APOBEC3D

gene
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Also known as ARP6APOBEC3DE

Summary

APOBEC3D (apolipoprotein B mRNA editing enzyme catalytic subunit 3D, HGNC:17354) is a protein-coding gene on chromosome 22q13.1, encoding DNA dC->dU-editing enzyme APOBEC-3D (Q96AK3). DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms.

This gene is a member of the cytidine deaminase gene family. It is one of a group of related genes found in a cluster, thought to result from gene duplication, on chromosome 22. Members of the cluster encode proteins that are structurally and functionally related to the C to U RNA-editing cytidine deaminase APOBEC1 and inhibit retroviruses, such as HIV, by deaminating cytosine residues in nascent retroviral cDNA.

Source: NCBI Gene 140564 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 88 total
  • MANE Select transcript: NM_152426

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17354
Approved symbolAPOBEC3D
Nameapolipoprotein B mRNA editing enzyme catalytic subunit 3D
Location22q13.1
Locus typegene with protein product
StatusApproved
AliasesARP6, APOBEC3DE
Ensembl geneENSG00000243811
Ensembl biotypeprotein_coding
OMIM609900
Entrez140564

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000216099, ENST00000427494, ENST00000622217, ENST00000891546, ENST00000951685

RefSeq mRNA: 2 — MANE Select: NM_152426 NM_001363781, NM_152426

CCDS: CCDS46709, CCDS87027

Canonical transcript exons

ENST00000216099 — 7 exons

ExonStartEnd
ENSE000018186163903219839033277
ENSE000038028933902282239023014
ENSE000038060823902555739025671
ENSE000038066683902507039025349
ENSE000038072123902936339029519
ENSE000038105463903169439031973
ENSE000038424883902112739021536

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 89.13.

FANTOM5 (CAGE): breadth broad, TPM avg 0.5507 / max 14.7425, expressed in 288 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1923040.5507288

Top tissues by expression

135 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009489.13gold quality
lymph nodeUBERON:000002984.49gold quality
spleenUBERON:000210680.10gold quality
bone marrow cellCL:000209279.21gold quality
bloodUBERON:000017878.86gold quality
vermiform appendixUBERON:000115478.72gold quality
leukocyteCL:000073875.16gold quality
right uterine tubeUBERON:000130274.99gold quality
monocyteCL:000057674.24gold quality
bone marrowUBERON:000237173.53gold quality
gall bladderUBERON:000211073.33gold quality
rectumUBERON:000105272.81gold quality
tonsilUBERON:000237272.80gold quality
duodenumUBERON:000211472.05gold quality
stromal cell of endometriumCL:000225572.04gold quality
colonic epitheliumUBERON:000039771.63gold quality
small intestine Peyer’s patchUBERON:000345471.45gold quality
small intestineUBERON:000210871.17gold quality
right ovaryUBERON:000211871.17gold quality
right adrenal gland cortexUBERON:003582771.17gold quality
fallopian tubeUBERON:000388971.02gold quality
smooth muscle tissueUBERON:000113570.45gold quality
ovaryUBERON:000099270.38gold quality
endocervixUBERON:000045870.01gold quality
left ovaryUBERON:000211969.95gold quality
uterine cervixUBERON:000000269.65gold quality
mucosa of transverse colonUBERON:000499169.52gold quality
right adrenal glandUBERON:000123369.46gold quality
left adrenal glandUBERON:000123469.30gold quality
placentaUBERON:000198769.22gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-MTAB-6058no31.93
E-ANND-3no1.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

44 targeting APOBEC3D, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4283100.0066.422097
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-311999.9271.342390
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-465899.7764.94514
HSA-MIR-6790-5P99.7765.24505
HSA-MIR-3150A-3P99.7664.441640
HSA-MIR-6763-5P99.7664.681767
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-317599.6566.302031
HSA-MIR-613499.6365.681537
HSA-MIR-443799.5265.291266
HSA-MIR-6731-5P99.2867.422375
HSA-MIR-808599.2867.562362
HSA-MIR-371A-5P99.0866.511914
HSA-MIR-328-5P99.0864.651000
HSA-MIR-6749-3P99.0065.731443
HSA-MIR-367-5P98.8467.18902
HSA-MIR-887-5P98.8265.901347
HSA-MIR-5197-3P98.7167.051905
HSA-MIR-6885-5P98.7164.33902
HSA-MIR-5008-5P98.4265.871019
HSA-MIR-3130-5P98.1466.00711
HSA-MIR-340-3P98.1168.25679
HSA-MIR-6827-3P98.0872.27651
HSA-MIR-30C-1-3P97.8066.361499

Literature-anchored findings (GeneRIF, showing 10)

  • Distinct determinants in HIV-1 Vif and human APOBEC3 proteins are required for the suppression of diverse host anti-viral proteins. (PMID:19088851)
  • endogenous levels of APOBEC3D, APOBEC3F, and APOBEC3G combine to restrict Vif-deficient HIV-1 and cause the hallmark dinucleotide hypermutation patterns in in the nonpermissive T cell line CEM2n (PMID:22807680)
  • The authors conclude that APOBEC3G exerts a greater restriction effect on HIV-1 than APOBEC3F and APOBEC3DE. (PMID:23097438)
  • We found that two common novel polymorphisms in APOBEC3D decrease antiviral activity against HIV-1, and one polymorphism decreases activity against Alu retrotransposons in the human population. (PMID:23755966)
  • APOBEC3 deaminases upregulated by IFN-beta induce E2 hypermutation of HPV16 in cervical keratinocytes. (PMID:24227842)
  • APOBEC3D/F and APOBEC3G fundamentally work as restriction factors against HIV-1 in vivo (PMID:25330146)
  • APOBEC3DE binds to itself, APOBEC3F, and APOBEC3G and antagonizes APOBEC3F and, to a lesser extent, APOBEC3G restriction of hepatitis B virus replication. (PMID:27289067)
  • APOBEC3DE inhibits human LINE-1 retrotransposition. (PMID:27428332)
  • These results indicate that APOBEC3 proteins can be copackaged and can comutate the same genomes, and can cooperate to inhibit HIV replication. (PMID:27439715)
  • Alternative splicing of APOBEC3D generates functional diversity and its role as a DNA mutator. (PMID:32533515)

Cross-species orthologs

0 orthologs

Paralogs (9): APOBEC3H (ENSG00000100298), APOBEC1 (ENSG00000111701), AICDA (ENSG00000111732), APOBEC2 (ENSG00000124701), APOBEC3A (ENSG00000128383), APOBEC3F (ENSG00000128394), APOBEC3B (ENSG00000179750), APOBEC3G (ENSG00000239713), APOBEC3C (ENSG00000244509)

Protein

Protein identifiers

DNA dC->dU-editing enzyme APOBEC-3DQ96AK3 (reviewed: Q96AK3)

All UniProt accessions (4): A0A087WX48, B2CML4, Q96AK3, Q6ICH2

UniProt curated annotations — full annotation on UniProt →

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 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. Also inhibits the mobility of LTR and non-LTR retrotransposons. (Microbial infection) Enhances hepatitis B virus/HBV replication by excluding restriction factors APOBEC3F and APOBEC3G from HBV capsids.

Subunit / interactions. Can form homo- and heterodimers with APOBEC3F and APOBEC3G. Interacts with L1RE1; this interaction inhibits LINE-1 retrotransposition. (Microbial infection) Interacts with HIV-1 Vif. This interaction triggers APOBEC3D polyubiquitylation and degradation by the 26S proteasome.

Subcellular location. Cytoplasm. P-body.

Tissue specificity. Expressed in lymphoid organs. Also detected in non-lymphoid tissues including lung.

Activity regulation. (Microbial infection) Antiviral activity is neutralized by the HIV-1 virion infectivity factor (Vif), that prevents its incorporation into progeny virions by both inhibiting its translation and/or by inducing its ubiquitination and subsequent degradation by the 26S proteasome.

Domain organisation. The CMP/dCMP deaminase domain 1 mediates RNA binding, RNA-dependent oligomerization and virion incorporation whereas the CMP/dCMP deaminase domain 2 confers deoxycytidine deaminase activity and substrate sequence specificity.

Miscellaneous. It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22.

Similarity. Belongs to the cytidine and deoxycytidylate deaminase family.

RefSeq proteins (2): NP_001350710, NP_689639* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002125CMP_dCMP_domDomain
IPR016192APOBEC/CMP_deaminase_Zn-bdBinding_site
IPR016193Cytidine_deaminase-likeHomologous_superfamily
IPR050610APOBEC_Cyt_DeaminaseFamily

Pfam: PF18782

Enzyme classification (BRENDA):

  • EC 3.5.4.38 — single-stranded DNA cytosine deaminase (BRENDA: 8 organisms, 58 substrates, 4 inhibitors, 11 Km, 10 kcat entries)

Substrate kinetics (BRENDA)

2 substrates with measured Km, best-characterized 2. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
CCCA0.001–0.0735
TTCA0.001–0.0195

Catalyzed reactions (Rhea), 1 shown:

  • a 2’-deoxycytidine in single-stranded DNA + H2O + H(+) = a 2’-deoxyuridine in single-stranded DNA + NH4(+) (RHEA:50948)

UniProt features (23 total): mutagenesis site 13, binding site 6, domain 2, chain 1, active site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96AK3-F187.720.64

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 264 (proton donor)

Ligand- & substrate-binding residues (6): 78; 109; 112; 262; 293; 296

Mutagenesis-validated functional residues (13):

PositionPhenotype
140about two-third loss of anti hiv-1 activity.
264no effect on vif binding.
268resistant to hiv-1 vif and abolishes vif binding.
271resistant to hiv-1 vif and abolishes vif binding.
272resistant to hiv-1 vif and reduces vif binding.
275–276resistant to hiv-1 vif and abolishes vif binding.
277resistant to hiv-1 vif and reduces vif binding.
282resistant to hiv-1 vif and abolishes vif binding.
302resistant to hiv-1 vif and abolishes vif binding.
303resistant to hiv-1 vif and abolishes vif binding.
307resistant to hiv-1 vif and abolishes vif binding.
337resistant to hiv-1 vif and reduces vif binding.
337resistant to hiv-1 vif and abolishes vif binding.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 76 (showing top): GOBP_NEGATIVE_REGULATION_OF_VIRAL_PROCESS, GOBP_DNA_MODIFICATION, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_RNA_MODIFICATION, GOBP_VIRAL_GENOME_REPLICATION, GOBP_VIRAL_LIFE_CYCLE, DOUGLAS_BMI1_TARGETS_DN, GOBP_DEFENSE_RESPONSE_TO_VIRUS, GOBP_REGULATION_OF_VIRAL_GENOME_REPLICATION, GOBP_NEGATIVE_REGULATION_OF_VIRAL_GENOME_REPLICATION, GOBP_RESPONSE_TO_VIRUS, GOCC_RIBONUCLEOPROTEIN_GRANULE, chr22q13, GOBP_DNA_METABOLIC_PROCESS, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_CARBON_NITROGEN_BUT_NOT_PEPTIDE_BONDS_IN_CYCLIC_AMIDINES

GO Biological Process (9): cytidine to uridine editing (GO:0016554), clearance of foreign intracellular DNA (GO:0044355), innate immune response (GO:0045087), negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869), defense response to virus (GO:0051607), DNA cytosine deamination (GO:0070383), immune system process (GO:0002376), negative regulation of macromolecule biosynthetic process (GO:0010558), defense response to symbiont (GO:0140546)

GO Molecular Function (6): RNA binding (GO:0003723), cytidine deaminase activity (GO:0004126), zinc ion binding (GO:0008270), catalytic activity (GO:0003824), hydrolase activity (GO:0016787), metal ion binding (GO:0046872)

GO Cellular Component (3): P-body (GO:0000932), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
base conversion or substitution editing1
clearance of foreign intracellular nucleic acids1
immune response1
defense response to symbiont1
single stranded viral RNA replication via double stranded DNA intermediate1
negative regulation of viral genome replication1
regulation of single stranded viral RNA replication via double stranded DNA intermediate1
negative regulation of RNA biosynthetic process1
defense response1
response to virus1
DNA deamination1
biological_process1
macromolecule biosynthetic process1
negative regulation of biosynthetic process1
regulation of macromolecule biosynthetic process1
negative regulation of macromolecule metabolic process1
defense response to other organism1
nucleic acid binding1
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines1
deaminase activity1
transition metal ion binding1
molecular_function1
catalytic activity1
cation binding1
cytoplasmic ribonucleoprotein granule1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

940 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
APOBEC3DCDAP32320866
APOBEC3DAPOBEC4Q8WW27819
APOBEC3DCBFBQ13951624
APOBEC3DCUL5Q93034600
APOBEC3DTRIM5Q9C035554
APOBEC3DELOBQ15370543
APOBEC3DSAMHD1Q9Y3Z3492
APOBEC3DAPOBP04114490
APOBEC3DBST2Q10589487
APOBEC3DUNGP13051481
APOBEC3DRNF7Q9UBF6481
APOBEC3DELOCQ15369465
APOBEC3DIL17CQ9P0M4396
APOBEC3DADARP55265378
APOBEC3DA1CFQ9NQ94373

IntAct

8 interactions, top by confidence:

ABTypeScore
Brwd3WDR91psi-mi:“MI:0914”(association)0.350
Gtf3c4YTHDC1psi-mi:“MI:0914”(association)0.350
MecomESYT2psi-mi:“MI:0914”(association)0.350
APOBEC3DIGF2BP3psi-mi:“MI:0914”(association)0.350
NRBM47psi-mi:“MI:0914”(association)0.350
GATA2EFCAB5psi-mi:“MI:0914”(association)0.350

ESM2 similar proteins: A2VDP6, A9QA56, G1SRW8, P0C7P3, P31941, P60704, P60705, Q08AF3, Q19Q52, Q1WBT4, Q2PT36, Q3SYR3, Q4VDN5, Q5RCA5, Q5XI89, Q68D06, Q694B4, Q694B5, Q694B6, Q694B7, Q694B8, Q694B9, Q694C0, Q694C1, Q694C2, Q694C4, Q694C5, Q6NTF7, Q75W64, Q7YR23, Q7YR24, Q7YR25, Q7Z7L1, Q8IUX4, Q8IXQ6, Q969Y0, Q96AK3, Q99J72, Q9BQQ7, Q9GZX7

Diamond homologs: A9QA56, P31941, P47855, P60704, P60705, Q19Q52, Q1WBT4, Q2PT36, Q3SYR3, Q4VDN5, Q694B4, Q694B5, Q694B6, Q694B7, Q694B8, Q694B9, Q694C0, Q694C1, Q694C2, Q694C4, Q694C5, Q6NTF7, Q75W64, Q7YR23, Q7YR24, Q7YR25, Q8IUX4, Q96AK3, Q99J72, Q9EQP0, Q9GZX7, Q9HC16, Q9NRW3, Q9UH17, Q9WV35, Q9WVE0, Q9Y235, P38483, P41238, P51908

SIGNOR signaling

1 interactions.

AEffectBMechanism
APOBEC3Dup-regulates“Clearance_of_foreign intracellular_DNA”

Disease & clinical

Clinical variants and AI predictions

ClinVar

88 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance69
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

949 predictions. Top by Δscore:

VariantEffectΔscore
22:39023011:GGAG:Gdonor_gain1.0000
22:39023012:G:GTdonor_gain1.0000
22:39032195:CAG:Cacceptor_loss1.0000
22:39032196:A:AGacceptor_gain1.0000
22:39032196:A:Tacceptor_loss1.0000
22:39032197:G:GAacceptor_gain1.0000
22:39032197:GATT:Gacceptor_gain1.0000
22:39023015:GT:Gdonor_loss0.9900
22:39023016:TAA:Tdonor_loss0.9900
22:39031770:C:Gacceptor_gain0.9900
22:39031940:G:GTdonor_gain0.9900
22:39031973:GGTG:Gdonor_loss0.9900
22:39031974:G:GAdonor_loss0.9900
22:39031975:T:Adonor_loss0.9900
22:39032197:GA:Gacceptor_gain0.9900
22:39032197:GAT:Gacceptor_gain0.9900
22:39032197:GATTT:Gacceptor_gain0.9900
22:39022813:T:TAacceptor_gain0.9800
22:39022820:A:AGacceptor_gain0.9800
22:39022821:G:GGacceptor_gain0.9800
22:39022916:G:GTdonor_gain0.9800
22:39023012:GAG:Gdonor_gain0.9800
22:39023015:G:GGdonor_gain0.9800
22:39029409:A:AGacceptor_gain0.9800
22:39029410:A:Gacceptor_gain0.9800
22:39031774:CTACG:Cacceptor_gain0.9800
22:39031974:G:GGdonor_gain0.9800
22:39022821:GA:Gacceptor_gain0.9700
22:39022994:C:Adonor_gain0.9700
22:39025123:T:TAacceptor_gain0.9700

AlphaMissense

2578 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:39022865:T:CF21L0.972
22:39022867:T:AF21L0.972
22:39022867:T:GF21L0.972
22:39025214:T:CF119L0.970
22:39025216:C:AF119L0.970
22:39025216:C:GF119L0.970
22:39029454:T:CF233L0.970
22:39029456:C:AF233L0.970
22:39029456:C:GF233L0.970
22:39025166:T:CF103L0.969
22:39025168:T:AF103L0.969
22:39025168:T:GF103L0.969
22:39031838:T:CF303L0.966
22:39031840:C:AF303L0.966
22:39031840:C:GF303L0.966
22:39022853:T:CF17L0.964
22:39022855:C:AF17L0.964
22:39022855:C:GF17L0.964
22:39029406:T:CF217L0.964
22:39029408:T:AF217L0.964
22:39029408:T:GF217L0.964
22:39025559:T:CF165L0.962
22:39025561:T:AF165L0.962
22:39025561:T:GF165L0.962
22:39029508:T:CF251L0.961
22:39029510:C:AF251L0.961
22:39029510:C:GF251L0.961
22:39025106:T:CF83L0.959
22:39025108:C:AF83L0.959
22:39025108:C:GF83L0.959

dbSNP variants (sampled 300 via entrez): RS1000336007 (22:39026238 C>T), RS1000485119 (22:39031060 G>A), RS1000951953 (22:39023185 A>G), RS1001185583 (22:39029491 TC>T), RS1001224052 (22:39032066 G>A,T), RS1001295741 (22:39023453 T>C), RS1001399987 (22:39025593 A>C), RS1001800557 (22:39020822 C>G), RS1001867103 (22:39029741 G>T), RS1002354832 (22:39022304 C>G), RS1002584405 (22:39020351 C>A,T), RS1002959925 (22:39032141 A>G), RS1003003154 (22:39020106 G>C), RS1003295276 (22:39033247 A>G), RS1003619991 (22:39033538 C>T)

Disease associations

OMIM: gene MIM:609900 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, increases expression, increases methylation3
triphenyl phosphateaffects expression1
bisphenol Adecreases methylation1
sodium arsenitedecreases expression, increases abundance1
aflatoxin B2decreases methylation1
nickel sulfateincreases expression1
Arsenicdecreases expression, increases abundance1
Cisplatinincreases expression1
Dactinomycinincreases expression1
Silicon Dioxidedecreases expression1
Smokedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Tretinoinincreases expression1
Urethanedecreases expression1
Valproic Acidincreases methylation1
Copper Sulfateincreases expression1
S-Nitrosoglutathioneincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.