TNRC18

gene
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Also known as CAGL79TNRC18AKIAA1856

Summary

TNRC18 (trinucleotide repeat containing 18, HGNC:11962) is a protein-coding gene on chromosome 7p22.1, encoding Trinucleotide repeat-containing gene 18 protein (O15417). Chromatin reader involved in the silencing of endogenous retroviruses (ERV) class-I elements, such as LTR12.

Predicted to enable chromatin binding activity. Located in cytosol; mitochondrion; and nucleus.

Source: NCBI Gene 84629 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 964 total
  • MANE Select transcript: NM_001080495

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11962
Approved symbolTNRC18
Nametrinucleotide repeat containing 18
Location7p22.1
Locus typegene with protein product
StatusApproved
AliasesCAGL79, TNRC18A, KIAA1856
Ensembl geneENSG00000182095
Ensembl biotypeprotein_coding
OMIM620902
Entrez84629

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 2 retained_intron

ENST00000328270, ENST00000399434, ENST00000399537, ENST00000413081, ENST00000430969, ENST00000434361, ENST00000440081, ENST00000455076, ENST00000464852, ENST00000497663

RefSeq mRNA: 1 — MANE Select: NM_001080495 NM_001080495

CCDS: CCDS47534

Canonical transcript exons

ENST00000430969 — 30 exons

ExonStartEnd
ENSE0000103620753615945361722
ENSE0000103621053703755371364
ENSE0000103621253593985359569
ENSE0000103621853626505362825
ENSE0000108622653518195352094
ENSE0000108622853455625345810
ENSE0000124332553618975362033
ENSE0000159826053068115308312
ENSE0000160340853760345376224
ENSE0000162569053205325320607
ENSE0000163676353250965325248
ENSE0000164337253779225378024
ENSE0000164924353740555374484
ENSE0000165659253125035313863
ENSE0000166561353768475376993
ENSE0000168388653904855390628
ENSE0000169336153210735321190
ENSE0000170244153569165357276
ENSE0000173427353326225333049
ENSE0000173706353088755308949
ENSE0000174205053159565316072
ENSE0000175609153091325309368
ENSE0000176388653242145324355
ENSE0000176539753203185320426
ENSE0000176630953876725389336
ENSE0000177133253773715377576
ENSE0000177746553149845315148
ENSE0000273328154210605421489
ENSE0000353221153944405394595
ENSE0000392194554234415423834

Expression profiles

Bgee: expression breadth ubiquitous, 248 present calls, max score 98.15.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.7869 / max 302.5122, expressed in 1745 samples.

FANTOM5 promoters (13 alternative TSS)

Promoter IDTPM avgSamples expressed
825738.94701651
825701.87281031
825661.8166735
825690.8920483
825720.8749440
825750.6998388
825710.6254321
825670.5471339
825770.4545237
825650.4527119

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
sural nerveUBERON:001548898.15gold quality
cardiac muscle of right atriumUBERON:000337997.71gold quality
upper arm skinUBERON:000426397.63gold quality
ventricular zoneUBERON:000305397.26gold quality
colonic epitheliumUBERON:000039797.06gold quality
kidney epitheliumUBERON:000481996.73gold quality
ganglionic eminenceUBERON:000402395.71gold quality
cortical plateUBERON:000534395.54gold quality
nasal cavity epitheliumUBERON:000538495.46gold quality
popliteal arteryUBERON:000225095.40gold quality
tibial arteryUBERON:000761095.39gold quality
left ventricle myocardiumUBERON:000656695.35silver quality
body of uterusUBERON:000985395.23gold quality
superficial temporal arteryUBERON:000161495.08gold quality
mucosa of stomachUBERON:000119994.96gold quality
lower esophagus muscularis layerUBERON:003583394.93gold quality
lower esophagusUBERON:001347394.90gold quality
aortaUBERON:000094794.84gold quality
muscle layer of sigmoid colonUBERON:003580594.83gold quality
pylorusUBERON:000116694.78gold quality
right coronary arteryUBERON:000162594.78gold quality
saphenous veinUBERON:000731894.78gold quality
esophagogastric junction muscularis propriaUBERON:003584194.72gold quality
left uterine tubeUBERON:000130394.67gold quality
renal medullaUBERON:000036294.63gold quality
cardia of stomachUBERON:000116294.60gold quality
cauda epididymisUBERON:000436094.52gold quality
thoracic aortaUBERON:000151594.11gold quality
descending thoracic aortaUBERON:000234594.08gold quality
ascending aortaUBERON:000149694.05gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.61
E-GEOD-98556no40.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

141 targeting TNRC18, 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-190A-3P100.0080.355520
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-5692A100.0074.406850
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-453499.9966.581907
HSA-MIR-1213699.9872.815713
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-480399.9871.993117
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-302E99.9670.742669
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-767-5P99.9570.85993
HSA-MIR-808299.9567.271170
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-185-3P99.9567.011743
HSA-MIR-101-3P99.9475.032230
HSA-MIR-144-3P99.9473.982698
HSA-MIR-6721-5P99.9368.922981

Literature-anchored findings (GeneRIF, showing 1)

  • Disruption of PCDH10 and TNRC18 Genes due to a Balanced Translocation. (PMID:32535594)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriotnrc18ENSDARG00000077052
mus_musculusTnrc18ENSMUSG00000039477
rattus_norvegicusTnrc18ENSRNOG00000024482
drosophila_melanogasterwgeFBGN0051151

Paralogs (2): BAHD1 (ENSG00000140320), BAHCC1 (ENSG00000266074)

Protein

Protein identifiers

Trinucleotide repeat-containing gene 18 proteinO15417 (reviewed: O15417)

Alternative names: Long CAG trinucleotide repeat-containing gene 79 protein

All UniProt accessions (8): O15417, A8MTZ4, C9J9K1, H7BXS9, H7C0N9, H7C177, H7C3U5, H9KVB4

UniProt curated annotations — full annotation on UniProt →

Function. Chromatin reader involved in the silencing of endogenous retroviruses (ERV) class-I elements, such as LTR12. Specifically binds histone H3 trimethylated at ‘Lys-9’ (H3K9me3) deposited by SETB1 at class-I ERV and directly mediates recruitment of corepressor complexes, such as Sin3-type and N-Cor complexes, leading to ERV silencing.

Subcellular location. Nucleus. Chromosome.

Domain organisation. The BAH domain specifically binds histone H3 trimethylated at ‘Lys-9’ (H3K9me3).

Miscellaneous. Dubious isoform produced through aberrant splice sites.

Isoforms (3)

UniProt IDNamesCanonical?
O15417-11yes
O15417-22
O15417-44

RefSeq proteins (1): NP_001073964* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001025BAH_domDomain
IPR043151BAH_sfHomologous_superfamily
IPR048924BAHCC1-like_TudorDomain
IPR052429BAH_domain_proteinFamily
IPR056841TNRC18_BAHCC1-like_SH3Domain

Pfam: PF01426, PF21744, PF24912

UniProt features (104 total): compositionally biased region 38, region of interest 14, strand 10, modified residue 9, mutagenesis site 8, sequence conflict 6, helix 5, splice variant 5, turn 3, coiled-coil region 2, chain 1, domain 1, cross-link 1, sequence variant 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
8DS8X-RAY DIFFRACTION1.84

Predicted structure (AlphaFold)

No AlphaFold model available for O15417 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

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 (10): 263, 611, 1127, 1136, 1540, 1857, 1863, 2146, 2771, 620

Mutagenesis-validated functional residues (8):

PositionPhenotype
760abolished interactiomn with sin3 (sin3a or sin3b), leading to endogenous retroviruses (erv) derepression.
2837abolished ability to bind histone h3 trimethylated at ’lys-9’ (h3k9me3).
2858abolished ability to bind histone h3 trimethylated at ’lys-9’ (h3k9me3), leading to endogenous retroviruses (erv) derepr
2860abolished ability to bind histone h3 trimethylated at ’lys-9’ (h3k9me3).
2864abolished ability to bind histone h3 trimethylated at ’lys-9’ (h3k9me3).
2908abolished ability to bind histone h3 trimethylated at ’lys-9’ (h3k9me3).
2910abolished ability to bind histone h3 trimethylated at ’lys-9’ (h3k9me3).
2912abolished ability to bind histone h3 trimethylated at ’lys-9’ (h3k9me3).

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 190 (showing top): chr7p22, GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC, GOBP_PROTEIN_LOCALIZATION_TO_CHROMATIN, GOBP_PROTEIN_LOCALIZATION_TO_CHROMOSOME, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_CHROMATIN_REMODELING, GOBP_HETEROCHROMATIN_ORGANIZATION, NIKOLSKY_BREAST_CANCER_7P22_AMPLICON, GOBP_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, GOCC_NUCLEAR_ENVELOPE, GOMF_CHROMATIN_BINDING, GOCC_NUCLEAR_MEMBRANE, VECCHI_GASTRIC_CANCER_EARLY_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GOCC_ORGANELLE_ENVELOPE

GO Biological Process (2): protein localization to chromatin (GO:0071168), transposable element silencing by heterochromatin formation (GO:0141005)

GO Molecular Function (3): chromatin binding (GO:0003682), histone H3K9me2/3 reader activity (GO:0062072), chromatin-protein adaptor activity (GO:0140463)

GO Cellular Component (6): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), mitochondrion (GO:0005739), cytosol (GO:0005829), nuclear membrane (GO:0031965)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
intracellular membrane-bounded organelle2
cytoplasm2
protein localization to chromosome1
transposable element silencing1
constitutive heterochromatin formation1
binding1
histone H3 reader activity1
chromatin binding1
chromatin organization1
protein-macromolecule adaptor activity1
chromosome1
nuclear lumen1
nucleus1
nuclear envelope1
organelle membrane1

Protein interactions and networks

STRING

1108 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TNRC18MRPL54Q6P161474
TNRC18OSBPL6Q9BZF3461
TNRC18NCAPH2Q6IBW4455
TNRC18DNPEPQ9ULA0446
TNRC18SIN3AQ96ST3444
TNRC18GALNT18Q6P9A2442
TNRC18SEZ6LQ9BYH1440
TNRC18RMND1Q9NWS8372
TNRC18FAM193AP78311359
TNRC18SLC66A1Q6ZP29358
TNRC18ZNF20P17024354
TNRC18RUNDC3BQ96NL0354
TNRC18MLLT11Q13015335
TNRC18BTBD18B2RXH4331
TNRC18GRHL2Q6ISB3326

IntAct

76 interactions, top by confidence:

ABTypeScore
HDAC1CDK2AP1psi-mi:“MI:0914”(association)0.840
HDAC1TNRC18psi-mi:“MI:0914”(association)0.790
RBBP4CDK2AP1psi-mi:“MI:0914”(association)0.790
HDAC1ZNF609psi-mi:“MI:0914”(association)0.730
RBBP7HAT1psi-mi:“MI:0914”(association)0.730
SINHCAFTNRC18psi-mi:“MI:0914”(association)0.640
CAMKVAP3B1psi-mi:“MI:0914”(association)0.640
SIN3BTNRC18psi-mi:“MI:0914”(association)0.530
PES1AP3B1psi-mi:“MI:0914”(association)0.530
MDKSETD1Apsi-mi:“MI:0914”(association)0.530
FHL2CNOT1psi-mi:“MI:0914”(association)0.530
EPB41L1AP3B1psi-mi:“MI:0914”(association)0.530
EDAAP3B1psi-mi:“MI:0914”(association)0.530
EPB41L3AP3B1psi-mi:“MI:0914”(association)0.530
RBBP4TNRC18psi-mi:“MI:0914”(association)0.530
RBBP7EPOPpsi-mi:“MI:0914”(association)0.530
SAP30TNRC18psi-mi:“MI:0914”(association)0.530
EPB41L1TNRC18psi-mi:“MI:0914”(association)0.530
DAXXTNRC18psi-mi:“MI:0914”(association)0.530

BioGRID (110): TNRC18 (Affinity Capture-MS), TNRC18 (Synthetic Lethality), TNRC18 (Affinity Capture-MS), TNRC18 (Affinity Capture-MS), TNRC18 (Affinity Capture-MS), TNRC18 (Affinity Capture-MS), TNRC18 (Affinity Capture-MS), TNRC18 (Affinity Capture-MS), TNRC18 (Affinity Capture-MS), TNRC18 (Affinity Capture-MS), TNRC18 (Affinity Capture-MS), TNRC18 (Affinity Capture-MS), TNRC18 (Affinity Capture-MS), TNRC18 (Affinity Capture-MS), TNRC18 (Affinity Capture-MS)

ESM2 similar proteins: A1YFU7, A2AJK6, A2BH40, A3RK75, D3YWE6, E9PYL2, E9Q4N7, O00512, O14497, O15417, O35126, O35740, O43365, P02831, P09026, P09027, P14651, P25822, P31249, P48634, P54258, P54259, P78414, P81068, P91613, P91716, P92203, Q06A37, Q08DG7, Q0VCT9, Q10571, Q24248, Q3UHR0, Q5IS70, Q5TM26, Q67FY3, Q7TQ40, Q80WC3, Q8CFT2, Q8NFD5

Diamond homologs: O15417, Q3LHL9, Q80WC3, Q9P281, Q497V6, Q8TBE0, F4JGB7, F4JL28, Q3UHR0, Q9FEN9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 71 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
HDACs deacetylate histones512.5×6e-03
Potential therapeutics for SARS511.9×6e-03

GO biological processes:

GO termPartnersFoldFDR
negative regulation of stem cell population maintenance897.3×4e-12
positive regulation of stem cell population maintenance949.1×4e-11
negative regulation of transforming growth factor beta receptor signaling pathway822.1×4e-07
negative regulation of cell migration915.9×5e-07
brain development78.8×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance714
Likely benign69
Benign113

Top pathogenic / likely-pathogenic (0)

SpliceAI

5725 predictions. Top by Δscore:

VariantEffectΔscore
7:5308309:CGCG:Cacceptor_gain1.0000
7:5308311:CG:Cacceptor_gain1.0000
7:5308312:GC:Gacceptor_loss1.0000
7:5308313:C:CCacceptor_gain1.0000
7:5308313:CT:Cacceptor_loss1.0000
7:5308871:CTA:Cdonor_loss1.0000
7:5308873:A:ACdonor_gain1.0000
7:5308873:ACC:Adonor_loss1.0000
7:5308873:ACCT:Adonor_gain1.0000
7:5308873:ACCTC:Adonor_gain1.0000
7:5308874:C:CCdonor_gain1.0000
7:5308874:CCT:Cdonor_gain1.0000
7:5308874:CCTC:Cdonor_gain1.0000
7:5308874:CCTCC:Cdonor_gain1.0000
7:5308889:T:TAdonor_gain1.0000
7:5308945:CAGTG:Cacceptor_gain1.0000
7:5308946:AGTG:Aacceptor_gain1.0000
7:5308947:GTG:Gacceptor_gain1.0000
7:5308947:GTGC:Gacceptor_loss1.0000
7:5308948:TG:Tacceptor_gain1.0000
7:5308948:TGC:Tacceptor_loss1.0000
7:5308949:GC:Gacceptor_loss1.0000
7:5308950:C:CCacceptor_gain1.0000
7:5308951:T:Aacceptor_loss1.0000
7:5308952:G:Cacceptor_gain1.0000
7:5308952:G:GCacceptor_gain1.0000
7:5308954:G:Cacceptor_gain1.0000
7:5308954:G:GCacceptor_gain1.0000
7:5309131:CCTGG:Cdonor_gain1.0000
7:5309153:G:Adonor_gain1.0000

AlphaMissense

19029 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:5308250:G:CC2921W1.000
7:5308252:A:GC2921R1.000
7:5309183:C:AW2858C1.000
7:5309183:C:GW2858C1.000
7:5309185:A:GW2858R1.000
7:5309185:A:TW2858R1.000
7:5309190:A:TV2856D1.000
7:5309196:A:TV2854D1.000
7:5309222:C:AW2845C1.000
7:5309222:C:GW2845C1.000
7:5309224:A:GW2845R1.000
7:5309224:A:TW2845R1.000
7:5309241:C:TG2839D1.000
7:5309242:C:GG2839R1.000
7:5309274:A:GL2828P1.000
7:5309276:G:CF2827L1.000
7:5309276:G:TF2827L1.000
7:5309277:A:CF2827C1.000
7:5309277:A:GF2827S1.000
7:5309278:A:GF2827L1.000
7:5309283:G:TA2825D1.000
7:5309322:A:TI2812N1.000
7:5309326:C:GA2811P1.000
7:5309332:A:CY2809D1.000
7:5309333:G:CF2808L1.000
7:5309333:G:TF2808L1.000
7:5309335:A:GF2808L1.000
7:5312521:C:AW2790C1.000
7:5312521:C:GW2790C1.000
7:5312523:A:GW2790R1.000

dbSNP variants (sampled 300 via entrez): RS1000024928 (7:5368894 C>G), RS1000028499 (7:5401649 G>A,C), RS1000031084 (7:5382094 C>A), RS1000047387 (7:5413799 G>A,C), RS1000064178 (7:5408905 G>A,T), RS1000073269 (7:5309553 C>T), RS1000081921 (7:5401868 G>A,T), RS1000116035 (7:5349779 A>C), RS1000122137 (7:5329736 G>A,C,T), RS1000128101 (7:5340007 T>C), RS1000146322 (7:5356473 G>A,C,T), RS1000162905 (7:5339868 C>A,T), RS1000183029 (7:5340790 A>T), RS1000203307 (7:5318914 G>T), RS1000224058 (7:5412174 G>A,C,T)

Disease associations

OMIM: gene MIM:620902 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST002183_6Relative hand skill in reading disability4.000000e-06
GCST006284_14Plasma proprotein convertase subtilisin/kexin type 9 levels in stable coronary artery disease2.000000e-06
GCST006284_5Plasma proprotein convertase subtilisin/kexin type 9 levels in stable coronary artery disease7.000000e-09
GCST011741_36LDL cholesterol levels in HIV infection3.000000e-07

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0009902handedness
EFO:0006899PCSK9 protein measurement
EFO:0004611low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs10234709TNRC180.000

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
methylmercuric chlorideincreases expression, affects cotreatment3
Air Pollutantsdecreases expression, increases abundance, affects expression, increases expression, affects cotreatment3
Ozonedecreases expression, increases abundance, affects expression, affects cotreatment3
sodium arseniteincreases expression2
methacrylaldehydedecreases expression, increases abundance, affects cotreatment2
Acroleinaffects cotreatment, decreases expression, increases abundance2
Benzo(a)pyrenedecreases expression, affects methylation2
Tetrachlorodibenzodioxindecreases methylation, increases abundance, affects expression2
Tobacco Smoke Pollutiondecreases expression, decreases methylation2
Valproic Aciddecreases expression, increases methylation2
aristolochic acid Iincreases expression1
FR900359affects phosphorylation1
TAK-243increases sumoylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, decreases expression, increases abundance1
bisphenol Aaffects cotreatment, increases methylation1
trichostatin Aaffects expression1
arseniteaffects binding, decreases reaction1
11-nor-delta(9)-tetrahydrocannabinol-9-carboxylic acidaffects methylation, increases abundance1
butyraldehydedecreases expression1
benzo(e)pyreneaffects methylation1
pentanaldecreases expression1
pentabromodiphenyl etherdecreases expression1
tebuconazoledecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Sdecreases methylation1
MT19c compounddecreases 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.