APOBEC3C

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

Basic information

Region (hg38): 22:39014257-39020352

Links

ENSG00000244509 ∙ NCBI:27350 ∙ OMIM:607750 ∙ HGNC:17353 ∙ Uniprot:Q9NRW3 ∙ 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 APOBEC3C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOBEC3C 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			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	1

Variants in APOBEC3C

This is a list of pathogenic ClinVar variants found in the APOBEC3C region.

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

Position	Type	Phenotype	Significance	ClinVar
22-39015611-A-G		not specified	Uncertain significance (Mar 22, 2022)
22-39015632-T-G		not specified	Uncertain significance (Oct 06, 2023)
22-39015650-T-C		not specified	Uncertain significance (Feb 28, 2023)
22-39015665-C-T		not specified	Uncertain significance (Apr 05, 2023)
22-39015723-C-G		not specified	Uncertain significance (Jun 05, 2023)
22-39015732-C-T		not specified	Uncertain significance (Sep 14, 2022)
22-39015735-G-T		not specified	Uncertain significance (May 30, 2022)
22-39017782-A-C		not specified	Likely benign (Aug 17, 2021)
22-39017787-C-T		not specified	Uncertain significance (Aug 04, 2023)
22-39017801-C-G		not specified	Uncertain significance (Sep 20, 2023)
22-39017825-C-G		not specified	Uncertain significance (Jan 31, 2024)
22-39017847-T-A		not specified	Uncertain significance (Jan 30, 2024)
22-39017866-C-T		not specified	Uncertain significance (Aug 30, 2021)
22-39017992-G-C		not specified	Uncertain significance (Mar 23, 2022)
22-39018327-G-C		not specified	Uncertain significance (Nov 13, 2023)
22-39018341-C-A		not specified	Uncertain significance (Sep 27, 2021)
22-39018377-G-T			Benign (May 17, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOBEC3C	protein_coding	protein_coding	ENST00000361441	4	6270

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0267	0.925	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.456	128	114	1.12	0.00000703	1267
Missense in Polyphen		36	39.63	0.90839		449
Synonymous	-0.916	51	43.3	1.18	0.00000278	334
Loss of Function	1.70	4	9.71	0.412	5.04e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.000218	0.000217
South Asian	0.00	0.00
Other	0.00	0.00

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. 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 against simian immunodeficiency virus (SIV), hepatitis B virus (HBV), herpes simplex virus 1 (HHV-1) and Epstein-Barr virus (EBV) and may inhibit the mobility of LTR and non-LTR retrotransposons. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation. {ECO:0000269|PubMed:12859895, ECO:0000269|PubMed:15466872, ECO:0000269|PubMed:16527742, ECO:0000269|PubMed:20062055, ECO:0000269|PubMed:21496894, ECO:0000269|PubMed:21632763}.
• Pathway: Metabolism of RNA;Formation of the Editosome;mRNA Editing: C to U Conversion;mRNA Editing (Consensus)

Recessive Scores

• pRec: 0.0592

Intolerance Scores

• loftool: 0.524
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.132
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.950

Gene Damage Prediction

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

Gene ontology

• Biological process: cytidine deamination;negative regulation of transposition;viral process;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;defense response to virus;DNA cytosine deamination;DNA demethylation
• Cellular component: P-body;nucleus;cytoplasm
• Molecular function: RNA binding;cytidine deaminase activity;protein binding;zinc ion binding