AIRIM

gene
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Also known as FLJ20508

Summary

AIRIM (AFG2 interacting ribosome maturation factor, HGNC:26039) is a protein-coding gene on chromosome 1p34.3, encoding AFG2-interacting ribosome maturation factor (Q9NX04). Part of the 55LCC heterohexameric ATPase complex which is chromatin-associated and promotes replisome proteostasis to maintain replication fork progression and genome stability. It is a common-essential gene (DepMap: required in 95.8% of cancer cell lines).

Involved in ribosomal large subunit biogenesis. Located in cytosol; nucleolus; and nucleoplasm.

Source: NCBI Gene 54955 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 9 total
  • Cancer dependency (DepMap): dependent in 95.8% of screened cell lines (common-essential)
  • MANE Select transcript: NM_001350770

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26039
Approved symbolAIRIM
NameAFG2 interacting ribosome maturation factor
Location1p34.3
Locus typegene with protein product
StatusApproved
AliasesFLJ20508
Ensembl geneENSG00000116922
Ensembl biotypeprotein_coding
OMIM614799
Entrez54955

Gene structure

Transcript identifiers

Ensembl transcripts: 35 — 29 protein_coding, 5 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000358011, ENST00000461359, ENST00000464085, ENST00000464178, ENST00000472584, ENST00000477060, ENST00000486637, ENST00000488137, ENST00000491797, ENST00000491981, ENST00000494120, ENST00000498448, ENST00000609516, ENST00000619962, ENST00000895429, ENST00000895430, ENST00000895431, ENST00000895432, ENST00000895433, ENST00000895434, ENST00000895435, ENST00000895436, ENST00000895437, ENST00000895438, ENST00000895439, ENST00000895440, ENST00000911431, ENST00000911432, ENST00000911433, ENST00000962186, ENST00000962187, ENST00000962188, ENST00000962189, ENST00000962190, ENST00000962191

RefSeq mRNA: 20 — MANE Select: NM_001350770 NM_001303030, NM_001303031, NM_001350755, NM_001350756, NM_001350757, NM_001350758, NM_001350759, NM_001350760, NM_001350761, NM_001350762, NM_001350763, NM_001350764, NM_001350765, NM_001350766, NM_001350767, NM_001350768, NM_001350769, NM_001350770, NM_001350771, NM_017850

CCDS: CCDS423

Canonical transcript exons

ENST00000486637 — 5 exons

ExonStartEnd
ENSE000018384453769000237690529
ENSE000035165723768157037683160
ENSE000037066633768960637689883
ENSE000037856753768331937683437
ENSE000037902393768627337686452

Expression profiles

Bgee: expression breadth ubiquitous, 265 present calls, max score 87.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.7536 / max 142.2393, expressed in 1741 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
117927.18631670
117932.56731386

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305387.46gold quality
stromal cell of endometriumCL:000225587.17gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099187.16gold quality
right coronary arteryUBERON:000162585.24gold quality
ganglionic eminenceUBERON:000402385.24gold quality
right ovaryUBERON:000211884.54gold quality
calcaneal tendonUBERON:000370184.42gold quality
left ovaryUBERON:000211984.12gold quality
body of uterusUBERON:000985383.31gold quality
popliteal arteryUBERON:000225083.30gold quality
tibial arteryUBERON:000761083.29gold quality
gall bladderUBERON:000211083.19gold quality
body of pancreasUBERON:000115083.18gold quality
left adrenal glandUBERON:000123483.16gold quality
right adrenal gland cortexUBERON:003582783.08gold quality
right adrenal glandUBERON:000123383.06gold quality
gastrocnemiusUBERON:000138882.98gold quality
minor salivary glandUBERON:000183082.80gold quality
ovaryUBERON:000099282.79gold quality
aortaUBERON:000094782.76gold quality
muscle of legUBERON:000138382.74gold quality
prefrontal cortexUBERON:000045182.66gold quality
adrenal glandUBERON:000236982.65gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.64gold quality
cortical plateUBERON:000534382.63gold quality
left adrenal gland cortexUBERON:003582582.63gold quality
left coronary arteryUBERON:000162682.57gold quality
lower esophagusUBERON:001347382.54gold quality
lower esophagus muscularis layerUBERON:003583382.54gold quality
skin of legUBERON:000151182.53gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-MTAB-4850no258.62
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

73 targeting AIRIM, 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-4262100.0073.263931
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-3134100.0066.43777
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-60799.9773.625593
HSA-MIR-314899.9775.066478
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-806399.9169.763146
HSA-MIR-153-5P99.8973.866317
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-369-3P99.8570.522264
HSA-MIR-449599.8272.083080
HSA-MIR-202-5P99.7867.65991
HSA-MIR-1273H-5P99.7766.322471
HSA-MIR-129999.7771.242389
HSA-MIR-548AG99.7769.251492
HSA-MIR-4766-5P99.7569.232662
HSA-MIR-4677-5P99.7070.091940
HSA-MIR-30B-3P99.7065.762325
HSA-MIR-3689A-3P99.7065.732306
HSA-MIR-3689B-3P99.7065.712311
HSA-MIR-3689C99.7065.712311
HSA-MIR-6779-5P99.7065.762363
HSA-MIR-548M99.7068.871749
HSA-MIR-379-3P99.6969.601524
HSA-MIR-411-3P99.6969.631524
HSA-MIR-548AI99.6969.241494

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 95.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 3)

  • our findings suggest that C1ORF109 may be the downstream target of protein kinase CK2 and involved in the regulation of cancer cell proliferation. (PMID:22548824)
  • Labeling of heterochronic ribosomes reveals C1ORF109 and SPATA5 control a late step in human ribosome assembly. (PMID:35354024)
  • C1orf109 promotes malignant phenotype of liver cancer via wnt signaling pathway in a CK2-dependent manner. (PMID:36988773)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioairimENSDARG00000012113
mus_musculusAirimENSMUSG00000044730
rattus_norvegicusAirimENSRNOG00000025065

Protein

Protein identifiers

AFG2-interacting ribosome maturation factorQ9NX04 (reviewed: Q9NX04)

Alternative names: Ribosome biogenesis protein C1orf109

All UniProt accessions (7): A0A087WUX7, Q9NX04, V9GY35, V9GYI2, V9GYN4, V9GYQ8, V9GYT8

UniProt curated annotations — full annotation on UniProt →

Function. Part of the 55LCC heterohexameric ATPase complex which is chromatin-associated and promotes replisome proteostasis to maintain replication fork progression and genome stability. Required for replication fork progression, sister chromatid cohesion, and chromosome stability. The ATPase activity is specifically enhanced by replication fork DNA and is coupled to cysteine protease-dependent cleavage of replisome substrates in response to replication fork damage. Uses ATPase activity to process replisome substrates in S-phase, facilitating their proteolytic turnover from chromatin to ensure DNA replication and mitotic fidelity. Involved in the cytoplasmic maturation steps of pre-60S ribosomal particles by promoting the release of shuttling protein RSL24D1/RLP24 from the pre-ribosomal particles.

Subunit / interactions. Part of the 55LCC heterohexameric ATPase complex composed at least of AIRIM, AFG2A, AFG2B and CINP. Does not associate with pre-60S ribosomal particles.

Subcellular location. Nucleus. Cytoplasm.

Post-translational modifications. Phosphorylated on serines by CK2 kinase.

Isoforms (2)

UniProt IDNamesCanonical?
Q9NX04-11yes
Q9NX04-22

RefSeq proteins (20): NP_001289959, NP_001289960, NP_001337684, NP_001337685, NP_001337686, NP_001337687, NP_001337688, NP_001337689, NP_001337690, NP_001337691, NP_001337692, NP_001337693, NP_001337694, NP_001337695, NP_001337696, NP_001337697, NP_001337698, NP_001337699, NP_001337700, NP_060320 (=MANE)

Domains & families (InterPro)

IDNameType
IPR029159CA109-likeFamily

Pfam: PF15011

UniProt features (9 total): mutagenesis site 6, splice variant 2, chain 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
9GWJX-RAY DIFFRACTION3.69
8RHNELECTRON MICROSCOPY4.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NX04-F194.170.88

Functional residue map

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

Mutagenesis-validated functional residues (6):

PositionPhenotype
63loss of interaction with cinp. no effect on interaction with interaction with afg2a and afg2b.
69loss of interaction with cinp. no effect on interaction with interaction with afg2a and afg2b.
73loss of interaction with cinp. no effect on interaction with interaction with afg2a and afg2b.
104abolishes phosphorylation by ck2 kinase; when associated with a-134 and a-182.
134abolishes phosphorylation by ck2 kinase; when associated with a-104 and a-182.
182abolishes phosphorylation by ck2 kinase; when associated with a-104 and a-134.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 115 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, WEI_MYCN_TARGETS_WITH_E_BOX, chr1p34, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, CCAGGGG_MIR331, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS, GOBP_DNA_REPLICATION, MARSON_BOUND_BY_E2F4_UNSTIMULATED, GOCC_ATPASE_COMPLEX, GOCC_NUCLEOLUS, GOBP_DNA_METABOLIC_PROCESS

GO Biological Process (2): ribosomal large subunit biogenesis (GO:0042273), ribosome biogenesis (GO:0042254)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
ribonucleoprotein complex biogenesis2
nuclear lumen2
ribosome biogenesis1
binding1
intracellular membrane-bounded organelle1
intracellular membraneless organelle1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

640 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
AIRIMCINPQ9BW66592
AIRIMTMEM239Q8WW34580
AIRIMMTBPQ96DY7472
AIRIMSPC24Q8NBT2455
AIRIMZBED8Q8IZ13432
AIRIMTTC33Q6PID6400
AIRIMLRRC61Q9BV99400
AIRIMRMP64Q6NW34397
AIRIMSNRNP48Q6IEG0389
AIRIMASPHD2Q6ICH7378
AIRIMAHCTF1Q8WYP5375
AIRIMTMEM60Q9H2L4369
AIRIMAUNIPQ9H7T9369
AIRIMAFG2BQ9BVQ7353
AIRIMIFFO1Q0D2I5351
AIRIMKIAA1586Q9HCI6351

IntAct

549 interactions, top by confidence:

ABTypeScore
AIRIMCINPpsi-mi:“MI:0915”(physical association)0.920
CINPAIRIMpsi-mi:“MI:0915”(physical association)0.920
AIRIMZBED1psi-mi:“MI:0915”(physical association)0.780
ZBED1AIRIMpsi-mi:“MI:0915”(physical association)0.780
AIRIMCEP55psi-mi:“MI:0915”(physical association)0.720
AIRIMNECAB2psi-mi:“MI:0915”(physical association)0.720
AIRIMTADA2Apsi-mi:“MI:0915”(physical association)0.720
STX11AIRIMpsi-mi:“MI:0915”(physical association)0.720
AIRIMKRT19psi-mi:“MI:0915”(physical association)0.720
AIRIMTRAF1psi-mi:“MI:0915”(physical association)0.720
KRT31AIRIMpsi-mi:“MI:0915”(physical association)0.720
RINT1AIRIMpsi-mi:“MI:0915”(physical association)0.720
AIRIMIHO1psi-mi:“MI:0915”(physical association)0.720
AIRIMVPS52psi-mi:“MI:0915”(physical association)0.720
AIRIMLZTS2psi-mi:“MI:0915”(physical association)0.720
KATNAL1AIRIMpsi-mi:“MI:0915”(physical association)0.720
TRIM54AIRIMpsi-mi:“MI:0915”(physical association)0.720
AIRIMRNF41psi-mi:“MI:0915”(physical association)0.720
AIRIMTFIP11psi-mi:“MI:0915”(physical association)0.720
AIRIMIKZF3psi-mi:“MI:0915”(physical association)0.720
NECAB2AIRIMpsi-mi:“MI:0915”(physical association)0.720
KRT19AIRIMpsi-mi:“MI:0915”(physical association)0.720
TRAF1AIRIMpsi-mi:“MI:0915”(physical association)0.720

BioGRID (191): C1orf109 (Two-hybrid), C1orf109 (Two-hybrid), C1orf109 (Two-hybrid), C1orf109 (Two-hybrid), C1orf109 (Two-hybrid), C1orf109 (Two-hybrid), C1orf109 (Two-hybrid), C1orf109 (Two-hybrid), C1orf109 (Two-hybrid), C1orf109 (Two-hybrid), C1orf109 (Two-hybrid), C1orf109 (Two-hybrid), C1orf109 (Two-hybrid), C1orf109 (Two-hybrid), C1orf109 (Two-hybrid)

ESM2 similar proteins: A0A0B4K7J2, A0A8W7Q4I4, A3N0I5, A4GCJ9, A5PK29, A7MEF1, A8C8J6, A8GDD4, A8GG50, B2SYW1, B3H1G2, B3R8A8, B4I608, B4QAF0, F7IW82, O84621, O86418, P03487, P0C267, P0DOF4, P0DOF7, P10355, P22047, P35937, P63234, P73889, P74103, Q0A2E3, Q13U06, Q2ICQ8, Q2PIK4, Q2PIM0, Q2PIM4, Q30NP9, Q38SQ6, Q3TC33, Q3YPZ3, Q44212, Q463X3, Q67161

Diamond homologs: Q28I03, Q499E6, Q8JHH5, Q9NX04

SIGNOR signaling

1 interactions.

AEffectBMechanism
AIRIM“form complex”“SPATA5-SPATA5L1 ATPase complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 70 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
Formation of the cornified envelope718.6×1e-05
Keratinization711.8×1e-04

GO biological processes:

GO termPartnersFoldFDR
morphogenesis of an epithelium739.5×2e-07
intermediate filament organization727.6×1e-06
epithelial cell differentiation514.4×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance2
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

955 predictions. Top by Δscore:

VariantEffectΔscore
1:37683158:TAT:Tacceptor_gain1.0000
1:37683158:TATCT:Tacceptor_loss1.0000
1:37683160:TCTGA:Tacceptor_loss1.0000
1:37683161:C:CCacceptor_gain1.0000
1:37683161:CT:Cacceptor_loss1.0000
1:37683162:T:Cacceptor_loss1.0000
1:37686272:CGA:Cdonor_gain1.0000
1:37686293:AATAT:Adonor_gain1.0000
1:37686336:A:ACdonor_gain1.0000
1:37686337:C:CCdonor_gain1.0000
1:37686337:CTG:Cdonor_gain1.0000
1:37686448:TGGCT:Tacceptor_gain1.0000
1:37686449:GGCT:Gacceptor_gain1.0000
1:37686450:GCTC:Gacceptor_loss1.0000
1:37686451:CT:Cacceptor_gain1.0000
1:37686452:TCTGC:Tacceptor_loss1.0000
1:37686453:C:CCacceptor_gain1.0000
1:37686453:CTGC:Cacceptor_loss1.0000
1:37686454:T:Gacceptor_loss1.0000
1:37689604:A:ACdonor_gain1.0000
1:37689604:ACAGC:Adonor_gain1.0000
1:37689605:C:CCdonor_gain1.0000
1:37689605:CAG:Cdonor_gain1.0000
1:37689605:CAGCC:Cdonor_gain1.0000
1:37689612:T:Adonor_gain1.0000
1:37689619:G:Cdonor_gain1.0000
1:37689656:A:ACdonor_gain1.0000
1:37689656:ACG:Adonor_gain1.0000
1:37689657:C:CCdonor_gain1.0000
1:37689657:CG:Cdonor_gain1.0000

AlphaMissense

715 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:37689683:G:CF66L0.949
1:37689683:G:TF66L0.949
1:37689685:A:GF66L0.949
1:37689663:A:GL73P0.923
1:37689735:A:GL49P0.897
1:37689799:A:GW28R0.887
1:37689799:A:TW28R0.887
1:37689827:G:CF18L0.879
1:37689827:G:TF18L0.879
1:37689829:A:GF18L0.879
1:37689840:A:GL14P0.876
1:37689828:A:GF18S0.873
1:37686432:C:GR99P0.871
1:37689756:A:GL42P0.864
1:37689730:C:GA51P0.862
1:37689639:C:TG81D0.853
1:37689653:C:AK76N0.848
1:37689653:C:GK76N0.848
1:37689737:C:AQ48H0.844
1:37689737:C:GQ48H0.844
1:37689744:G:TA46E0.837
1:37689675:A:GL69S0.836
1:37689745:C:GA46P0.830
1:37689828:A:CF18C0.824
1:37689756:A:TL42H0.823
1:37689797:C:AW28C0.819
1:37689797:C:GW28C0.819
1:37686423:A:TV102D0.805
1:37689640:C:GG81R0.804
1:37689684:A:GF66S0.800

dbSNP variants (sampled 300 via entrez): RS1000159373 (1:37687826 G>C), RS1000316293 (1:37688188 C>T), RS1000468782 (1:37691486 C>T), RS1000496392 (1:37686764 G>A,T), RS1000823175 (1:37691036 G>C), RS1001104245 (1:37692150 A>C), RS1001147502 (1:37690485 A>C,T), RS1001206307 (1:37690624 C>T), RS1001287945 (1:37687448 T>A), RS1001416104 (1:37684448 C>G,T), RS1001764068 (1:37684179 A>C,T), RS1001945945 (1:37692632 C>A), RS1002159646 (1:37691930 C>A,G,T), RS1002211938 (1:37692100 A>G), RS1002363912 (1:37685507 A>G)

Disease associations

OMIM: gene MIM:614799 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST002115_4Axial length4.000000e-13
GCST003476_2Eyebrow thickness7.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0005318axial length measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsincreases oxidation, increases expression, affects cotreatment, decreases expression, increases abundance3
Tetrachlorodibenzodioxindecreases expression2
Particulate Matterdecreases expression, increases abundance, increases expression2
aristolochic acid Iincreases expression1
alpha-pineneaffects cotreatment, decreases expression, increases oxidation, increases abundance1
bisphenol Aaffects cotreatment, decreases methylation1
sodium arseniteincreases expression1
methacrylaldehydeincreases oxidation, increases abundance, affects cotreatment, decreases expression1
2-palmitoylglycerolincreases expression1
Bortezomibincreases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Acroleinincreases abundance, affects cotreatment, decreases expression, increases oxidation1
Benzo(a)pyrenedecreases methylation1
Estradiolincreases expression1
Hydrogen Peroxidedecreases expression1
Ozonedecreases expression, increases oxidation, increases abundance, affects cotreatment1
Phthalic Acidsaffects methylation1
Silicon Dioxideincreases expression1
Smokedecreases expression1
Dronabinoldecreases expression1
Tobacco Smoke Pollutionincreases expression1
Valproic Acidincreases expression, increases methylation1
Cyclosporineincreases expression1
Volatile Organic Compoundsaffects cotreatment, decreases expression, increases oxidation1

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.