Seroatlas · Human Serome Atlas

APOBEC3D

DNA dC->dU-editing enzyme APOBEC-3D

Also known as: ABC3D_HUMAN, APOBEC3DE, APOBEC3E, ARP6

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q96AK3
Gene: APOBEC3D
Ensembl: ENSG00000243811
Chromosome: 22
Canonical length: 386 aa
Protein class: Enzymes, Predicted intracellular proteins

OverviewNCBI Gene

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. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

386 residues, UniProt reviewed canonical sequence.

>Q96AK3|APOBEC3D
     1  MNPQIRNPME RMYRDTFYDN FENEPILYGR SYTWLCYEVK IKRGRSNLLW DTGVFRGPVL
    61  PKRQSNHRQE VYFRFENHAE MCFLSWFCGN RLPANRRFQI TWFVSWNPCL PCVVKVTKFL
   121  AEHPNVTLTI SAARLYYYRD RDWRWVLLRL HKAGARVKIM DYEDFAYCWE NFVCNEGQPF
   181  MPWYKFDDNY ASLHRTLKEI LRNPMEAMYP HIFYFHFKNL LKACGRNESW LCFTMEVTKH
   241  HSAVFRKRGV FRNQVDPETH CHAERCFLSW FCDDILSPNT NYEVTWYTSW SPCPECAGEV
   301  AEFLARHSNV NLTIFTARLC YFWDTDYQEG LCSLSQEGAS VKIMGYKDFV SCWKNFVYSD
   361  DEPFKPWKGL QTNFRLLKRR LREILQ

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against APOBEC3D can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.27
Highest tissue expression: 14 nTPM

Expression across tissuesHPA

Tissue

lymph node: 14 nTPM
spleen: 13 nTPM
tonsil: 13 nTPM
appendix: 8.1 nTPM
thymus: 7.1 nTPM
small intestine: 6.1 nTPM

Single-cell type

parietal cells: 5.3 nCPM
gastric chief cells: 3.3 nCPM
ependymal cells: 2.7 nCPM
respiratory ionocytes: 2.5 nCPM
t-cells: 2.3 nCPM
epididymal clear cells: 2 nCPM

Immune cell

gdT-cell: 7.8 nTPM
memory CD8 T-cell: 7.1 nTPM
memory B-cell: 6.6 nTPM
naive B-cell: 6.5 nTPM
non-classical monocyte: 6.4 nTPM
memory CD4 T-cell: 5.7 nTPM

Brain region

medulla oblongata: 4.1 nTPM
cerebellum: 3.7 nTPM
spinal cord: 3.6 nTPM
white matter: 3.6 nTPM
cerebral cortex: 3.4 nTPM
amygdala: 3.2 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 1.66
gnomAD pLI: 0
gnomAD missense Z: -1.09
DepMap mean gene effect: 0.01
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of APOBEC3D in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

L1RE1

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads APOBEC3D as an antibody target. Whether an autoantibody or antibody against APOBEC3D could matter depends on whether native APOBEC3D is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

APOBEC3D is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label APOBEC3D as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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