OGFOD3

2-oxoglutarate and iron dependent oxygenase domain containing 3

Basic information

Region (hg38): 17:82389210-82418637

Previous symbols: [ "C17orf101" ]

Links

ENSG00000181396 ∙ NCBI:79701 ∙ ∙ HGNC:26174 ∙ Uniprot:Q6PK18 ∙ 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 OGFOD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OGFOD3 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					1	1
missense			30	3		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	3	1

Variants in OGFOD3

This is a list of pathogenic ClinVar variants found in the OGFOD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-82394400-G-T		not specified	Uncertain significance (Jun 29, 2023)
17-82394435-T-C		not specified	Uncertain significance (Jan 16, 2024)
17-82394444-G-A		not specified	Uncertain significance (Jun 18, 2021)
17-82394471-C-G		not specified	Uncertain significance (Dec 11, 2023)
17-82394472-C-G		not specified	Uncertain significance (Dec 11, 2023)
17-82394483-C-A		not specified	Uncertain significance (Jan 26, 2023)
17-82394492-G-A		not specified	Uncertain significance (Feb 12, 2024)
17-82394516-C-T		not specified	Uncertain significance (Apr 13, 2023)
17-82394519-G-T		not specified	Uncertain significance (Feb 06, 2024)
17-82394524-C-T		not specified	Uncertain significance (Oct 03, 2023)
17-82394528-C-T		not specified	Uncertain significance (Apr 13, 2022)
17-82394530-G-T		not specified	Uncertain significance (Dec 26, 2023)
17-82398213-G-A		not specified	Uncertain significance (May 03, 2023)
17-82398246-C-T		not specified	Uncertain significance (Jul 27, 2021)
17-82398250-C-A		not specified	Uncertain significance (Oct 04, 2022)
17-82398306-G-T		not specified	Uncertain significance (May 24, 2023)
17-82398315-G-C		not specified	Uncertain significance (Oct 10, 2023)
17-82403950-G-A		not specified	Uncertain significance (Apr 25, 2023)
17-82403986-G-A		not specified	Uncertain significance (May 14, 2024)
17-82403992-T-C		not specified	Uncertain significance (Dec 16, 2022)
17-82403998-C-A		not specified	Uncertain significance (Dec 19, 2022)
17-82405325-G-A		not specified	Uncertain significance (Nov 27, 2023)
17-82405373-C-T		not specified	Uncertain significance (Sep 01, 2021)
17-82406443-C-G		not specified	Uncertain significance (Jan 08, 2024)
17-82409409-C-T		not specified	Likely benign (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OGFOD3	protein_coding	protein_coding	ENST00000329197	9	29415

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.63e-9	0.221	124427	4	1317	125748	0.00527

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.557	196	219	0.894	0.0000151	2116
Missense in Polyphen		56	72.238	0.77521		684
Synonymous	0.437	91	96.5	0.943	0.00000733	668
Loss of Function	0.580	15	17.6	0.851	9.14e-7	201

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00859	0.00860
Ashkenazi Jewish	0.0186	0.0186
East Asian	0.000653	0.000653
Finnish	0.00139	0.00134
European (Non-Finnish)	0.00759	0.00754
Middle Eastern	0.000653	0.000653
South Asian	0.000632	0.000621
Other	0.00572	0.00572

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.82
• rvis_percentile_EVS: 88.04

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ogfod3
• Phenotype: hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: oxidation-reduction process
• Cellular component: membrane;integral component of membrane
• Molecular function: iron ion binding;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;L-ascorbic acid binding;dioxygenase activity