LIN9

gene
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Also known as TGS

Summary

LIN9 (lin-9 DREAM MuvB core complex component, HGNC:30830) is a protein-coding gene on chromosome 1q42.12, encoding Protein lin-9 homolog (Q5TKA1). Acts as a tumor suppressor.

This gene encodes a tumor suppressor protein that inhibits DNA synthesis and oncogenic transformation through association with the retinoblastoma 1 protein. The encoded protein also interacts with a complex of other cell cycle regulators to repress cell cycle-dependent gene expression in non-dividing cells. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 286826 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 61 total
  • MANE Select transcript: NM_001366245

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30830
Approved symbolLIN9
Namelin-9 DREAM MuvB core complex component
Location1q42.12
Locus typegene with protein product
StatusApproved
AliasesTGS
Ensembl geneENSG00000183814
Ensembl biotypeprotein_coding
OMIM609375
Entrez286826

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 protein_coding

ENST00000328205, ENST00000359525, ENST00000366808, ENST00000460719, ENST00000481685, ENST00000681046, ENST00000899464, ENST00000899465, ENST00000899466, ENST00000899467, ENST00000918994, ENST00000918995

RefSeq mRNA: 9 — MANE Select: NM_001366245 NM_001270409, NM_001270410, NM_001366237, NM_001366238, NM_001366239, NM_001366240, NM_001366241, NM_001366245, NM_173083

CCDS: CCDS1553, CCDS91164, CCDS91165

Canonical transcript exons

ENST00000681046 — 15 exons

ExonStartEnd
ENSE00001292598226277775226277932
ENSE00001293826226266213226266332
ENSE00001300920226295842226295946
ENSE00001306222226250839226250919
ENSE00001312187226286333226286458
ENSE00001313449226267957226268090
ENSE00001321890226287664226287797
ENSE00001324549226265533226265634
ENSE00001337987226233096226233193
ENSE00001337989226233344226233523
ENSE00001337990226238971226239096
ENSE00001442658226231157226232606
ENSE00003498432226301173226301205
ENSE00003593168226297719226297813
ENSE00003912496226309109226309164

Expression profiles

Bgee: expression breadth ubiquitous, 185 present calls, max score 86.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.5988 / max 149.6492, expressed in 1348 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
177485.54621338
177500.052613

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305386.67gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.34gold quality
ganglionic eminenceUBERON:000402384.35gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.77gold quality
heart left ventricleUBERON:000208479.42gold quality
cardiac ventricleUBERON:000208279.24gold quality
secondary oocyteCL:000065579.07silver quality
heart right ventricleUBERON:000208078.28silver quality
oocyteCL:000002377.32gold quality
heartUBERON:000094875.96gold quality
apex of heartUBERON:000209875.71gold quality
cortical plateUBERON:000534375.66gold quality
calcaneal tendonUBERON:000370175.35gold quality
rectumUBERON:000105273.70gold quality
right atrium auricular regionUBERON:000663173.02gold quality
smooth muscle tissueUBERON:000113573.00gold quality
cardiac atriumUBERON:000208172.01gold quality
stromal cell of endometriumCL:000225571.17gold quality
testisUBERON:000047370.36gold quality
muscle of legUBERON:000138370.22gold quality
islet of LangerhansUBERON:000000670.08gold quality
gastrocnemiusUBERON:000138869.87gold quality
vermiform appendixUBERON:000115469.77gold quality
bone marrow cellCL:000209269.72silver quality
right testisUBERON:000453469.65gold quality
lymph nodeUBERON:000002969.39gold quality
ovaryUBERON:000099269.04gold quality
left testisUBERON:000453368.86gold quality
leukocyteCL:000073868.62gold quality
esophagus mucosaUBERON:000246968.53gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes10.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

100 targeting LIN9, 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-4795-3P100.0074.624024
HSA-MIR-3163100.0077.238605
HSA-MIR-5692A100.0074.406850
HSA-MIR-126-5P100.0072.713180
HSA-MIR-340-5P100.0072.504437
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-428299.9975.366408
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-480399.9871.993117
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-1213699.9872.815713
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-60799.9773.625593
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-3065-5P99.9771.563281

Literature-anchored findings (GeneRIF, showing 12)

  • Human Lin-9 has tumor-suppressing activities and the ability of hLin-9 to inhibit transformation is mediated through its association with pRB. (PMID:15538385)
  • Mutation of BARA/LIN-9 restores the expression of E2F target genes. (PMID:16730350)
  • Mip/LIN-9 is required for the expression of B-Myb, and both proteins collaborate in the control of the cell cycle progression via the regulation of S phase and cyclin A, cyclin B, and CDK1 (PMID:17098733)
  • human LIN-9, together with B-MYB, has a critical role in the activation of genes that are essential for progression into mitosis (PMID:17159899)
  • The repressor complex that Mip/LIN-9 forms with p107 takes functional precedence over the transcriptional activation linked to the Mip/LIN-9 and B-Myb interaction. (PMID:17563750)
  • inactivation of LIN9, a subunit of DREAM, results in premature senescence, which can be overcome by the SV40 large T (LT) antigen (PMID:21860417)
  • Study links hTRM9L and tRNA modifications to inhibition of tumour growth via LIN9 and HIF1-alpha-dependent mechanisms. (PMID:23381944)
  • Results show that E7 interacts with the B-Myb, FoxM1 and LIN9 components of this activator complex, leading to cooperative transcriptional activation of mitotic genes in primary cells and E7 recruitment to the corresponding promoters. (PMID:24141769)
  • LIN-9 phosphorylation on threonine-96 is required for transcriptional activation of LIN-9 target genes and promotes cell cycle progression. (PMID:24475316)
  • The MuvB multiprotein complex, together with B-MYB and FOXM1 (MMB-FOXM1) regulate the expression of mitotic kinesins in breast cancer cells. (PMID:28061449)
  • High LIN9 expression is associated with Triple-negative breast cancers. (PMID:28807940)
  • LIN9 and NEK2 Are Core Regulators of Mitotic Fidelity That Can Be Therapeutically Targeted to Overcome Taxane Resistance. (PMID:32054769)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriolin9ENSDARG00000028475
mus_musculusLin9ENSMUSG00000058729
rattus_norvegicusLin9ENSRNOG00000023304
drosophila_melanogasteralyFBGN0004372
drosophila_melanogastermip130FBGN0023509
caenorhabditis_elegansWBGENE00002998

Protein

Protein identifiers

Protein lin-9 homologQ5TKA1 (reviewed: Q5TKA1)

Alternative names: Beta subunit-associated regulator of apoptosis, TUDOR gene similar protein, Type I interferon receptor beta chain-associated protein, pRB-associated protein

All UniProt accessions (5): Q5TKA1, B1B047, C9J5J4, H0Y322, H7C4T7

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a tumor suppressor. Inhibits DNA synthesis. Its ability to inhibit oncogenic transformation is mediated through its association with RB1. Plays a role in the expression of genes required for the G1/S transition.

Subunit / interactions. Component of the DREAM complex (also named LINC complex) at least composed of E2F4, E2F5, LIN9, LIN37, LIN52, LIN54, MYBL1, MYBL2, RBL1, RBL2, RBBP4, TFDP1 and TFDP2. The complex exists in quiescent cells where it represses cell cycle-dependent genes. It dissociates in S phase when LIN9, LIN37, LIN52 and LIN54 form a subcomplex that binds to MYBL2. Interacts with RB1.

Subcellular location. Nucleus. Nucleoplasm.

Tissue specificity. Expressed in thymus and testis.

Similarity. Belongs to the lin-9 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q5TKA1-11, Lin9-L, Long formyes
Q5TKA1-22
Q5TKA1-33, Lin9-S, Short form

RefSeq proteins (9): NP_001257338, NP_001257339, NP_001353166, NP_001353167, NP_001353168, NP_001353169, NP_001353170, NP_001353174, NP_775106 (=MANE)

Domains & families (InterPro)

IDNameType
IPR010561LIN-9/ALY1Family
IPR033471DIRPDomain
IPR045831LIN9_CDomain

Pfam: PF06584, PF19438

UniProt features (36 total): helix 10, modified residue 7, strand 7, turn 3, splice variant 2, sequence conflict 2, initiator methionine 1, chain 1, cross-link 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
6C48X-RAY DIFFRACTION2.32
7N40X-RAY DIFFRACTION2.55
7R1DELECTRON MICROSCOPY3.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5TKA1-F171.210.28

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 (8): 321, 21, 2, 65, 95, 96, 304, 309

Function

Pathways and Gene Ontology

Reactome pathways

14 pathways

IDPathway
R-HSA-1362277Transcription of E2F targets under negative control by DREAM complex
R-HSA-1362300Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1
R-HSA-1538133G0 and Early G1
R-HSA-156711Polo-like kinase mediated events
R-HSA-69202Cyclin E associated events during G1/S transition
R-HSA-69205G1/S-Specific Transcription
R-HSA-69656Cyclin A:Cdk2-associated events at S phase entry
R-HSA-1640170Cell Cycle
R-HSA-453274Mitotic G2-G2/M phases
R-HSA-453279Mitotic G1 phase and G1/S transition
R-HSA-69206G1/S Transition
R-HSA-69242S Phase
R-HSA-69275G2/M Transition
R-HSA-69278Cell Cycle, Mitotic

MSigDB gene sets: 196 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, TAATAAT_MIR126, REACTOME_G1_S_SPECIFIC_TRANSCRIPTION, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, TATTATA_MIR374, LE_EGR2_TARGETS_UP, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_DNA_BIOSYNTHETIC_PROCESS, DODD_NASOPHARYNGEAL_CARCINOMA_UP, FISCHER_DREAM_TARGETS, BERENJENO_TRANSFORMED_BY_RHOA_UP, TTTGCAC_MIR19A_MIR19B, DURCHDEWALD_SKIN_CARCINOGENESIS_DN, GOCC_RNA_POLYMERASE_II_TRANSCRIPTION_REGULATOR_COMPLEX

GO Biological Process (4): DNA-templated transcription (GO:0006351), regulation of transcription by RNA polymerase II (GO:0006357), regulation of cell cycle (GO:0051726), DNA biosynthetic process (GO:0071897)

GO Molecular Function (2): DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (3): nucleoplasm (GO:0005654), transcription repressor complex (GO:0017053), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-8 pathways:

CategoryPathways
Cell Cycle, Mitotic3
G0 and Early G12
Mitotic G1 phase and G1/S transition2
G1/S Transition2
G2/M Transition1
S Phase1
Mitotic G2-G2/M phases1
Cell Cycle1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
gene expression1
RNA biosynthetic process1
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
cell cycle1
regulation of cellular process1
DNA metabolic process1
nucleic acid biosynthetic process1
nucleic acid binding1
binding1
nuclear lumen1
cellular anatomical structure1
transcription regulator complex1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

944 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LIN9LIN37Q96GY3999
LIN9RBBP4P31149999
LIN9LIN54Q6MZP7999
LIN9LIN52Q52LA3998
LIN9MYBL2P10244994
LIN9E2F4Q16254939
LIN9RBL2Q08999897
LIN9FOXM1Q08050753
LIN9RB1P06400740
LIN9E2F5Q15329701
LIN9MYBL1P10243679
LIN9MSI1O43347665
LIN9DPP6P42658638
LIN9RBBP7Q16576625
LIN9E2F1Q01094608

IntAct

81 interactions, top by confidence:

ABTypeScore
CDK2CCNE2psi-mi:“MI:0914”(association)0.940
RBBP7CDK2AP1psi-mi:“MI:0914”(association)0.840
RBBP4CDK2AP1psi-mi:“MI:0914”(association)0.790
LIN37RBL2psi-mi:“MI:0914”(association)0.770
LIN37MYBL2psi-mi:“MI:0914”(association)0.730
LIN9MYBL2psi-mi:“MI:0914”(association)0.720
LIN9MYBL2psi-mi:“MI:0915”(physical association)0.720
MYBL2LIN9psi-mi:“MI:0915”(physical association)0.720
LIN9RBL2psi-mi:“MI:0914”(association)0.700
LIN9RBL2psi-mi:“MI:0915”(physical association)0.700
RBL2LIN9psi-mi:“MI:0914”(association)0.700
E2F4LIN9psi-mi:“MI:0915”(physical association)0.670
LIN54RBL2psi-mi:“MI:0914”(association)0.620
TCF19E2F6psi-mi:“MI:0914”(association)0.620
LIN54MYBL2psi-mi:“MI:0914”(association)0.560
RBL2LIN52psi-mi:“MI:0914”(association)0.560

BioGRID (208): LIN9 (Affinity Capture-RNA), LIN9 (Affinity Capture-RNA), LIN9 (Affinity Capture-RNA), LIN9 (Affinity Capture-MS), LIN9 (Affinity Capture-MS), LIN9 (Affinity Capture-MS), LIN9 (Proximity Label-MS), LIN9 (Affinity Capture-MS), LIN9 (Affinity Capture-MS), LIN9 (Affinity Capture-MS), MYBL2 (Affinity Capture-Western), LIN9 (Affinity Capture-MS), LIN9 (Affinity Capture-MS), MYBL2 (Affinity Capture-MS), LIN54 (Affinity Capture-MS)

ESM2 similar proteins: A0AUQ6, A2BE76, O14645, O18973, O35427, O35473, O55003, O88447, O88597, P50503, Q05B58, Q12983, Q13901, Q14457, Q14AM7, Q14CZ0, Q28HY5, Q32KN2, Q32PE4, Q4A1L3, Q4A1L4, Q4A1L5, Q4R3K5, Q4R8N2, Q4RLT3, Q52LA3, Q5JSJ4, Q5NVP8, Q5R878, Q5RBU4, Q5TKA1, Q5ZHS3, Q5ZJQ3, Q68FJ8, Q6DKA1, Q6GMH0, Q6GP52, Q6PAX8, Q6X4M3, Q7TSU0

Diamond homologs: P30630, Q4R8N2, Q5RHQ8, Q5TKA1, Q6A331, Q6A333, Q8C735, Q6A332

SIGNOR signaling

2 interactions.

AEffectBMechanism
CDK3up-regulatesLIN9phosphorylation
CyclinE1/CDK3“up-regulates activity”LIN9phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 73 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
G0 and Early G11180.5×1e-16
Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1880.1×3e-12
Transcription of E2F targets under negative control by DREAM complex872.5×6e-12
Polo-like kinase mediated events663.4×2e-08
Cyclin E associated events during G1/S transition1047.6×1e-12
G1/S-Specific Transcription847.6×3e-10
Cyclin A:Cdk2-associated events at S phase entry1044.3×2e-12
G1/S Transition623.3×1e-05

GO biological processes:

GO termPartnersFoldFDR
G1/S transition of mitotic cell cycle617.2×2e-04
chromatin remodeling88.3×5e-04
transcription by RNA polymerase II88.1×5e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance43
Likely benign0
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2294 predictions. Top by Δscore:

VariantEffectΔscore
1:226233092:TTAC:Tdonor_loss1.0000
1:226233093:TA:Tdonor_loss1.0000
1:226233094:ACCTG:Adonor_loss1.0000
1:226233095:CCT:Cdonor_loss1.0000
1:226233189:AGACA:Aacceptor_gain1.0000
1:226233190:GACA:Gacceptor_gain1.0000
1:226233191:ACA:Aacceptor_gain1.0000
1:226233192:CA:Cacceptor_gain1.0000
1:226233192:CAC:Cacceptor_gain1.0000
1:226233193:ACTAA:Aacceptor_loss1.0000
1:226233194:C:CCacceptor_gain1.0000
1:226234555:T:TAdonor_gain1.0000
1:226238966:CTTA:Cdonor_loss1.0000
1:226238967:TTA:Tdonor_loss1.0000
1:226238968:TAC:Tdonor_loss1.0000
1:226238969:A:ACdonor_gain1.0000
1:226238969:AC:Adonor_gain1.0000
1:226238969:ACCT:Adonor_gain1.0000
1:226238969:ACCTC:Adonor_loss1.0000
1:226238970:C:CTdonor_gain1.0000
1:226238970:CC:Cdonor_gain1.0000
1:226238970:CCT:Cdonor_gain1.0000
1:226238970:CCTC:Cdonor_gain1.0000
1:226238970:CCTCA:Cdonor_gain1.0000
1:226239092:GATTT:Gacceptor_gain1.0000
1:226239093:ATTT:Aacceptor_gain1.0000
1:226239094:TTT:Tacceptor_gain1.0000
1:226239095:TT:Tacceptor_gain1.0000
1:226239096:TCTGA:Tacceptor_loss1.0000
1:226239097:C:CCacceptor_gain1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000015635 (1:226242792 C>T), RS1000063352 (1:226272721 C>T), RS1000110835 (1:226302913 C>T), RS1000149119 (1:226281776 C>T), RS1000201485 (1:226306004 T>C), RS1000217648 (1:226255064 A>C), RS1000244189 (1:226281574 G>C), RS1000307871 (1:226306248 C>T), RS1000392661 (1:226293828 T>A), RS1000407826 (1:226268111 T>C), RS1000429070 (1:226255289 T>C), RS1000490239 (1:226300181 G>A,C,T), RS1000516214 (1:226305027 G>A), RS1000544749 (1:226261140 A>T), RS1000545526 (1:226256616 T>C)

Disease associations

OMIM: gene MIM:609375 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST009257_10Caudate nucleus volume2.000000e-06
GCST010105_147Nicotine dependence symptom count6.000000e-06
GCST010816_6Gut microbiota beta diversity (weighted UniFrac distance)8.000000e-06
GCST012489_97Heel bone mineral density x serum urate levels interaction9.000000e-09
GCST90002390_340Mean corpuscular hemoglobin3.000000e-11
GCST90002395_508Mean platelet volume5.000000e-12

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0004830caudate nucleus volume
EFO:0009262nicotine dependence symptom count
EFO:0007874gut microbiome measurement
EFO:0004531urate measurement
EFO:0009270heel bone mineral density
EFO:0004527mean corpuscular hemoglobin

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression4
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
propionaldehydedecreases expression1
bisphenol Aincreases methylation1
arsenitedecreases reaction, affects binding1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
aflatoxin B2decreases methylation1
coumarinincreases phosphorylation1
epigallocatechin gallateaffects cotreatment, decreases expression1
2-palmitoylglycerolincreases expression1
(+)-JQ1 compounddecreases expression1
Sunitinibdecreases expression1
Ethanoldecreases expression1
Atrazinedecreases expression1
Benzo(a)pyreneincreases methylation1
Caffeineaffects phosphorylation1
Calcitrioldecreases expression, affects cotreatment1
Cisplatinincreases expression1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Leadaffects expression1
Lucanthonedecreases expression1
Testosteronedecreases expression, affects cotreatment1
Tetrachlorodibenzodioxinaffects expression1
Thimerosalincreases expression1
Tobacco Smoke Pollutiondecreases expression1
Tretinoindecreases 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.