OGG1

8-oxoguanine DNA glycosylase, the group of DNA glycosylases

Basic information

Region (hg38): 3:9749943-9788219

Links

ENSG00000114026 ∙ NCBI:4968 ∙ OMIM:601982 ∙ HGNC:8125 ∙ Uniprot:O15527 ∙ 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 OGG1 gene.

• Inborn genetic diseases (28 variants)
• not provided (7 variants)
• Nonpapillary renal cell carcinoma (1 variants)
• Clear cell carcinoma of kidney (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OGG1 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			16	4	1	21
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			12	1		13
Total	0	0	29	5	1

Variants in OGG1

This is a list of pathogenic ClinVar variants found in the OGG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-9750414-A-T		not specified	Uncertain significance (Aug 17, 2021)
3-9750416-T-C		not specified	Uncertain significance (Mar 02, 2023)
3-9750423-G-A		Clear cell carcinoma of kidney	Uncertain significance (Jul 31, 2021)
3-9750981-A-T		OGG1-related disorder	Likely benign (Sep 05, 2019)
3-9751003-C-G		not specified	Uncertain significance (Apr 08, 2023)
3-9751100-A-G		not specified	Uncertain significance (Jul 20, 2021)
3-9751135-T-C		not specified	Uncertain significance (Aug 08, 2022)
3-9751138-C-T		not specified	Uncertain significance (May 16, 2022)
3-9751159-T-C		not specified	Likely benign (Apr 12, 2022)
3-9751785-G-T		not specified	Uncertain significance (Aug 24, 2023)
3-9751790-G-A		not specified	Uncertain significance (Jan 10, 2023)
3-9751830-A-G			Uncertain significance (Sep 24, 2021)
3-9751913-A-T		not specified	Uncertain significance (Jun 23, 2021)
3-9754716-A-G		not specified	Uncertain significance (Aug 21, 2023)
3-9754784-C-A		not specified	Uncertain significance (Jan 23, 2024)
3-9756522-G-T		not specified	Uncertain significance (Mar 21, 2023)
3-9756779-G-A		not specified	Uncertain significance (Sep 16, 2021)
3-9756791-G-A		OGG1-related disorder	Likely benign (Mar 01, 2023)
3-9756823-G-A			Likely benign (May 11, 2018)
3-9757056-T-C		OGG1-related disorder	Benign/Likely benign (Feb 05, 2020)
3-9757089-C-G		OGG1-related disorder	Benign (Oct 17, 2019)
3-9757095-A-G		not specified	Likely benign (Nov 07, 2022)
3-9757096-T-C		OGG1-related disorder	Likely benign (Mar 11, 2019)
3-9757113-C-T		not specified	Uncertain significance (Jul 12, 2022)
3-9757118-C-T		not specified	Uncertain significance (Sep 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OGG1	protein_coding	protein_coding	ENST00000302036	7	38276

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.93e-12	0.0928	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.572	271	246	1.10	0.0000139	2715
Missense in Polyphen		72	67.55	1.0659		775
Synonymous	-1.21	115	99.6	1.15	0.00000545	894
Loss of Function	0.493	19	21.5	0.885	0.00000134	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000757	0.000756
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.000327	0.000326
South Asian	0.000556	0.000555
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA repair enzyme that incises DNA at 8-oxoG residues. Excises 7,8-dihydro-8-oxoguanine and 2,6-diamino-4-hydroxy-5-N- methylformamidopyrimidine (FAPY) from damaged DNA. Has a beta- lyase activity that nicks DNA 3' to the lesion.
• Pathway: Base excision repair - Homo sapiens (human);DNA Repair;Recognition and association of DNA glycosylase with site containing an affected purine;Cleavage of the damaged purine;Depurination;Recognition and association of DNA glycosylase with site containing an affected pyrimidine;Cleavage of the damaged pyrimidine ;Depyrimidination;Base-Excision Repair, AP Site Formation;Resolution of Abasic Sites (AP sites);Base Excision Repair;Validated transcriptional targets of TAp63 isoforms;Displacement of DNA glycosylase by APEX1;APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway (Consensus)

Recessive Scores

• pRec: 0.466

Intolerance Scores

• loftool: 0.557
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.73

Haploinsufficiency Scores

• pHI: 0.265
• hipred: N
• hipred_score: 0.438
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.985

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ogg1
• Phenotype: neoplasm; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: ogg1
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: acute inflammatory response;base-excision repair;base-excision repair, AP site formation;regulation of transcription, DNA-templated;cellular response to DNA damage stimulus;response to oxidative stress;aging;response to radiation;response to light stimulus;response to estradiol;nucleotide-excision repair, DNA incision;negative regulation of apoptotic process;depurination;depyrimidination;response to ethanol;response to folic acid;cellular response to cadmium ion;negative regulation of double-strand break repair via single-strand annealing
• Cellular component: nucleus;nucleoplasm;mitochondrion;nuclear matrix;nuclear speck;protein-containing complex
• Molecular function: damaged DNA binding;endonuclease activity;protein binding;microtubule binding;oxidized purine nucleobase lesion DNA N-glycosylase activity;oxidized purine DNA binding;8-oxo-7,8-dihydroguanine DNA N-glycosylase activity;class I DNA-(apurinic or apyrimidinic site) endonuclease activity