DDX28

gene
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Also known as MDDX28FLJ11282

Summary

DDX28 (DEAD-box helicase 28, HGNC:17330) is a protein-coding gene on chromosome 16q22.1, encoding Probable ATP-dependent RNA helicase DDX28 (Q9NUL7). Plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. It is a selective cancer dependency (DepMap: 22.6% of cell lines).

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 the DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene is intronless. It encodes an RNA-dependent ATPase. The encoded protein is localized in the mitochondria and the nucleus, and can be transported between the mitochondria and the nucleus.

Source: NCBI Gene 55794 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 74 total
  • Cancer dependency (DepMap): dependent in 22.6% of screened cell lines
  • MANE Select transcript: NM_018380

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17330
Approved symbolDDX28
NameDEAD-box helicase 28
Location16q22.1
Locus typegene with protein product
StatusApproved
AliasesMDDX28, FLJ11282
Ensembl geneENSG00000182810
Ensembl biotypeprotein_coding
OMIM607618
Entrez55794

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000332395

RefSeq mRNA: 1 — MANE Select: NM_018380 NM_018380

CCDS: CCDS10858

Canonical transcript exons

ENST00000332395 — 1 exons

ExonStartEnd
ENSE000013006726802091668023232

Expression profiles

Bgee: expression breadth ubiquitous, 248 present calls, max score 93.57.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.7764 / max 52.2658, expressed in 1730 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1578476.77641730

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
oocyteCL:000002393.57gold quality
secondary oocyteCL:000065591.61gold quality
endometrium epitheliumUBERON:000481183.27silver quality
gastrocnemiusUBERON:000138882.88gold quality
granulocyteCL:000009482.85gold quality
monocyteCL:000057682.68gold quality
leukocyteCL:000073882.68gold quality
mononuclear cellCL:000084282.62gold quality
muscle of legUBERON:000138381.77gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.62gold quality
right adrenal gland cortexUBERON:003582781.50gold quality
right adrenal glandUBERON:000123380.98gold quality
left adrenal glandUBERON:000123480.11gold quality
apex of heartUBERON:000209879.73gold quality
gingival epitheliumUBERON:000194979.69gold quality
hindlimb stylopod muscleUBERON:000425279.65gold quality
muscle organUBERON:000163079.41gold quality
left adrenal gland cortexUBERON:003582579.18gold quality
amniotic fluidUBERON:000017379.02gold quality
adrenal cortexUBERON:000123578.28gold quality
mucosa of transverse colonUBERON:000499178.21gold quality
adrenal glandUBERON:000236977.91gold quality
heart left ventricleUBERON:000208477.90gold quality
gingivaUBERON:000182877.48gold quality
cardiac ventricleUBERON:000208277.46gold quality
bloodUBERON:000017877.40gold quality
placentaUBERON:000198776.78gold quality
skin of abdomenUBERON:000141676.68gold quality
skin of legUBERON:000151176.58gold quality
bone marrowUBERON:000237176.53gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes2.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting DDX28, 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-569699.9872.364487
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-568099.9169.833421
HSA-MIR-94499.8270.853042
HSA-MIR-472999.6972.184233
HSA-MIR-7161-5P99.6868.921592
HSA-MIR-548U99.6567.781463
HSA-MIR-942-5P99.4168.401977
HSA-MIR-520E-5P99.2768.901513
HSA-MIR-3691-3P97.9065.97791
HSA-MIR-7112-3P97.6768.77948
HSA-MIR-431-5P96.1666.50652
HSA-MIR-7108-3P94.3764.79183
HSA-MIR-425890.6862.19164

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 22.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • Three domains in the N-terminal half of the protein and its RNA binding ability were essential for nucleolar localization as well as transcription-inhibition-dependent localization to nuclear subcompartments and two were the nuclear localization signal (PMID:12663657)
  • The authors have identified the DEAD box protein family member DDX28 as an interactor and negative regulator of HIF-2alpha that suppresses HIF-2alpha’s ability to activate eIF4E2-directed translation. (PMID:31907278)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioddx28ENSDARG00000060411
mus_musculusDdx28ENSMUSG00000045538
rattus_norvegicusDdx28ENSRNOG00000019817
drosophila_melanogasterDbp21E2FBGN0086130

Paralogs (38): DDX20 (ENSG00000064703), DDX3Y (ENSG00000067048), DDX1 (ENSG00000079785), DDX43 (ENSG00000080007), DDX18 (ENSG00000088205), DDX24 (ENSG00000089737), DDX17 (ENSG00000100201), DDX49 (ENSG00000105671), DDX50 (ENSG00000107625), DDX5 (ENSG00000108654), DDX25 (ENSG00000109832), DDX6 (ENSG00000110367), DDX55 (ENSG00000111364), DDX59 (ENSG00000118197), DDX54 (ENSG00000123064), DDX39A (ENSG00000123136), DDX27 (ENSG00000124228), DDX31 (ENSG00000125485), DDX56 (ENSG00000136271), EIF4A3 (ENSG00000141543), DDX46 (ENSG00000145833), DDX4 (ENSG00000152670), EIF4A2 (ENSG00000156976), DDX19B (ENSG00000157349), EIF4A1 (ENSG00000161960), DDX21 (ENSG00000165732), DDX19A (ENSG00000168872), TDRD12 (ENSG00000173809), DDX23 (ENSG00000174243), DDX10 (ENSG00000178105), DDX41 (ENSG00000183258), DDX53 (ENSG00000184735), DDX51 (ENSG00000185163), DDX42 (ENSG00000198231), DDX39B (ENSG00000198563), DDX47 (ENSG00000213782), DDX3X (ENSG00000215301), DDX52 (ENSG00000278053)

Protein

Protein identifiers

Probable ATP-dependent RNA helicase DDX28Q9NUL7 (reviewed: Q9NUL7)

Alternative names: Mitochondrial DEAD box protein 28

All UniProt accessions (1): Q9NUL7

UniProt curated annotations — full annotation on UniProt →

Function. Plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. May be involved in RNA processing or transport. Has RNA and Mg(2+)-dependent ATPase activity.

Subunit / interactions. Monomer. Found in a complex with GRSF1, DHX30, FASTKD2 and FASTKD5. Associates with the 16S mitochondrial rRNA (16S mt-rRNA) and with the mitochondrial ribosome large subunit (39S).

Subcellular location. Nucleus. Mitochondrion. Mitochondrion matrix. Mitochondrion nucleoid.

Tissue specificity. Expressed in all tissues tested, including brain, placenta, lung, liver, skeletal muscle, kidney, pancreas, leukocytes, colon, small intestine, ovary and prostate.

Similarity. Belongs to the DEAD box helicase family.

RefSeq proteins (1): NP_060850* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001650Helicase_C-likeDomain
IPR011545DEAD/DEAH_box_helicase_domDomain
IPR014001Helicase_ATP-bdDomain
IPR014014RNA_helicase_DEAD_Q_motifDomain
IPR027417P-loop_NTPaseHomologous_superfamily
IPR050079DEAD_box_RNA_helicaseFamily

Pfam: PF00270, PF00271

Catalyzed reactions (Rhea), 1 shown:

  • ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)

UniProt features (10 total): short sequence motif 5, domain 2, chain 1, binding site 1, sequence variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
9UU7X-RAY DIFFRACTION2.6
7OI6ELECTRON MICROSCOPY5.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NUL7-F183.490.48

Functional residue map

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

Ligand- & substrate-binding residues (1): 172–179

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 144 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, GOBP_RIBOSOME_BIOGENESIS, chr16q22, GOBP_RIBOSOME_ASSEMBLY, GOBP_RIBOSOMAL_LARGE_SUBUNIT_ASSEMBLY, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, CREB_Q2_01, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, DELASERNA_MYOD_TARGETS_DN, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, CREBP1CJUN_01, SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY

GO Biological Process (2): mitochondrial large ribosomal subunit assembly (GO:1902775), ribosome biogenesis (GO:0042254)

GO Molecular Function (9): RNA binding (GO:0003723), RNA helicase activity (GO:0003724), ATP binding (GO:0005524), ATP hydrolysis activity (GO:0016887), rRNA binding (GO:0019843), nucleotide binding (GO:0000166), nucleic acid binding (GO:0003676), helicase activity (GO:0004386), hydrolase activity (GO:0016787)

GO Cellular Component (8): nucleoplasm (GO:0005654), nucleolus (GO:0005730), mitochondrion (GO:0005739), cytosol (GO:0005829), ribonucleoprotein granule (GO:0035770), mitochondrial nucleoid (GO:0042645), nucleus (GO:0005634), mitochondrial matrix (GO:0005759)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular membraneless organelle3
ATP-dependent activity2
nuclear lumen2
cellular anatomical structure2
cytoplasm2
intracellular membrane-bounded organelle2
mitochondrion2
ribosomal large subunit assembly1
mitochondrial ribosome assembly1
ribonucleoprotein complex biogenesis1
nucleic acid binding1
helicase activity1
ATP-dependent activity, acting on RNA1
catalytic activity, acting on RNA1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
ribonucleoside triphosphate phosphatase activity1
RNA binding1
nucleoside phosphate binding1
heterocyclic compound binding1
binding1
nucleic acid conformation isomerase activity1
catalytic activity, acting on a nucleic acid1
catalytic activity1
supramolecular complex1
mitochondrial matrix1
nucleoid1
intracellular organelle lumen1

Protein interactions and networks

STRING

3451 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DDX28MRM3Q9HC36802
DDX28DHX30Q7L2E3792
DDX28MTERF3Q96E29777
DDX28GRSF1Q12849758
DDX28GTPBP10A4D1E9754
DDX28ERAL1O75616752
DDX28MTG1Q9BT17740
DDX28MALSU1Q96EH3731
DDX28GTPBP6O43824691
DDX28MTG2Q9H4K7678
DDX28FASTKD2Q9NYY8671
DDX28NSUN4Q96CB9669
DDX28MTERF4Q7Z6M4667
DDX28GTPBP8Q8N3Z3666
DDX28RPUSD3Q6P087639

IntAct

119 interactions, top by confidence:

ABTypeScore
YBX1HNRNPRpsi-mi:“MI:0915”(physical association)0.770
MRPS30GTPBP10psi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
DDX28PTCD1psi-mi:“MI:0914”(association)0.530
NNOP56psi-mi:“MI:0914”(association)0.530
NRBM47psi-mi:“MI:0914”(association)0.530
MRPL2GTPBP10psi-mi:“MI:0914”(association)0.530
PSME1POLR3Apsi-mi:“MI:0914”(association)0.530
CLEC11AVWA8psi-mi:“MI:0914”(association)0.530
MRPL13GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL18GTPBP10psi-mi:“MI:0914”(association)0.530
ZNRD2MYO9Apsi-mi:“MI:0914”(association)0.530
ABT1ZNF316psi-mi:“MI:0914”(association)0.530
MAGEB2GTPBP10psi-mi:“MI:0914”(association)0.530
PNMA2CCDC85Cpsi-mi:“MI:0914”(association)0.530
ZNRD2CCDC85Cpsi-mi:“MI:0914”(association)0.530
NDUFAB1MIEF1psi-mi:“MI:0915”(physical association)0.490
Ybx1MRPS18Bpsi-mi:“MI:0915”(physical association)0.400
Ubr5SFI1psi-mi:“MI:0914”(association)0.350
Ercc6lRPL17psi-mi:“MI:0914”(association)0.350
MPHOSPH8HCFC1psi-mi:“MI:0914”(association)0.350
MATR3BCLAF3psi-mi:“MI:0914”(association)0.350
EMC2TBL2psi-mi:“MI:0914”(association)0.350
HSCBRBP5psi-mi:“MI:0914”(association)0.350
k8RGL2psi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
CUL3PXDNLpsi-mi:“MI:0914”(association)0.350

BioGRID (280): DDX28 (Affinity Capture-MS), DDX28 (Affinity Capture-MS), DDX28 (Affinity Capture-MS), DDX28 (Affinity Capture-MS), DDX28 (Affinity Capture-MS), DDX28 (Affinity Capture-MS), DDX28 (Affinity Capture-MS), DDX28 (Affinity Capture-MS), DDX28 (Affinity Capture-MS), DDX28 (Affinity Capture-MS), DDX28 (Affinity Capture-MS), RPUSD4 (Affinity Capture-MS), METAP2 (Affinity Capture-MS), TRUB2 (Affinity Capture-MS), PTCD1 (Affinity Capture-MS)

ESM2 similar proteins: A0JMH2, A5K3F9, A6XGL0, A8IRK7, B0BNM1, B7QDG3, C3YDS7, D3ZEY4, D3ZU57, E2QRY6, E7FCP8, F6W8I0, F7DL67, F7FIH8, O14976, O88444, P16386, P51828, P52333, P52824, P53370, P70563, Q08828, Q0PIT9, Q17QN2, Q2KI13, Q2KI24, Q3TIU4, Q4R4T6, Q5GA22, Q5RAR6, Q5ZHX9, Q6AXQ5, Q6DHK1, Q6L8Q7, Q6P5E8, Q6QRN6, Q8CH40, Q8K2J9, Q8K4Z3

Diamond homologs: A1CHL3, A1CR32, A1CX72, A1D405, A2QIL2, A2RB17, A2XKG2, A3LQ55, A3LS22, A3LSN3, A4RGD1, A5DLE0, A5DQF1, A5E6W6, A5F3R4, A6QRQ7, A6RW56, A6ZSX1, A6ZT77, A7EML8, A7TK63, A7TS37, B0RWT6, C3LQR1, P0A9P6, P0A9P7, P0A9P8, P0CR00, P0CR01, P25888, P33906, P34580, P38712, P38719, P46942, Q0CIQ3, Q0U6X2, Q0UK12, Q0UWC8, Q1E1N5

SIGNOR signaling

1 interactions.

AEffectBMechanism
DDX28up-regulatesStress_granules

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 128 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Mitochondrial ribosome-associated quality control1015.7×3e-07
Mitochondrial translation initiation813.0×2e-05
Mitochondrial translation elongation813.0×2e-05
Mitochondrial translation712.3×9e-05
Mitochondrial translation termination811.3×4e-05
rRNA processing59.4×9e-03
Translation108.0×4e-05
mRNA Polyadenylation66.8×1e-02

GO biological processes:

GO termPartnersFoldFDR
mitochondrial large ribosomal subunit assembly546.3×2e-05
mitochondrial translation1016.2×4e-07
translation87.7×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance72
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

62 predictions. Top by Δscore:

VariantEffectΔscore
16:68023171:G:Tdonor_gain0.9900
16:68023035:G:GTdonor_gain0.9700
16:68023035:G:Tdonor_gain0.9700
16:68023172:A:Tdonor_gain0.9300
16:68023171:G:GTdonor_gain0.8900
16:68023170:G:GTdonor_gain0.8300
16:68023125:GACC:Gdonor_gain0.7200
16:68023194:T:Adonor_gain0.7100
16:68023111:T:Adonor_gain0.7000
16:68023152:G:GTdonor_gain0.6900
16:68023106:GGG:Gdonor_gain0.6700
16:68023107:GGG:Gdonor_gain0.6700
16:68023129:G:GGdonor_gain0.6600
16:68023133:G:GTdonor_gain0.6600
16:68023034:G:GTdonor_gain0.6500
16:68023187:GCCGC:Gdonor_gain0.6400
16:68023128:C:CGdonor_gain0.6300
16:68023105:AGG:Adonor_gain0.6200
16:68023014:T:TAdonor_gain0.6000
16:68023163:TC:Tdonor_gain0.5800
16:68023124:GGACC:Gdonor_gain0.5700
16:68023125:GACCG:Gdonor_gain0.5700
16:68023134:G:Tdonor_gain0.5600
16:68023212:A:AGdonor_gain0.5300
16:68023213:G:GGdonor_gain0.5300
16:68023107:G:GAdonor_gain0.4900
16:68023104:C:Tdonor_gain0.4700
16:68023167:G:GTdonor_gain0.4700
16:68023190:GC:Gdonor_gain0.4500
16:68023191:C:Gdonor_gain0.4500

AlphaMissense

3414 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:68021700:A:CS501R0.998
16:68021700:A:TS501R0.998
16:68021702:T:GS501R0.998
16:68021994:G:CF403L0.997
16:68021994:G:TF403L0.997
16:68021996:A:GF403L0.997
16:68021752:C:GR484T0.995
16:68021844:G:CC453W0.995
16:68021751:T:AR484S0.994
16:68021751:T:GR484S0.994
16:68021752:C:AR484I0.994
16:68021833:G:TA457D0.994
16:68021756:G:CH483D0.992
16:68021695:A:TV503E0.991
16:68021790:A:CN471K0.991
16:68021790:A:TN471K0.991
16:68021842:G:AT454I0.991
16:68022096:A:CF369L0.991
16:68022096:A:TF369L0.991
16:68022098:A:GF369L0.991
16:68022343:T:AE287V0.991
16:68022914:A:GW97R0.991
16:68022914:A:TW97R0.991
16:68021845:C:TC453Y0.990
16:68021991:A:CC404W0.990
16:68022097:A:GF369S0.990
16:68022689:C:GA172P0.989
16:68022912:C:AW97C0.988
16:68022912:C:GW97C0.988
16:68021668:A:TV512D0.987

dbSNP variants (sampled 300 via entrez): RS1001226438 (16:68024708 G>A,C), RS1001294787 (16:68023348 C>T), RS1001410260 (16:68023215 G>A), RS1003636025 (16:68024980 C>T), RS1005554272 (16:68022754 T>C,G), RS1005752688 (16:68025032 A>G), RS1006547812 (16:68023470 A>C,G,T), RS1006892845 (16:68020716 A>AT), RS1007309444 (16:68023969 A>C), RS1007333464 (16:68021175 G>A), RS1008901624 (16:68024564 CTT>C,CTTT), RS1009315620 (16:68024733 A>C), RS1010178962 (16:68024350 C>G,T), RS1013985028 (16:68022117 C>T), RS1014198314 (16:68020587 T>A)

Disease associations

OMIM: gene MIM:607618 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST002539_84Schizophrenia2.000000e-08
GCST006803_42Schizophrenia4.000000e-08
GCST010002_113Refractive error2.000000e-14

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
GSK-J4decreases expression1
sodium arsenitedecreases expression1
ferrous chloridedecreases expression1
di-n-butylphosphoric acidaffects expression1
2,3,5-(triglutathion-S-yl)hydroquinoneincreases ADP-ribosylation1
cylindrospermopsinincreases expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
teriflunomidedecreases expression1
Decitabineaffects expression1
Acetaminophendecreases expression1
Atrazinedecreases expression1
Benzo(a)pyreneincreases methylation1
Cisplatinaffects expression1
Formaldehydedecreases expression1
Methotrexatedecreases expression1
Nickelincreases expression1
Ribonucleotidesaffects binding1
Silverdecreases expression1
Smokedecreases expression1
Dronabinoldecreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethanedecreases expression1
Cyclosporinedecreases expression1
Aflatoxin B1increases methylation1
Antirheumatic Agentsdecreases expression1
Cadmium Chloridedecreases expression1
Copper Sulfatedecreases 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.