MAK16

gene
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Also known as MAK16L

Summary

MAK16 (MAK16 homolog, HGNC:13703) is a protein-coding gene on chromosome 8p12, encoding Protein MAK16 homolog (Q9BXY0). It is a common-essential gene (DepMap: required in 100.0% of cancer cell lines).

Enables RNA binding activity. Predicted to be involved in maturation of 5.8S rRNA and maturation of LSU-rRNA. Located in nucleolus.

Source: NCBI Gene 84549 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 66 total — 1 pathogenic
  • Phenotypes (HPO): 1
  • Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
  • MANE Select transcript: NM_032509

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13703
Approved symbolMAK16
NameMAK16 homolog
Location8p12
Locus typegene with protein product
StatusApproved
AliasesMAK16L
Ensembl geneENSG00000198042
Ensembl biotypeprotein_coding
Entrez84549

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 6 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000360128, ENST00000517567, ENST00000518389, ENST00000519089, ENST00000520763, ENST00000929667, ENST00000929668, ENST00000929669, ENST00000929670, ENST00000954019

RefSeq mRNA: 1 — MANE Select: NM_032509 NM_032509

CCDS: CCDS6089

Canonical transcript exons

ENST00000360128 — 10 exons

ExonStartEnd
ENSE000009116083348898833489139
ENSE000009116093349028533490339
ENSE000014215313349843233501262
ENSE000021317263348518233485221
ENSE000035154913348837833488427
ENSE000035336333348852033488629
ENSE000035936283349554233495616
ENSE000036168803348873433488798
ENSE000036316903349662533496741
ENSE000036670453349723233497297

Expression profiles

Bgee: expression breadth ubiquitous, 275 present calls, max score 90.15.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.5906 / max 633.0842, expressed in 1795 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
8839224.20801794
883941.3826781

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370190.15gold quality
secondary oocyteCL:000065589.88gold quality
oocyteCL:000002388.99gold quality
tendonUBERON:000004387.23gold quality
tibialis anteriorUBERON:000138586.54gold quality
deltoidUBERON:000147686.05silver quality
buccal mucosa cellCL:000233685.70silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.55gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.43gold quality
oviduct epitheliumUBERON:000480484.66gold quality
cervix squamous epitheliumUBERON:000692284.54silver quality
gluteal muscleUBERON:000200084.34gold quality
parietal pleuraUBERON:000240083.71gold quality
biceps brachiiUBERON:000150783.67gold quality
adrenal tissueUBERON:001830383.60gold quality
pleuraUBERON:000097783.28gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451183.00silver quality
endometriumUBERON:000129582.94gold quality
islet of LangerhansUBERON:000000682.71gold quality
palpebral conjunctivaUBERON:000181282.60gold quality
cartilage tissueUBERON:000241882.48gold quality
stromal cell of endometriumCL:000225582.28gold quality
skeletal muscle tissueUBERON:000113482.23gold quality
gastrocnemiusUBERON:000138882.06gold quality
muscle of legUBERON:000138382.02gold quality
colonic epitheliumUBERON:000039782.01gold quality
fallopian tubeUBERON:000388981.86gold quality
visceral pleuraUBERON:000240181.74gold quality
epithelium of mammary glandUBERON:000324481.65gold quality
mucosa of urinary bladderUBERON:000125981.63gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.90

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

157 targeting MAK16, 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-5692A100.0074.406850
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-4533100.0069.482758
HSA-MIR-9-5P100.0072.282361
HSA-MIR-428299.9975.366408
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-480399.9871.993117
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-548N99.9871.944170
HSA-MIR-1213699.9872.815713
HSA-MIR-569699.9872.364487
HSA-MIR-548P99.9872.253784
HSA-MIR-314899.9775.066478
HSA-MIR-365899.9673.874379
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-9-3P99.9670.882068
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-493-5P99.9672.472382
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-548AB99.9571.313488
HSA-MIR-55999.9572.283609
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriomak16ENSDARG00000003527
mus_musculusMak16ENSMUSG00000031578
rattus_norvegicusMak16ENSRNOG00000010783
drosophila_melanogasterRbm13FBGN0030067
caenorhabditis_elegansWBGENE00015811

Protein

Protein identifiers

Protein MAK16 homologQ9BXY0 (reviewed: Q9BXY0)

Alternative names: NNP78, Protein RBM13

All UniProt accessions (2): Q9BXY0, H0YBV6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus. Nucleolus.

Similarity. Belongs to the MAK16 family.

RefSeq proteins (1): NP_115898* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006958Mak16Family
IPR029004Ribosomal_eL28/Mak16Domain

Pfam: PF01778, PF04874

UniProt features (15 total): modified residue 5, compositionally biased region 3, cross-link 2, sequence conflict 2, chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

4 structures.

PDBMethodResolution (Å)
8FKVELECTRON MICROSCOPY2.47
8FKTELECTRON MICROSCOPY2.81
8FKPELECTRON MICROSCOPY2.85
8FKRELECTRON MICROSCOPY2.89

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BXY0-F175.200.49

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 (7): 55, 151, 1, 197, 200, 229, 232

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 155 (showing top): GOBP_RIBOSOME_BIOGENESIS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, PUJANA_CHEK2_PCC_NETWORK, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_MATURATION_OF_LSU_RRNA, GATA1_01, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP, chr8p12, GOBP_MATURATION_OF_5_8S_RRNA, SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS, BERENJENO_TRANSFORMED_BY_RHOA_UP, CAIRO_LIVER_DEVELOPMENT_UP, GOCC_PRERIBOSOME

GO Biological Process (2): maturation of 5.8S rRNA (GO:0000460), maturation of LSU-rRNA (GO:0000470)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (3): nucleolus (GO:0005730), preribosome, large subunit precursor (GO:0030687), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
rRNA processing2
ribosomal large subunit biogenesis1
nucleic acid binding1
binding1
nuclear lumen1
intracellular membraneless organelle1
preribosome1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

2305 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MAK16WDR12Q9GZL7678
MAK16NIFKQ9BYG3671
MAK16RSL1D1O76021663
MAK16PA2G4Q9UQ80627
MAK16NIP7Q9Y221597
MAK16PUS7Q96PZ0597
MAK16GTPBP4Q9BZE4572
MAK16POLR1BQ9H9Y6570
MAK16PAK1IP1Q9NWT1558
MAK16WDR74Q6RFH5523
MAK16RRP36Q96EU6520
MAK16EBNA1BP2Q99848517
MAK16GNL3Q9BVP2515
MAK16RSPH14Q9UHP6509
MAK16RAB14P35287492

IntAct

107 interactions, top by confidence:

ABTypeScore
MAK16FRMD6psi-mi:“MI:0915”(physical association)0.670
FRMD6MAK16psi-mi:“MI:0915”(physical association)0.670
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
NPM1NVLpsi-mi:“MI:0914”(association)0.610
MAK16LIN7Bpsi-mi:“MI:0915”(physical association)0.560
RPL28MAGEB2psi-mi:“MI:0914”(association)0.560
HNRNPH2PLOD2psi-mi:“MI:0914”(association)0.530
H1-4IGF2BP3psi-mi:“MI:0914”(association)0.530
ZNF2MPHOSPH10psi-mi:“MI:0914”(association)0.530
MACROH2A2PPM1Gpsi-mi:“MI:0914”(association)0.530
MAK16NVLpsi-mi:“MI:0914”(association)0.530
ZBTB48ZBTB24psi-mi:“MI:0914”(association)0.530
RPF1ZNF324psi-mi:“MI:0914”(association)0.530
MAGEB2POLRMTpsi-mi:“MI:0914”(association)0.530
H1-4RRP8psi-mi:“MI:0914”(association)0.530
KRR1MPHOSPH10psi-mi:“MI:0914”(association)0.530
NHSL3NCK2psi-mi:“MI:0914”(association)0.530
ZNF71DKC1psi-mi:“MI:0914”(association)0.530
MAK16CSNK2A1psi-mi:“MI:0217”(phosphorylation reaction)0.440
CSNK2A2WDR46psi-mi:“MI:0914”(association)0.350
SMC6IFT88psi-mi:“MI:0914”(association)0.350
TSNAXpsi-mi:“MI:0914”(association)0.350
Cep85lCLK2psi-mi:“MI:0914”(association)0.350
PDGFRARNPS1psi-mi:“MI:0914”(association)0.350

BioGRID (231): MAK16 (Affinity Capture-MS), BRIX1 (Co-fractionation), MAK16 (Co-fractionation), MAK16 (Affinity Capture-MS), MAK16 (Affinity Capture-MS), MAK16 (Affinity Capture-MS), MAK16 (Affinity Capture-MS), MAK16 (Affinity Capture-MS), MAK16 (Affinity Capture-MS), MAK16 (Affinity Capture-MS), MAK16 (Affinity Capture-MS), MAK16 (Affinity Capture-MS), FRMD6 (Affinity Capture-MS), WDR74 (Affinity Capture-MS), TUBA8 (Affinity Capture-MS)

ESM2 similar proteins: A1CQN6, A3GGT2, A3GGV1, A5DNZ1, A5E203, A7A241, A7TJT3, A7TSJ7, A8P353, B4PKZ7, C5E1C7, F5HI87, O14015, O14218, O49691, O59835, O60153, P0C9Y6, P13200, P29832, P36103, P41884, P43587, P46583, P53222, Q09356, Q11091, Q196X1, Q1DR50, Q4R309, Q59ZU1, Q59ZW4, Q6BSZ8, Q6CNA0, Q6DDH0, Q6FUM5, Q6GLB0, Q6R7J4, Q750F0, Q88889

Diamond homologs: P10962, P46435, Q1RML7, Q55DJ3, Q66L33, Q6NYD4, Q6P7N1, Q7ZYG5, Q8BGS0, Q9BXY0, Q9UTE6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 121 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
Peptide chain elongation914.8×4e-07
Viral mRNA Translation914.8×4e-07
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA914.7×4e-07
rRNA modification in the nucleus and cytosol614.6×5e-05
Selenocysteine synthesis914.1×4e-07
Eukaryotic Translation Termination914.1×4e-07
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)913.8×4e-07
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA913.8×4e-07

GO biological processes:

GO termPartnersFoldFDR
ribosomal large subunit biogenesis623.8×2e-05
cytoplasmic translation1016.5×1e-07
ribosomal small subunit biogenesis816.3×6e-06
rRNA processing1215.2×1e-08
regulation of alternative mRNA splicing, via spliceosome613.1×6e-04
regulation of RNA splicing59.8×9e-03
translation109.2×2e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance42
Likely benign9
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
88868NM_001102401.4(TTI2):c.1307T>A (p.Ile436Asn)Pathogenic

SpliceAI

1198 predictions. Top by Δscore:

VariantEffectΔscore
8:33485222:G:GGdonor_gain1.0000
8:33488372:TTGCA:Tacceptor_loss1.0000
8:33488373:TGCA:Tacceptor_loss1.0000
8:33488374:GCA:Gacceptor_loss1.0000
8:33488375:CA:Cacceptor_loss1.0000
8:33488376:AGGT:Aacceptor_loss1.0000
8:33488377:GGTT:Gacceptor_gain1.0000
8:33488428:G:GAdonor_loss1.0000
8:33488513:A:AGacceptor_gain1.0000
8:33488514:T:Gacceptor_gain1.0000
8:33488518:A:AGacceptor_gain1.0000
8:33488519:G:GTacceptor_gain1.0000
8:33488519:GA:Gacceptor_gain1.0000
8:33488519:GAA:Gacceptor_gain1.0000
8:33488519:GAAC:Gacceptor_gain1.0000
8:33488519:GAACC:Gacceptor_gain1.0000
8:33488625:GAAAG:Gdonor_gain1.0000
8:33488626:AAAGG:Adonor_loss1.0000
8:33488627:AAGGT:Adonor_loss1.0000
8:33488628:AG:Adonor_loss1.0000
8:33488629:GGTA:Gdonor_loss1.0000
8:33488630:G:Tdonor_loss1.0000
8:33488631:T:Adonor_loss1.0000
8:33488733:GGACA:Gacceptor_gain1.0000
8:33489140:G:GGdonor_gain1.0000
8:33495427:G:GTdonor_gain1.0000
8:33495540:A:ACacceptor_loss1.0000
8:33495612:A:Gdonor_gain1.0000
8:33495617:G:GGdonor_gain1.0000
8:33496614:AT:Aacceptor_gain1.0000

AlphaMissense

1995 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:33488384:T:AW8R0.999
8:33488384:T:CW8R0.999
8:33488569:T:CC39R0.999
8:33488584:T:CC44R0.999
8:33488609:C:AA52D0.999
8:33488790:T:AW78R0.999
8:33488790:T:CW78R0.999
8:33488792:G:CW78C0.999
8:33488792:G:TW78C0.999
8:33489040:T:CL98P0.999
8:33489074:T:GC109W0.999
8:33489077:G:CK110N0.999
8:33489077:G:TK110N0.999
8:33489106:T:CL120P0.999
8:33489112:G:CR122P0.999
8:33489124:T:CL126P0.999
8:33495558:C:AA155D0.999
8:33495560:G:CA156P0.999
8:33495561:C:AA156D0.999
8:33495575:G:CA161P0.999
8:33495579:T:AI162N0.999
8:33495591:T:CL166S0.999
8:33495603:T:CL170P0.999
8:33488386:G:CW8C0.998
8:33488386:G:TW8C0.998
8:33488411:T:CC17R0.998
8:33488412:G:AC17Y0.998
8:33488539:T:CC29R0.998
8:33488540:G:AC29Y0.998
8:33488541:C:GC29W0.998

dbSNP variants (sampled 300 via entrez): RS1000107618 (8:33492491 A>G), RS1000497496 (8:33484529 T>A,C), RS1000609111 (8:33497389 C>T), RS1000774633 (8:33484737 C>A,T), RS1001079798 (8:33490710 T>C), RS1001490144 (8:33498739 A>C), RS1001543862 (8:33495695 T>A,G), RS1001696454 (8:33489384 T>C), RS1001704809 (8:33483452 G>C), RS1001940541 (8:33493815 C>T), RS1002127451 (8:33489609 A>C), RS1002340675 (8:33500461 T>C), RS1002544993 (8:33494330 C>T), RS1002867055 (8:33500754 A>C,G), RS1003265715 (8:33488080 C>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:615541

GenCC curated gene-disease

Mondo (2): severe intellectual disability-short stature-behavioral abnormalities-facial dysmorphism syndrome (MONDO:0014238), microcephaly (MONDO:0001149)

Orphanet (1): Severe intellectual disability-short stature-behavioral abnormalities-facial dysmorphism syndrome (Orphanet:391307)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPOTerm
HP:0000252Microcephaly

GWAS associations

2 associations (top):

StudyTraitp-value
GCST006626_14Pulse pressure1.000000e-09
GCST009391_574Metabolite levels7.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0005763pulse pressure measurement
EFO:0021604hypoxanthine measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D008831MicrocephalyC05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects methylation, decreases expression2
sodium arseniteaffects cotreatment, increases abundance, increases expression, decreases expression2
Resveratrolaffects cotreatment, decreases expression, increases expression2
Estradiolincreases expression2
FR900359affects phosphorylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
tetrahydropalmatinedecreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
1-nitropyreneincreases expression1
di-n-butylphosphoric acidaffects expression1
perfluoro-n-nonanoic acidincreases expression1
bisphenol Saffects expression1
jinfukangdecreases expression1
Temozolomideincreases expression1
Sunitinibincreases expression1
Leflunomideincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicincreases expression, affects cotreatment, increases abundance1
Benzo(a)pyreneincreases methylation1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Ethyl Methanesulfonatedecreases expression1
Ivermectindecreases expression1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Manganeseaffects cotreatment, increases abundance, increases expression1
Methyl Methanesulfonatedecreases expression1
Plant Extractsincreases expression, affects cotreatment1
Ribonucleotidesaffects binding1
Smokedecreases expression1
Dronabinoldecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT05518188PHASE1/PHASE2RECRUITINGMelpida: Recombinant Adeno-associated Virus (serotype 9) Encoding a Codon Optimized Human AP4M1 Transgene (hAP4M1opt)
NCT00001639Not specifiedCOMPLETEDEvaluation of Patients With Unresolved Chromosome Abnormalities
NCT01151462Not specifiedWITHDRAWNPostnatal HCMV Infection in Very Preterm Infants. Implications, Morbidity, Growth and Neurodevelopmental Outcomes.
NCT01565005Not specifiedCOMPLETEDMicrocephaly Genetic Deficiency in Neural Progenitors
NCT02510170Not specifiedCOMPLETEDFetal and Maternal Head Circumference During Pregnancy in Israeli Population
NCT02741882Not specifiedCOMPLETEDZika and Microcephaly: Case-control Study
NCT02943304Not specifiedCOMPLETEDNeurodevelopment Outcome of Newborns Exposed to Zika Virus (ZIKV) in Utero
NCT03255369Not specifiedUNKNOWNVertical Exposure to Zika Virus and Its Consequences for Child Neurodevelopment (ZIKVIRUSIFF)
NCT03325946Not specifiedRECRUITINGThe FBRI VTC Neuromotor Research Clinic
NCT03330600Not specifiedCOMPLETEDEfficacy of Aquatic Physiotherapy in Children With Microcephaly by Zika Virus Congenital Syndrome
NCT03548779Not specifiedCOMPLETEDNorth Carolina Genomic Evaluation by Next-generation Exome Sequencing, 2
NCT03651687Not specifiedCOMPLETEDGuangzhou Surveillance and Clinical Study in Microcephaly (GSCSM)
NCT03922594Not specifiedTERMINATEDSurveillance of Zika-related Microcephaly in Sub-Saharan Africa and Asia
NCT04816175Not specifiedCOMPLETEDIntensive Therapy for Children With Microcephaly, Hyperkinetic Movements, or Global Developmental Delay
NCT05322980Not specifiedCOMPLETEDSummary of Infants Weighing 500 Grams or Less
NCT06019182Not specifiedRECRUITINGMEHMO Natural History and Biomarkers
NCT06566066Not specifiedRECRUITINGRegister for Patients With Thyroid Hormone Resistance.