CENATAC

gene
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Also known as DLNB14

Summary

CENATAC (centrosomal AT-AC splicing factor, HGNC:30460) is a protein-coding gene on chromosome 11q23.3, encoding Centrosomal AT-AC splicing factor (Q86UT8). Component of the minor spliceosome that promotes splicing of a specific, rare minor intron subtype. It is a common-essential gene (DepMap: required in 99.3% of cancer cell lines).

This gene encodes a protein thought to contain a coiled coil motif. No function has been determined for the encoded protein. A pseudogene of this gene is located on chromosome 20. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 338657 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): mosaic variegated aneuploidy syndrome 4 (Limited, GenCC)
  • Clinical variants (ClinVar): 87 total — 2 pathogenic
  • Phenotypes (HPO): 4
  • Cancer dependency (DepMap): dependent in 99.3% of screened cell lines (common-essential)
  • MANE Select transcript: NM_198489

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30460
Approved symbolCENATAC
Namecentrosomal AT-AC splicing factor
Location11q23.3
Locus typegene with protein product
StatusApproved
AliasesDLNB14
Ensembl geneENSG00000186166
Ensembl biotypeprotein_coding
OMIM620142
Entrez338657

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 6 retained_intron, 3 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000334418, ENST00000524670, ENST00000526463, ENST00000527356, ENST00000528088, ENST00000532132, ENST00000533787, ENST00000534656, ENST00000580556, ENST00000583842, ENST00000891520, ENST00000937690

RefSeq mRNA: 1 — MANE Select: NM_198489 NM_198489

CCDS: CCDS8405

Canonical transcript exons

ENST00000334418 — 11 exons

ExonStartEnd
ENSE00001336373119011221119011283
ENSE00001336377119015538119015793
ENSE00001336378118998138118998317
ENSE00003471497119015307119015439
ENSE00003476708118998430118998593
ENSE00003536694118999011118999109
ENSE00003555622119012149119012254
ENSE00003555873119014994119015083
ENSE00003565648119010764119010830
ENSE00003637325119013232119013262
ENSE00003691033119011939119012003

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 95.95.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.2985 / max 198.2184, expressed in 1784 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
11708015.25601770
1170780.5539340
1170790.4886288

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cerebellar cortexUBERON:000212995.95gold quality
cerebellar hemisphereUBERON:000224595.93gold quality
mucosa of stomachUBERON:000119995.86gold quality
cerebellumUBERON:000203795.86gold quality
sural nerveUBERON:001548895.74gold quality
adenohypophysisUBERON:000219695.58gold quality
right hemisphere of cerebellumUBERON:001489095.43gold quality
metanephros cortexUBERON:001053395.32gold quality
granulocyteCL:000009495.15gold quality
pituitary glandUBERON:000000795.15gold quality
upper lobe of left lungUBERON:000895295.14gold quality
spleenUBERON:000210695.11gold quality
left lobe of thyroid glandUBERON:000112094.95gold quality
right lungUBERON:000216794.93gold quality
apex of heartUBERON:000209894.87gold quality
right lobe of thyroid glandUBERON:000111994.84gold quality
primary visual cortexUBERON:000243694.83gold quality
tibial nerveUBERON:000132394.68gold quality
thyroid glandUBERON:000204694.63gold quality
skin of legUBERON:000151194.62gold quality
skin of abdomenUBERON:000141694.61gold quality
zone of skinUBERON:000001494.60gold quality
small intestine Peyer’s patchUBERON:000345494.36gold quality
right uterine tubeUBERON:000130294.19gold quality
cortex of kidneyUBERON:000122593.97gold quality
ectocervixUBERON:001224993.79gold quality
uterine cervixUBERON:000000293.72gold quality
thoracic mammary glandUBERON:000520093.68gold quality
body of pancreasUBERON:000115093.65gold quality
endocervixUBERON:000045893.60gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.56
E-MTAB-4850no128.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting CENATAC, 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-186-5P99.9970.833707
HSA-MIR-477599.9875.006394
HSA-MIR-314899.9775.066478
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-493-5P99.9672.472382
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-105-5P99.5469.242060
HSA-MIR-7853-5P99.5469.302055
HSA-MIR-4762-3P99.4369.722363
HSA-MIR-471898.5568.61814
HSA-MIR-654-3P98.3867.61905
HSA-MIR-218-2-3P98.0867.21601
HSA-MIR-152-5P96.4266.59960
HSA-MIR-584-5P95.8268.05848

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.3% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 2)

  • CCDC84 Acetylation Oscillation Regulates Centrosome Duplication by Modulating HsSAS-6 Degradation. (PMID:31722219)
  • Chromosomal instability by mutations in the novel minor spliceosome component CENATAC. (PMID:34009673)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriocenatacENSDARG00000059606
mus_musculusCenatacENSMUSG00000043923
rattus_norvegicusCenatacENSRNOG00000012137

Protein

Protein identifiers

Centrosomal AT-AC splicing factorQ86UT8 (reviewed: Q86UT8)

Alternative names: Coiled-coil domain-containing protein 84

All UniProt accessions (3): E9PJ16, E9PPT8, Q86UT8

UniProt curated annotations — full annotation on UniProt →

Function. Component of the minor spliceosome that promotes splicing of a specific, rare minor intron subtype. Negative regulator of centrosome duplication. Constrains centriole number by modulating the degradation of the centrosome-duplication-associated protein SASS6 in an acetylation-dependent manner. SIRT1 deacetylates CENATAC in G1 phase, allowing for SASS6 accumulation on the centrosome and subsequent procentriole assembly. The CENATAC acetylation level is restored in mitosis by NAT10, promoting SASS6 proteasome degradation by facilitating SASS6 binding to APC/C E3 ubiquitin-protein ligase complex/FZR1.

Subunit / interactions. Interacts with SASS6; the interaction increases with CENATAC acetylation.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome.

Post-translational modifications. Acetylated. Acetylation oscillates throughout the cell cycle, and the acetylation state at Lys-31 is regulated by the deacetylase SIRT1 and the acetyltransferase NAT10. Deacetylated CENATAC is responsible for its centrosome targeting, and acetylated CENATAC promotes SASS6 degradation by enhancing the binding affinity of SASS6 for APC/C E3 ubiquitin-protein ligase complex/FZR1.

Disease relevance. Mosaic variegated aneuploidy syndrome 4 (MVA4) [MIM:620153] A form of mosaic variegated aneuploidy syndrome, a severe disorder characterized by mosaic aneuploidies, predominantly trisomies and monosomies, involving multiple different chromosomes and tissues. Affected individuals typically present with severe intrauterine growth retardation and microcephaly. Eye anomalies, mild dysmorphism, variable developmental delay, and a broad spectrum of additional congenital abnormalities and medical conditions may also occur. The risk of malignancy is high, with rhabdomyosarcoma, Wilms tumor and leukemia reported in several cases. MVA4 inheritance is autosomal recessive. The disease is caused by variants affecting the gene represented in this entry.

RefSeq proteins (1): NP_940891* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR028015CCDC84-likeFamily

Pfam: PF14968

UniProt features (9 total): region of interest 2, mutagenesis site 2, chain 1, coiled-coil region 1, compositionally biased region 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
8Y6OELECTRON MICROSCOPY3.38

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86UT8-F176.920.44

Functional residue map

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

Post-translational modifications (1): 31

Mutagenesis-validated functional residues (2):

PositionPhenotype
31increases interaction with sass6.
31strongly reduces acetylation. no effect on interaction with sass6.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 104 (showing top): GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_CHROMOSOME_SEPARATION, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_SPLICEOSOMAL_TRI_SNRNP_COMPLEX_ASSEMBLY, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE_PROCESS, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE, GOBP_REGULATION_OF_CELL_CYCLE, GOCC_CENTROSOME, GOBP_REGULATION_OF_CENTROSOME_CYCLE, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_RNA_SPLICING

GO Biological Process (6): mRNA splicing, via spliceosome (GO:0000398), negative regulation of centrosome duplication (GO:0010826), regulation of protein catabolic process (GO:0042176), chromosome separation (GO:0051304), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

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

GO Cellular Component (3): centrosome (GO:0005813), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA processing2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile1
mRNA processing1
regulation of centrosome duplication1
negative regulation of centrosome cycle1
centrosome duplication1
regulation of catabolic process1
protein catabolic process1
regulation of protein metabolic process1
chromosome segregation1
cell cycle process1
mRNA metabolic process1
binding1
centriole1
microtubule organizing center1
intracellular anatomical structure1
cellular anatomical structure1
intracellular membraneless organelle1

Protein interactions and networks

STRING

430 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CENATACC6orf52Q5T4I8613
CENATACENTR1Q96C92528
CENATACDYNC1LI2O43237499
CENATACCCDC107Q8WV48489
CENATACMRPL40Q9NQ50484
CENATACTMEM87AQ8NBN3475
CENATACCCDC190Q86UF4431
CENATACCCP110O43303427
CENATACTEPSINQ96N21426
CENATACCCDC169A6NNP5424
CENATACKATNIPO60303423
CENATACCCDC74BQ96LY2419
CENATACSNRNP48Q6IEG0419
CENATACTMEM208Q9BTX3418
CENATACINTS10Q9NVR2407

IntAct

53 interactions, top by confidence:

ABTypeScore
SNRPFGEMIN2psi-mi:“MI:0914”(association)0.910
CENATACTXNL4Bpsi-mi:“MI:0915”(physical association)0.770
SNRPEGEMIN2psi-mi:“MI:0914”(association)0.770
PRPF3PRPF4psi-mi:“MI:0914”(association)0.730
SNRPGGEMIN2psi-mi:“MI:0914”(association)0.710
SNRPBSART1psi-mi:“MI:0914”(association)0.640
CENATACZNF114psi-mi:“MI:0915”(physical association)0.560
CENATACMRPL38psi-mi:“MI:0915”(physical association)0.560
MESDCENATACpsi-mi:“MI:0915”(physical association)0.560
CENATACPPIL3psi-mi:“MI:0915”(physical association)0.560
CENATACNDOR1psi-mi:“MI:0915”(physical association)0.560
KLC2KIF5Bpsi-mi:“MI:0914”(association)0.530
G3BP1COX5Apsi-mi:“MI:0914”(association)0.530
SNRPEPRMT5psi-mi:“MI:0914”(association)0.530
CENATACGINS1psi-mi:“MI:0914”(association)0.530
SNRPESNRPGP15psi-mi:“MI:0914”(association)0.530
ADARB1SPTY2D1psi-mi:“MI:0914”(association)0.530
MAGEB2GTPBP10psi-mi:“MI:0914”(association)0.530
ECE1CENATACpsi-mi:“MI:0915”(physical association)0.370
YWHAZWDR62psi-mi:“MI:0914”(association)0.350
PRPF4psi-mi:“MI:0914”(association)0.350
Srp72psi-mi:“MI:0914”(association)0.350
Mtx2NRDCpsi-mi:“MI:0914”(association)0.350
Juppsi-mi:“MI:0914”(association)0.350
PIM2NUP98psi-mi:“MI:0914”(association)0.350
Tgs1EFCAB5psi-mi:“MI:0914”(association)0.350

BioGRID (74): PRPF3 (Affinity Capture-MS), TUT1 (Affinity Capture-MS), SART3 (Affinity Capture-MS), WDR83 (Affinity Capture-MS), DCAF5 (Affinity Capture-MS), TXNL4B (Affinity Capture-MS), CCDC84 (Affinity Capture-MS), CCDC84 (Affinity Capture-MS), CCDC84 (Affinity Capture-MS), CCDC84 (Affinity Capture-MS), CCDC84 (Affinity Capture-MS), CCDC84 (Affinity Capture-MS), CCDC84 (Affinity Capture-MS), CCDC84 (Affinity Capture-MS), CCDC84 (Affinity Capture-MS)

ESM2 similar proteins: A4D161, A6H7A8, E1BGQ2, O70524, O75391, P29084, P29540, P70445, Q14161, Q15650, Q28J59, Q2KJF9, Q2NL14, Q2VPL9, Q32LC9, Q32NC0, Q3ZK22, Q4V8D7, Q4VA36, Q5R595, Q5R802, Q5R9D9, Q5RFL7, Q5XI52, Q5ZJK1, Q66H91, Q6AY70, Q7TNE3, Q861R7, Q86UT8, Q8BND4, Q8BQR4, Q8BXK4, Q8C790, Q8IWR0, Q8K2I9, Q8NFZ0, Q8VDD9, Q8WWQ0, Q922H9

Diamond homologs: F4JRR5, Q4VA36, Q86UT8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 44 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
Metabolism of non-coding RNA5117.5×4e-08
snRNP Assembly754.8×5e-09
SARS-CoV-2 modulates host translation machinery541.5×2e-06
RNA Polymerase II Transcription Termination540.7×2e-06
mRNA Splicing624.4×2e-06
SARS-CoV-2-host interactions522.0×4e-05
Processing of Capped Intron-Containing Pre-mRNA618.3×1e-05
mRNA Splicing - Major Pathway918.2×4e-08

GO biological processes:

GO termPartnersFoldFDR
spliceosomal snRNP assembly7109.9×4e-11
mRNA splicing, via spliceosome1024.8×6e-10
RNA splicing716.7×9e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic0
Uncertain significance71
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
2627019NM_198489.3(CENATAC):c.805+2_805+19delPathogenic
2627020NM_198489.3(CENATAC):c.803A>T (p.Glu268Val)Pathogenic

SpliceAI

1695 predictions. Top by Δscore:

VariantEffectΔscore
11:118998291:G:GTdonor_gain1.0000
11:118998314:CCAG:Cdonor_loss1.0000
11:118998315:CAGGT:Cdonor_loss1.0000
11:118998316:AGG:Adonor_loss1.0000
11:118998317:GGTG:Gdonor_loss1.0000
11:118999006:TTCA:Tacceptor_loss1.0000
11:118999007:TCA:Tacceptor_loss1.0000
11:118999009:A:AGacceptor_gain1.0000
11:118999010:G:GCacceptor_gain1.0000
11:118999010:GC:Gacceptor_gain1.0000
11:118999010:GCCC:Gacceptor_gain1.0000
11:118999010:GCCCA:Gacceptor_gain1.0000
11:119010829:AGG:Adonor_loss1.0000
11:119010831:G:Cdonor_loss1.0000
11:119010832:T:Adonor_loss1.0000
11:119014989:TTCA:Tacceptor_loss1.0000
11:119014990:TCA:Tacceptor_loss1.0000
11:119014991:CAG:Cacceptor_loss1.0000
11:119014992:A:AGacceptor_gain1.0000
11:119014992:AG:Aacceptor_gain1.0000
11:119014992:AGGT:Aacceptor_gain1.0000
11:119014993:G:GAacceptor_gain1.0000
11:119014993:GG:Gacceptor_gain1.0000
11:119014993:GGT:Gacceptor_gain1.0000
11:119014993:GGTG:Gacceptor_gain1.0000
11:119014993:GGTGC:Gacceptor_gain1.0000
11:119015079:AGAAA:Adonor_gain1.0000
11:119015080:GAAA:Gdonor_gain1.0000
11:119015080:GAAAG:Gdonor_gain1.0000
11:119015081:A:Tdonor_gain1.0000

AlphaMissense

2182 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:119015399:T:CF300L0.999
11:119015401:T:AF300L0.999
11:119015401:T:GF300L0.999
11:119015411:T:AW304R0.999
11:119015411:T:CW304R0.999
11:119015413:G:CW304C0.999
11:119015413:G:TW304C0.999
11:119015008:T:AW244R0.998
11:119015008:T:CW244R0.998
11:119015387:T:AW296R0.998
11:119015387:T:CW296R0.998
11:119015357:T:CF286L0.997
11:119015359:T:AF286L0.997
11:119015359:T:GF286L0.997
11:119015389:G:CW296C0.996
11:119015389:G:TW296C0.996
11:119015403:G:AG301D0.996
11:119015412:G:CW304S0.996
11:119015426:C:AR309S0.996
11:119015545:T:CF316L0.996
11:119015547:C:AF316L0.996
11:119015547:C:GF316L0.996
11:119015343:G:CR281P0.995
11:119015400:T:GF300C0.995
11:119015010:G:CW244C0.994
11:119015010:G:TW244C0.994
11:118999040:T:CF105S0.993
11:118999042:T:AW106R0.993
11:118999042:T:CW106R0.993
11:119015349:G:AG283E0.993

dbSNP variants (sampled 300 via entrez): RS1000121364 (11:119015770 A>G), RS1000313978 (11:118996719 C>T), RS1000433036 (11:119010632 C>A,T), RS1000448558 (11:119011864 C>A,G,T), RS1000559872 (11:119005258 A>C,G), RS1000762085 (11:118999526 TC>T), RS1000816683 (11:119013502 C>A,G,T), RS1000998911 (11:119006202 T>G), RS1001030223 (11:119006617 C>G), RS1001085941 (11:119000537 T>C), RS1001411603 (11:118996996 A>G), RS1001464050 (11:118997314 T>C,G), RS1001526503 (11:119011226 A>G), RS1001746295 (11:119016060 G>A), RS1001757740 (11:119002495 C>G,T)

Disease associations

OMIM: gene MIM:620142 | disease phenotypes: MIM:620153

GenCC curated gene-disease

DiseaseClassificationInheritance
mosaic variegated aneuploidy syndrome 4LimitedAutosomal recessive

Mondo (1): mosaic variegated aneuploidy syndrome 4 (MONDO:0859329)

Orphanet (0):

HPO phenotypes

4 total (4 of 4 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000252Microcephaly
HP:0003220Abnormality of chromosome stability
HP:0011342Mild global developmental delay

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression3
bisphenol Aincreases expression, affects cotreatment, decreases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Particulate Matterdecreases expression, decreases reaction2
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arseniteaffects cotreatment, decreases expression, increases abundance1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
CGP 52608affects binding, increases reaction1
K 7174increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrineincreases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amidedecreases expression, decreases reaction1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Saffects cotreatment, decreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Decitabineaffects expression1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Atrazinedecreases expression1
Vehicle Emissionsdecreases expression, decreases reaction1
Cadmiumdecreases expression, increases abundance1
Carbamazepineaffects expression1
Cisplatinaffects expression1
Dexamethasoneaffects cotreatment, decreases expression1
Formaldehydeincreases expression1
Indomethacinaffects cotreatment, decreases expression1
Manganesedecreases expression, increases abundance, affects cotreatment1
Methyl Methanesulfonateincreases expression1
Silicon Dioxideincreases expression1
Silverincreases expression1
Smokedecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.