APOBEC3G

apolipoprotein B mRNA editing enzyme catalytic subunit 3G, the group of Apolipoprotein B mRNA editing enzyme catalytic subunits

Basic information

Region (hg38): 22:39077066-39087743

Links

ENSG00000239713 ∙ NCBI:60489 ∙ OMIM:607113 ∙ HGNC:17357 ∙ Uniprot:Q9HC16 ∙ 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 APOBEC3G gene.

• Inborn genetic diseases (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOBEC3G 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in APOBEC3G

This is a list of pathogenic ClinVar variants found in the APOBEC3G region.

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

Position	Type	Phenotype	Significance	ClinVar
22-39078950-G-A		not specified	Uncertain significance (Jan 25, 2023)
22-39079002-C-T		not specified	Uncertain significance (Sep 25, 2023)
22-39080960-G-A		not specified	Uncertain significance (Apr 19, 2023)
22-39080967-G-A		not specified	Uncertain significance (Nov 10, 2022)
22-39080975-C-G		not specified	Uncertain significance (Jun 16, 2023)
22-39080985-G-C		not specified	Uncertain significance (Oct 03, 2022)
22-39081125-C-T		not specified	Uncertain significance (Jan 24, 2023)
22-39083738-A-G		not specified	Uncertain significance (Dec 02, 2022)
22-39086341-T-G		not specified	Uncertain significance (May 23, 2023)
22-39086357-G-T		not specified	Uncertain significance (Dec 03, 2021)
22-39086361-T-C		not specified	Uncertain significance (Dec 12, 2023)
22-39086387-T-G		not specified	Uncertain significance (Dec 02, 2022)
22-39086437-C-A		not specified	Uncertain significance (May 26, 2022)
22-39086478-C-T		not specified	Uncertain significance (May 24, 2023)
22-39086481-G-A		not specified	Uncertain significance (Jun 29, 2022)
22-39086519-C-T		not specified	Uncertain significance (Dec 14, 2023)
22-39086541-C-A		not specified	Uncertain significance (Jan 19, 2024)
22-39087050-G-T		not specified	Uncertain significance (Oct 10, 2023)
22-39087092-A-G		not specified	Uncertain significance (Mar 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOBEC3G	protein_coding	protein_coding	ENST00000407997	8	46825

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.67e-21	0.000217	125493	2	253	125748	0.00101

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.151	227	233	0.972	0.0000137	2569
Missense in Polyphen		75	75.993	0.98694		1003
Synonymous	0.00267	86	86.0	1.00	0.00000514	672
Loss of Function	-0.985	28	22.9	1.22	0.00000119	243

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.000999
Ashkenazi Jewish	0.00119	0.00119
East Asian	0.000163	0.000163
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000714	0.000712
Middle Eastern	0.000163	0.000163
South Asian	0.00431	0.00426
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. Exhibits potent antiviral activity against vif-deficient HIV-1. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination- independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single-or double- stranded RNA. Exhibits antiviral activity also against simian immunodeficiency viruses (SIVs), hepatitis B virus (HBV), equine infectious anemia virus (EIAV), xenotropic MuLV-related virus (XMRV) and simian foamy virus (SFV). May inhibit the mobility of LTR and non-LTR retrotransposons. {ECO:0000269|PubMed:12167863, ECO:0000269|PubMed:12808465, ECO:0000269|PubMed:12808466, ECO:0000269|PubMed:12809610, ECO:0000269|PubMed:12859895, ECO:0000269|PubMed:12970355, ECO:0000269|PubMed:14528300, ECO:0000269|PubMed:14557625, ECO:0000269|PubMed:15031497, ECO:0000269|PubMed:16378963, ECO:0000269|PubMed:16527742, ECO:0000269|PubMed:18288108, ECO:0000269|PubMed:19458006, ECO:0000269|PubMed:20219927, ECO:0000269|PubMed:20335265, ECO:0000269|PubMed:21123384, ECO:0000269|PubMed:21835787, ECO:0000269|PubMed:22791714, ECO:0000269|PubMed:22807680, ECO:0000269|PubMed:22915799, ECO:0000269|PubMed:23097438, ECO:0000269|PubMed:23152537}.
• Pathway: Dual hijack model of Vif in HIV infection;Disease;hiv-1 defeats host-mediated resistance by cem15;Host Interactions of HIV factors;HIV Infection;Infectious disease;APOBEC3G mediated resistance to HIV-1 infection;Vif-mediated degradation of APOBEC3G (Consensus)

Recessive Scores

• pRec: 0.0568

Intolerance Scores

• loftool: 0.860
• rvis_EVS: 0.07
• rvis_percentile_EVS: 58.96

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.401
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.894

Gene Damage Prediction

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

Gene ontology

• Biological process: positive regulation of defense response to virus by host;cytidine deamination;negative regulation of transposition;viral process;base conversion or substitution editing;cytidine to uridine editing;negative regulation of viral genome replication;innate immune response;negative regulation of single stranded viral RNA replication via double stranded DNA intermediate;negative regulation of viral process;defense response to virus;DNA cytosine deamination;DNA demethylation
• Cellular component: P-body;nucleus;cytoplasm;cytosol;apolipoprotein B mRNA editing enzyme complex;ribonucleoprotein complex
• Molecular function: RNA binding;cytidine deaminase activity;protein binding;zinc ion binding;dCTP deaminase activity;identical protein binding;protein homodimerization activity;deoxycytidine deaminase activity