertain significance (Jul 14, 2024)
12-122978814-T-C		not specified	Uncertain significance (Aug 14, 2023)
12-122978820-C-T		not specified	Uncertain significance (May 20, 2024)
12-122978864-G-A		not specified	Uncertain significance (Dec 20, 2023)
12-122978873-C-T		not specified	Uncertain significance (Aug 29, 2024)
12-122978910-T-A		not specified	Uncertain significance (Oct 16, 2024)
12-122978919-G-A		not specified	Uncertain significance (May 16, 2023)
12-122978939-G-A		not specified	Uncertain significance (May 18, 2023)
12-122978951-A-G		not specified	Uncertain significance (Feb 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OGFOD2	protein_coding	protein_coding	ENST00000397389	6	5464

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.44e-12	0.0124	124714	0	77	124791	0.000309

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.16	249	203	1.23	0.0000142	1837
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00139	0.00133
Ashkenazi Jewish	0.000100	0.0000994
East Asian	0.000224	0.000222
Finnish	0.00	0.00
European (Non-Finnish)	0.000341	0.000336
Middle Eastern	0.000224	0.000222
South Asian	0.000295	0.000294
Other	0.000168	0.000165

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.331
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.46

Haploinsufficiency Scores

• pHI: 0.133
• hipred: N
• hipred_score: 0.204
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.904

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ogfod2

Gene ontology

• 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