Seroatlas · Human Serome Atlas

DDX56

Probable ATP-dependent RNA helicase DDX56

Also known as: DDX56_HUMAN, NOH61

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

Protein identityUniProt · HPA

UniProt accession: Q9NY93
Gene: DDX56
Ensembl: ENSG00000136271
Chromosome: 7
Canonical length: 547 aa
Protein class: Enzymes, Predicted intracellular proteins
Subcellular location: Nucleoli,Mitotic chromosome

OverviewNCBI Gene

This gene encodes a member of the DEAD box protein family. DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The protein encoded by this gene shows ATPase activity in the presence of polynucleotides and associates with nucleoplasmic 65S preribosomal particles. This gene may be involved in ribosome synthesis, most likely during assembly of the large 60S ribosomal subunit. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2012]

Canonical amino-acid sequenceUniProt

547 residues, UniProt reviewed canonical sequence.

>Q9NY93|DDX56
     1  MEDSEALGFE HMGLDPRLLQ AVTDLGWSRP TLIQEKAIPL ALEGKDLLAR ARTGSGKTAA
    61  YAIPMLQLLL HRKATGPVVE QAVRGLVLVP TKELARQAQS MIQQLATYCA RDVRVANVSA
   121  AEDSVSQRAV LMEKPDVVVG TPSRILSHLQ QDSLKLRDSL ELLVVDEADL LFSFGFEEEL
   181  KSLLCHLPRI YQAFLMSATF NEDVQALKEL ILHNPVTLKL QESQLPGPDQ LQQFQVVCET
   241  EEDKFLLLYA LLKLSLIRGK SLLFVNTLER SYRLRLFLEQ FSIPTCVLNG ELPLRSRCHI
   301  ISQFNQGFYD CVIATDAEVL GAPVKGKRRG RGPKGDKASD PEAGVARGID FHHVSAVLNF
   361  DLPPTPEAYI HRAGRTARAN NPGIVLTFVL PTEQFHLGKI EELLSGENRG PILLPYQFRM
   421  EEIEGFRYRC RDAMRSVTKQ AIREARLKEI KEELLHSEKL KTYFEDNPRD LQLLRHDLPL
   481  HPAVVKPHLG HVPDYLVPPA LRGLVRPHKK RKKLSSSCRK AKRAKSQNPL RSFKHKGKKF
   541  RPTAKPS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against DDX56 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): 0.3
Highest tissue expression: 46 nTPM

Expression across tissuesHPA

Tissue

skeletal muscle: 46 nTPM
liver: 43 nTPM
choroid plexus: 40 nTPM
esophagus: 37 nTPM
skin: 36 nTPM
spleen: 36 nTPM

Single-cell type

esophageal basal cells: 73 nCPM
cytotrophoblasts: 67 nCPM
migrating cytotrophoblasts: 61 nCPM
esophageal suprabasal cells: 59 nCPM
extravillous trophoblasts: 55 nCPM
decidual stromal cells: 54 nCPM

Immune cell

non-classical monocyte: 68 nTPM
intermediate monocyte: 66 nTPM
myeloid DC: 64 nTPM
NK-cell: 63 nTPM
total PBMC: 60 nTPM
naive B-cell: 55 nTPM

Brain region

white matter: 17 nTPM
pons: 17 nTPM
medulla oblongata: 17 nTPM
basal ganglia: 16 nTPM
cerebral cortex: 16 nTPM
cerebellum: 16 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): 0.85
gnomAD pLI: 0
gnomAD missense Z: -0.23
DepMap mean gene effect: -1.99
DepMap dependency class: pan

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 12% 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 DDX56 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads DDX56 as an antibody target. Whether an autoantibody or antibody against DDX56 could matter depends on whether native DDX56 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

DDX56 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 DDX56 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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