APOBEC3D

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

Basic information

Region (hg38): 22:39021112-39033277

Previous symbols: [ "APOBEC3E" ]

Links

ENSG00000243811 ∙ NCBI:140564 ∙ OMIM:609900 ∙ HGNC:17354 ∙ Uniprot:Q96AK3 ∙ 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 APOBEC3D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOBEC3D 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			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	0

Variants in APOBEC3D

This is a list of pathogenic ClinVar variants found in the APOBEC3D region.

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

Position	Type	Phenotype	Significance	ClinVar
22-39022859-G-A		not specified	Uncertain significance (Aug 30, 2021)
22-39022893-G-A		not specified	Uncertain significance (Jan 31, 2023)
22-39022977-C-T		not specified	Uncertain significance (Oct 06, 2021)
22-39022992-G-T		not specified	Likely benign (Dec 28, 2023)
22-39025079-C-T		not specified	Uncertain significance (Oct 27, 2021)
22-39025094-G-C		not specified	Uncertain significance (Dec 09, 2023)
22-39025107-T-G		not specified	Uncertain significance (Sep 15, 2021)
22-39025218-T-C		not specified	Uncertain significance (Apr 18, 2023)
22-39025220-G-T		not specified	Uncertain significance (Dec 13, 2023)
22-39025224-A-G		not specified	Uncertain significance (Aug 08, 2022)
22-39025233-A-G		not specified	Uncertain significance (Jun 11, 2021)
22-39025290-G-A		not specified	Uncertain significance (Jul 09, 2021)
22-39025294-G-T		not specified	Uncertain significance (May 10, 2022)
22-39025325-C-T		not specified	Uncertain significance (Jan 26, 2022)
22-39025336-C-G		not specified	Uncertain significance (May 01, 2024)
22-39025575-A-C		not specified	Uncertain significance (Jun 29, 2023)
22-39025653-C-T		not specified	Uncertain significance (Dec 09, 2023)
22-39025668-T-G		not specified	Uncertain significance (May 26, 2024)
22-39029431-G-A		not specified	Uncertain significance (Jan 30, 2024)
22-39029434-G-A		not specified	Uncertain significance (Sep 06, 2022)
22-39029463-G-C		not specified	Uncertain significance (May 26, 2024)
22-39029475-C-T		not specified	Uncertain significance (Apr 15, 2024)
22-39029490-T-G		not specified	Uncertain significance (Dec 13, 2021)
22-39029494-G-T		not specified	Uncertain significance (Aug 02, 2021)
22-39029505-G-C		not specified	Uncertain significance (Mar 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOBEC3D	protein_coding	protein_coding	ENST00000216099	7	18914

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.36e-18	0.000768	125631	0	116	125747	0.000461

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.09	279	232	1.20	0.0000142	2566
Missense in Polyphen		65	62.098	1.0467		774
Synonymous	-0.551	93	86.5	1.08	0.00000511	698
Loss of Function	-0.817	25	21.0	1.19	0.00000114	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00176	0.00174
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000217	0.000217
Finnish	0.00208	0.00208
European (Non-Finnish)	0.000224	0.000220
Middle Eastern	0.000217	0.000217
South Asian	0.000196	0.000196
Other	0.000327	0.000326

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 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. May inhibit the mobility of LTR and non-LTR retrotransposons. {ECO:0000269|PubMed:12859895, ECO:0000269|PubMed:20062055, ECO:0000269|PubMed:21835787, ECO:0000269|PubMed:22807680, ECO:0000269|PubMed:23097438, ECO:0000269|PubMed:23152537}.

Recessive Scores

• pRec: 0.0492

Intolerance Scores

• loftool: 0.792
• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.06

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.132
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00463

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;cytidine to uridine editing;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;zinc ion binding