CIAO3

gene
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Also known as FLJ21988PRNHPRNIOP1NAR1

Summary

CIAO3 (cytosolic iron-sulfur assembly component 3, HGNC:14179) is a protein-coding gene on chromosome 16p13.3, encoding Cytosolic iron-sulfur assembly component 3 (Q9H6Q4). Component of the cytosolic iron-sulfur protein assembly (CIA) complex, a multiprotein complex that mediates the incorporation of iron-sulfur cluster into extramitochondrial Fe/S proteins. It is a common-essential gene (DepMap: required in 99.8% of cancer cell lines).

Predicted to enable 4 iron, 4 sulfur cluster binding activity and metal ion binding activity. Involved in several processes, including intracellular oxygen homeostasis; iron-sulfur cluster assembly; and response to hypoxia. Part of cytosolic [4Fe-4S] assembly targeting complex.

Source: NCBI Gene 64428 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): pulmonary arteriovenous malformation (Limited, GenCC)
  • GWAS associations: 8
  • Clinical variants (ClinVar): 116 total
  • Cancer dependency (DepMap): dependent in 99.8% of screened cell lines (common-essential)
  • MANE Select transcript: NM_022493

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14179
Approved symbolCIAO3
Namecytosolic iron-sulfur assembly component 3
Location16p13.3
Locus typegene with protein product
StatusApproved
AliasesFLJ21988, PRN, HPRN, IOP1, NAR1
Ensembl geneENSG00000103245
Ensembl biotypeprotein_coding
OMIM611118
Entrez64428

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 12 protein_coding, 6 protein_coding_CDS_not_defined, 5 retained_intron, 4 nonsense_mediated_decay

ENST00000251588, ENST00000540986, ENST00000562421, ENST00000562752, ENST00000562862, ENST00000563051, ENST00000563534, ENST00000564285, ENST00000565065, ENST00000565341, ENST00000565425, ENST00000565693, ENST00000566614, ENST00000566650, ENST00000567172, ENST00000567403, ENST00000567455, ENST00000568545, ENST00000569759, ENST00000570066, ENST00000570289, ENST00000873908, ENST00000873909, ENST00000873910, ENST00000938080, ENST00000938081, ENST00000946067

RefSeq mRNA: 2 — MANE Select: NM_022493 NM_001304799, NM_022493

CCDS: CCDS10425, CCDS76798

Canonical transcript exons

ENST00000251588 — 11 exons

ExonStartEnd
ENSE00001804243729765730655
ENSE00003479322734229734347
ENSE00003483053739643739738
ENSE00003484486730843731000
ENSE00003543550732301732373
ENSE00003569553731565731702
ENSE00003611661734737734871
ENSE00003632127740920740997
ENSE00003667404737186737329
ENSE00003671916733298733427
ENSE00003756943736266736398

Expression profiles

Bgee: expression breadth ubiquitous, 195 present calls, max score 93.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.3209 / max 100.7958, expressed in 1802 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
15578413.34801798
1557820.3810199
1557830.3712167
1557800.191356
1557810.029415

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
apex of heartUBERON:000209893.76gold quality
right hemisphere of cerebellumUBERON:001489093.27gold quality
cerebellar hemisphereUBERON:000224592.65gold quality
cerebellar cortexUBERON:000212992.50gold quality
lower esophagus mucosaUBERON:003583491.79gold quality
right frontal lobeUBERON:000281091.68gold quality
mucosa of transverse colonUBERON:000499191.26gold quality
metanephros cortexUBERON:001053391.26gold quality
right uterine tubeUBERON:000130291.08gold quality
cerebellumUBERON:000203791.05gold quality
prefrontal cortexUBERON:000045189.88gold quality
anterior cingulate cortexUBERON:000983589.81gold quality
cingulate cortexUBERON:000302789.78gold quality
skin of legUBERON:000151189.68gold quality
pancreatic ductal cellCL:000207989.55silver quality
adenohypophysisUBERON:000219689.39gold quality
hindlimb stylopod muscleUBERON:000425289.32gold quality
skin of abdomenUBERON:000141689.18gold quality
Brodmann (1909) area 9UBERON:001354089.03gold quality
transverse colonUBERON:000115788.86gold quality
right lobe of liverUBERON:000111488.80gold quality
small intestine Peyer’s patchUBERON:000345488.80gold quality
pituitary glandUBERON:000000788.69gold quality
minor salivary glandUBERON:000183088.67gold quality
sural nerveUBERON:001548888.67gold quality
body of stomachUBERON:000116188.60gold quality
right lobe of thyroid glandUBERON:000111988.55gold quality
C1 segment of cervical spinal cordUBERON:000646988.39gold quality
putamenUBERON:000187488.21gold quality
neocortexUBERON:000195088.03gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes3.29
E-GEOD-110499no59.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting CIAO3, 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-6870-5P99.9968.552115
HSA-MIR-50799.9770.111915
HSA-MIR-477999.8666.501583
HSA-MIR-127599.4767.902749
HSA-MIR-532-3P99.3465.761195
HSA-MIR-607199.1667.771780
HSA-MIR-939-3P98.9765.072347
HSA-MIR-426098.7865.37848
HSA-MIR-6801-3P98.0464.64805
HSA-MIR-6810-3P97.9664.571023
HSA-MIR-466097.7967.441328
HSA-MIR-1224-3P97.2465.92851

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 6)

  • IOP1 is involved in mammalian cytosolic Fe-S protein maturation. (PMID:18270200)
  • human IscA1 plays an important role in both mitochondrial and cytosolic iron-sulfur cluster biogenesis, and a notable component of the latter is the interaction between IscA1 and IOP1. (PMID:19864422)
  • MMS19 interacts with target proteins. MIP18 has a role to bridge MMS19 and CIAO1. CIAO1 also binds IOP1. (PMID:23585563)
  • we concluded that the Ser161Ile mutant induced NARFL deficiency and eventually diffuse PAVMs probably through VEGF pathway. In a word, we detected a functional mutation in NARFL, which might be the pathogenic gene in this pedigree. (PMID:27835862)
  • CIAO3 protein forms a stable ternary complex with two key players of the human cytosolic iron-sulfur cluster assembly machinery. (PMID:32222833)
  • NARFL deficiency caused mitochondrial dysfunction in lung cancer cells by HIF-1alpha-DNMT1 axis. (PMID:37821486)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerionarflENSDARG00000062216
mus_musculusCiao3ENSMUSG00000002280
rattus_norvegicusCiao3ENSRNOG00000019522

Paralogs (2): NDUFS1 (ENSG00000023228), NARF (ENSG00000141562)

Protein

Protein identifiers

Cytosolic iron-sulfur assembly component 3Q9H6Q4 (reviewed: Q9H6Q4)

Alternative names: Cytosolic Fe-S cluster assembly factor NARFL, Iron-only hydrogenase-like protein 1, Nuclear prelamin A recognition factor-like protein, Protein related to Narf

All UniProt accessions (8): Q9H6Q4, B4DEE7, H3BPX8, H3BQ03, H3BSH2, H3BSJ7, H3BUF3, I3L2A3

UniProt curated annotations — full annotation on UniProt →

Function. Component of the cytosolic iron-sulfur protein assembly (CIA) complex, a multiprotein complex that mediates the incorporation of iron-sulfur cluster into extramitochondrial Fe/S proteins. Seems to negatively regulate the level of HIF1A expression, although this effect could be indirect.

Subunit / interactions. External component of the CIA complex. In the CIA complex, interacts directly with CIAO1 and MMS19.

Tissue specificity. Widely expressed.

Similarity. Belongs to the NARF family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9H6Q4-11yes
Q9H6Q4-22
Q9H6Q4-33

RefSeq proteins (2): NP_001291728, NP_071938* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003149Fe_hydrogenase_ssuDomain
IPR004108Fe_hydrogenase_lsu_CDomain
IPR009016Fe_hydrogenaseHomologous_superfamily
IPR050340Cytosolic_Fe-S_CAFFamily

Pfam: PF02256, PF02906

UniProt features (16 total): binding site 8, splice variant 2, sequence variant 2, initiator methionine 1, chain 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H6Q4-F186.630.72

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 (8): 24; 71; 74; 77; 190; 246; 395; 399

Post-translational modifications (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-2564830Cytosolic iron-sulfur cluster assembly

MSigDB gene sets: 74 (showing top): VERHAAK_AML_WITH_NPM1_MUTATED_DN, GOBP_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, GOBP_RESPONSE_TO_OXYGEN_LEVELS, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_HOMEOSTATIC_PROCESS, GOBP_CHEMICAL_HOMEOSTASIS, NIKOLSKY_BREAST_CANCER_16P13_AMPLICON, GOMF_METAL_CLUSTER_BINDING, GOMF_4_IRON_4_SULFUR_CLUSTER_BINDING, GOBP_INTRACELLULAR_OXYGEN_HOMEOSTASIS, GOCC_CYTOSOLIC_4FE_4S_ASSEMBLY_TARGETING_COMPLEX, VALK_AML_CLUSTER_13, REACTOME_CYTOSOLIC_IRON_SULFUR_CLUSTER_ASSEMBLY, GSE5503_MLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, DACH1_TARGET_GENES

GO Biological Process (5): response to hypoxia (GO:0001666), hematopoietic progenitor cell differentiation (GO:0002244), regulation of gene expression (GO:0010468), iron-sulfur cluster assembly (GO:0016226), intracellular oxygen homeostasis (GO:0032364)

GO Molecular Function (4): metal ion binding (GO:0046872), 4 iron, 4 sulfur cluster binding (GO:0051539), protein binding (GO:0005515), iron-sulfur cluster binding (GO:0051536)

GO Cellular Component (1): cytosolic [4Fe-4S] assembly targeting complex (GO:0097361)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
response to stress1
response to decreased oxygen levels1
hemopoiesis1
cell differentiation1
gene expression1
regulation of macromolecule biosynthetic process1
metallo-sulfur cluster assembly1
intracellular chemical homeostasis1
cation binding1
iron-sulfur cluster binding1
binding1
metal cluster binding1
intracellular protein-containing complex1
iron-sulfur cluster assembly complex1

Protein interactions and networks

STRING

890 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CIAO3MMS19Q96T76975
CIAO3CIAO1O76071971
CIAO3NUBP1P53384906
CIAO3CIAPIN1Q6FI81889
CIAO3CIAO2BQ9Y3D0878
CIAO3ISCA1Q9BUE6793
CIAO3LYRM4Q9HD34745
CIAO3NFS1Q9Y697742
CIAO3ISCUQ9H1K1713
CIAO3ABCB7O75027709
CIAO3NDOR1Q9UHB4709
CIAO3NUBP2Q9Y5Y2709
CIAO3CIAO2AQ9H5X1702
CIAO3EGLN1Q9GZT9687
CIAO3ABCE1P61221665

IntAct

31 interactions, top by confidence:

ABTypeScore
CIAO2ACIAO1psi-mi:“MI:0915”(physical association)0.950
CIAO2BCIAO1psi-mi:“MI:0915”(physical association)0.950
CIAO2ACIAO1psi-mi:“MI:0914”(association)0.950
MMS19CIAO1psi-mi:“MI:0914”(association)0.910
TULP3GGPS1psi-mi:“MI:0914”(association)0.640
CIAO3psi-mi:“MI:0407”(direct interaction)0.560
CIAO3INPPL1psi-mi:“MI:0914”(association)0.530
ZBTB39FOXK2psi-mi:“MI:0914”(association)0.530
DTX3ITSN1psi-mi:“MI:0914”(association)0.530
MMS19CIAO3psi-mi:“MI:0407”(direct interaction)0.520
NAA10OFD1psi-mi:“MI:0914”(association)0.480
CIAO1CIAO3psi-mi:“MI:0407”(direct interaction)0.440
MYH9PLEKHG3psi-mi:“MI:0914”(association)0.350
RGS20PGPpsi-mi:“MI:0914”(association)0.350
DTX3NDUFS6psi-mi:“MI:0914”(association)0.350
ZBTB39FOXK1psi-mi:“MI:0914”(association)0.350
NUBP2POTEFpsi-mi:“MI:0914”(association)0.350
CCNOFOXN3psi-mi:“MI:0914”(association)0.350
NAA11DVL2psi-mi:“MI:0914”(association)0.350
CIAO2Apsi-mi:“MI:0914”(association)0.350
NUBP2TK2psi-mi:“MI:0914”(association)0.350
DTX3RAD50psi-mi:“MI:0914”(association)0.350
CIAO2AMAP2K7psi-mi:“MI:0914”(association)0.350
CIAO3NUBP1psi-mi:“MI:0914”(association)0.350
FAXCHAT1psi-mi:“MI:0914”(association)0.350
DSCR9CIAO3psi-mi:“MI:0915”(physical association)0.000

BioGRID (64): NARFL (Affinity Capture-RNA), NARFL (Affinity Capture-MS), NARFL (Affinity Capture-Western), NARFL (Affinity Capture-MS), NARFL (Affinity Capture-MS), NARFL (Affinity Capture-MS), NARFL (Affinity Capture-MS), NARFL (Affinity Capture-MS), ARNT (Affinity Capture-MS), WDFY1 (Affinity Capture-MS), INPPL1 (Affinity Capture-MS), NARFL (Affinity Capture-Western), NARFL (Affinity Capture-MS), NARFL (Affinity Capture-MS), NARFL (Affinity Capture-Western)

ESM2 similar proteins: A2RRV9, A4FV58, A4QN59, A7SDA8, A8PGQ3, A8WH18, A8XZU0, B0WU52, B3N018, B3NKH7, B4GXC8, B4IMH3, B4ISL0, B4JBE6, B4KFU7, B4LQR5, B4MUM8, B4NSS7, B5DK31, B6K2N0, O43837, O77784, P29696, P37223, P41565, P51553, P70404, Q16ML2, Q28479, Q2YDU6, Q58CP0, Q5BK18, Q5RBT4, Q5RF36, Q68FX0, Q6CFR3, Q6DE00, Q6DHP6, Q6GP25, Q6ING7

Diamond homologs: A1CIC2, A1CWD8, A2Q9A9, A2RRV9, A3LYR2, A4FV58, A5DKC0, A5DSI2, A6RR15, A6ZRK3, A7E7C4, A7SDA8, A7TQP0, A8PGQ3, A8WH18, A8XZU0, B0WU52, B0Y4F9, B3N018, B3NKH7, B4GXC8, B4IMH3, B4ISL0, B4JBE6, B4KFU7, B4LQR5, B4MUM8, B4NSS7, B5DK31, B6HUC4, B6K2N0, B6QQH9, B8N122, B9W8S4, P0CP10, P0CP11, P23503, P53998, Q0CR17, Q0UM75

SIGNOR signaling

2 interactions.

AEffectBMechanism
CIAO3“form complex”“CIAO2B cytosolic iron-sulfur protein assembly complex”binding
CIAO3“form complex”“CIAO1-CIAO2A-CIAO3 cytosolic iron-sulfur protein assembly complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 32 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
Cytosolic iron-sulfur cluster assembly5173.0×7e-09

GO biological processes:

GO termPartnersFoldFDR
protein maturation527.3×2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance85
Likely benign11
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

2394 predictions. Top by Δscore:

VariantEffectΔscore
16:730656:C:CCacceptor_gain1.0000
16:730656:CTAT:Cacceptor_loss1.0000
16:730657:T:Cacceptor_loss1.0000
16:730802:C:CAdonor_gain1.0000
16:730863:T:TAdonor_gain1.0000
16:730886:C:CAdonor_gain1.0000
16:731001:C:CAacceptor_loss1.0000
16:731001:C:CCacceptor_gain1.0000
16:731002:T:Aacceptor_loss1.0000
16:731561:TGA:Tdonor_loss1.0000
16:731563:A:Tdonor_loss1.0000
16:731564:C:Tdonor_loss1.0000
16:732295:A:ACdonor_gain1.0000
16:732296:C:CCdonor_gain1.0000
16:732296:CGTA:Cdonor_gain1.0000
16:732297:GTACA:Gdonor_loss1.0000
16:732298:TAC:Tdonor_loss1.0000
16:732299:A:ACdonor_gain1.0000
16:732299:A:Cdonor_loss1.0000
16:732299:ACAGG:Adonor_gain1.0000
16:732300:C:CTdonor_gain1.0000
16:732300:CA:Cdonor_gain1.0000
16:732300:CAGG:Cdonor_gain1.0000
16:732300:CAGGC:Cdonor_gain1.0000
16:732371:CTC:Cacceptor_gain1.0000
16:732372:TCCTG:Tacceptor_loss1.0000
16:732374:C:CCacceptor_gain1.0000
16:732374:C:Tacceptor_loss1.0000
16:733292:CCGCA:Cdonor_loss1.0000
16:733293:CGCA:Cdonor_loss1.0000

AlphaMissense

3098 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:734345:A:GW193R0.995
16:734345:A:TW193R0.995
16:733375:T:AK249I0.994
16:733383:G:CC246W0.994
16:733384:C:TC246Y0.994
16:733385:A:GC246R0.994
16:730925:G:CF370L0.993
16:730925:G:TF370L0.993
16:730927:A:GF370L0.993
16:734332:G:TA197D0.993
16:734743:A:GC190R0.993
16:730852:A:GC395R0.992
16:733357:C:GR255T0.992
16:734328:C:AE198D0.992
16:734328:C:GE198D0.992
16:737279:G:CC71W0.992
16:733374:T:AK249N0.991
16:733374:T:GK249N0.991
16:737281:A:GC71R0.991
16:730850:G:CC395W0.990
16:730926:A:GF370S0.990
16:733364:C:GA253P0.990
16:734741:G:CC190W0.990
16:734742:C:TC190Y0.990
16:737280:C:GC71S0.990
16:737281:A:TC71S0.990
16:730851:C:TC395Y0.989
16:734264:C:GG220R0.988
16:734333:C:GA197P0.988
16:737262:C:GC77S0.988

dbSNP variants (sampled 300 via entrez): RS1000006549 (16:738058 C>T), RS1000147633 (16:738283 TGGTTCA>T), RS1000322096 (16:734248 T>C), RS1000398460 (16:730102 G>A), RS1000441451 (16:738219 A>G), RS1000769425 (16:729928 C>A,G,T), RS1000982054 (16:729804 G>A), RS1001010041 (16:729924 AC>A,ACC,ACCC,ACCCC), RS1001520964 (16:737800 G>A,T), RS1001553578 (16:737980 C>A,T), RS1001644485 (16:731438 TCCAAAC>T), RS1001820836 (16:729673 G>A,C), RS1002381940 (16:741581 T>C), RS1002418827 (16:739298 C>G), RS1002492694 (16:739530 C>A,G)

Disease associations

OMIM: gene MIM:611118 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
pulmonary arteriovenous malformationLimitedAutosomal recessive

Mondo (1): (MONDO:0009930)

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

StudyTraitp-value
GCST000817_82Height1.000000e-13
GCST002702_92Height6.000000e-08
GCST008163_25Height4.000000e-06
GCST008839_40Height1.000000e-07
GCST012226_378Waist circumference adjusted for body mass index7.000000e-15
GCST012227_358Hip circumference adjusted for BMI8.000000e-21
GCST90000025_245Appendicular lean mass3.000000e-40
GCST90020028_1482Hip circumference adjusted for BMI3.000000e-12

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0007789BMI-adjusted waist circumference
EFO:0008039BMI-adjusted hip circumference
EFO:0004980appendicular lean mass

MeSH disease descriptors (1)

DescriptorNameTree numbers
C562404Pulmonary Arteriovenous Fistulas (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Faffects cotreatment, increases methylation, increases expression2
sodium arseniteaffects expression, decreases expression2
alpha-pineneincreases abundance, affects cotreatment, increases oxidation1
methacrylaldehydeincreases abundance, affects cotreatment, increases oxidation1
di-n-butylphosphoric acidaffects expression1
2-palmitoylglycerolincreases expression1
pyrimidifendecreases expression1
abrineincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation1
Arsenicaffects methylation1
Atrazinedecreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Indomethacinaffects cotreatment, increases expression1
Ozoneincreases oxidation, increases abundance, affects cotreatment1
Rotenonedecreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Valproic Acidincreases methylation1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Cyclosporinedecreases methylation1
Acrylamidedecreases expression1
Volatile Organic Compoundsaffects cotreatment, 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.