DNTTIP2

gene
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Also known as HSU15552ERBPTdIF2

Summary

DNTTIP2 (deoxynucleotidyltransferase terminal interacting protein 2, HGNC:24013) is a protein-coding gene on chromosome 1p22.1, encoding Deoxynucleotidyltransferase terminal-interacting protein 2 (Q5QJE6). Regulates the transcriptional activity of DNTT and ESR1. It is a selective cancer dependency (DepMap: 73.4% of cell lines).

This gene is thought to be involved in chromatin remodeling and gene transcription. The encoded nuclear protein binds to and enhances the transcriptional activity of the estrogen receptor alpha, and also interacts with terminal deoxynucleotidyltransferase. The expression profile of this gene is a potential biomarker for chronic obstructive pulmonary disease.

Source: NCBI Gene 30836 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 112 total
  • Cancer dependency (DepMap): dependent in 73.4% of screened cell lines
  • MANE Select transcript: NM_014597

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24013
Approved symbolDNTTIP2
Namedeoxynucleotidyltransferase terminal interacting protein 2
Location1p22.1
Locus typegene with protein product
StatusApproved
AliasesHSU15552, ERBP, TdIF2
Ensembl geneENSG00000067334
Ensembl biotypeprotein_coding
OMIM611199
Entrez30836

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding_CDS_not_defined, 2 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000359208, ENST00000436063, ENST00000460191, ENST00000462746, ENST00000496535, ENST00000496672, ENST00000528680

RefSeq mRNA: 1 — MANE Select: NM_014597 NM_014597

CCDS: CCDS44174

Canonical transcript exons

ENST00000436063 — 7 exons

ExonStartEnd
ENSE000007770899387564593875783
ENSE000017744329386628493869944
ENSE000022019769387907793879206
ENSE000034645639387626893877862
ENSE000035514979387311993873214
ENSE000036412629387068393870792
ENSE000036553939387207293872236

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 96.45.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.2469 / max 531.0837, expressed in 1787 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1334621.93651774
133473.26261393
133380.047825

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370196.45gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099195.82gold quality
gingival epitheliumUBERON:000194995.66gold quality
cervix squamous epitheliumUBERON:000692295.40gold quality
gingivaUBERON:000182895.39gold quality
islet of LangerhansUBERON:000000695.36gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047395.03gold quality
ventricular zoneUBERON:000305395.01gold quality
gluteal muscleUBERON:000200094.89gold quality
tongue squamous epitheliumUBERON:000691994.89gold quality
biceps brachiiUBERON:000150794.88gold quality
tendonUBERON:000004394.84gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450294.73gold quality
olfactory segment of nasal mucosaUBERON:000538694.67gold quality
heart right ventricleUBERON:000208094.56gold quality
cranial nerve IIUBERON:000094194.47gold quality
gastrocnemiusUBERON:000138894.11gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451194.07gold quality
deltoidUBERON:000147693.93gold quality
ganglionic eminenceUBERON:000402393.89gold quality
endothelial cellCL:000011593.83gold quality
skin of hipUBERON:000155493.81gold quality
cervix epitheliumUBERON:000480193.79gold quality
cortical plateUBERON:000534393.73gold quality
bronchial epithelial cellCL:000232893.69gold quality
tibialis anteriorUBERON:000138593.65gold quality
nasal cavity epitheliumUBERON:000538493.56gold quality
muscle of legUBERON:000138393.41gold quality
bone marrow cellCL:000209293.40gold quality
colonic epitheliumUBERON:000039793.40gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-CURD-53no672.50
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): KAT5

miRNA regulators (miRDB)

21 targeting DNTTIP2, 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-366299.9973.825684
HSA-MIR-570-3P99.9672.414910
HSA-MIR-153-5P99.8973.866317
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-449599.8272.083080
HSA-MIR-200A-5P99.7669.10949
HSA-MIR-200B-5P99.7669.05948
HSA-MIR-33A-3P99.7070.273362
HSA-MIR-7152-5P99.6069.332094
HSA-MIR-409-3P99.5066.331192
HSA-MIR-302B-5P99.5069.491857
HSA-MIR-302D-5P99.5069.341863
HSA-MIR-32-3P99.3668.202517
HSA-MIR-148A-5P99.3068.271141
HSA-MIR-224-3P98.9168.421815
HSA-MIR-522-3P98.9168.561817
HSA-MIR-5007-5P97.9564.71614
HSA-MIR-193A-5P95.7065.33613
HSA-MIR-4694-5P94.6265.39532
HSA-MIR-758-5P93.9964.46534

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 73.4% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • The TdIF2 might promote hrDNAP activity by suppressing Tip60’s HAT activity and promoting UBF acetylation. (PMID:21668587)
  • Depletion of DNTTIP2 Induces Cell Cycle Arrest in Pancreatic Cancer Cells. (PMID:38151292)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriodnttip2ENSDARG00000057648
mus_musculusDnttip2ENSMUSG00000039756
rattus_norvegicusDnttip2ENSRNOG00000025025
drosophila_melanogasterCG1142FBGN0037504
caenorhabditis_elegansWBGENE00021715

Protein

Protein identifiers

Deoxynucleotidyltransferase terminal-interacting protein 2Q5QJE6 (reviewed: Q5QJE6)

Alternative names: Estrogen receptor-binding protein, LPTS-interacting protein 2, Terminal deoxynucleotidyltransferase-interacting factor 2

All UniProt accessions (3): Q5QJE6, E9PRB3, J3KP30

UniProt curated annotations — full annotation on UniProt →

Function. Regulates the transcriptional activity of DNTT and ESR1. May function as a chromatin remodeling protein. Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome.

Subunit / interactions. Forms a ternary complex with DNTT and core histone; interaction with PCNA releases DNTT and H2A/H2B histones from this ternary complex. Interacts with ESR1, ESR2, PPARG and RXRA. Part of the small subunit (SSU) processome, composed of more than 70 proteins and the RNA chaperone small nucleolar RNA (snoRNA) U3.

Subcellular location. Nucleus. Nucleolus.

Tissue specificity. Widely expressed with higher levels in testis.

RefSeq proteins (1): NP_055412* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR014810Fcf2_CDomain
IPR039883Fcf2/DNTTIP2Family

Pfam: PF08698

UniProt features (53 total): modified residue 19, cross-link 15, compositionally biased region 5, sequence variant 5, region of interest 4, sequence conflict 3, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
7MQAELECTRON MICROSCOPY2.7
7MQ8ELECTRON MICROSCOPY3.6
7MQ9ELECTRON MICROSCOPY3.87

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5QJE6-F154.470.16

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 (34): 21, 117, 129, 141, 145, 148, 184, 194, 232, 239, 251, 253, 324, 330, 381, 434, 512, 569, 610, 217 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 135 (showing top): SHEPARD_BMYB_MORPHOLINO_UP, GOBP_RIBOSOME_BIOGENESIS, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, SHEPARD_CRASH_AND_BURN_MUTANT_UP, GOBP_MATURATION_OF_SSU_RRNA, PUJANA_CHEK2_PCC_NETWORK, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GARY_CD5_TARGETS_DN, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, chr1p22, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GCM_DDX5, VANTVEER_BREAST_CANCER_BRCA1_UP

GO Biological Process (2): RNA processing (GO:0006396), ribosomal small subunit biogenesis (GO:0042274)

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

GO Cellular Component (5): nucleoplasm (GO:0005654), chromosome (GO:0005694), nucleolus (GO:0005730), small-subunit processome (GO:0032040), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
nuclear lumen2
intracellular membraneless organelle2
gene expression1
RNA biosynthetic process1
primary metabolic process1
ribonucleoprotein complex biogenesis1
ribosome biogenesis1
nucleic acid binding1
binding1
cellular anatomical structure1
nucleolus1
preribosome1
t-UTP complex1
nuclear protein-containing complex1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

2001 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DNTTIP2FCF1Q9Y324965
DNTTIP2FAF1Q9UNN5834
DNTTIP2UTP3Q9NQZ2770
DNTTIP2DNTTP04053767
DNTTIP2WDR46O15213724
DNTTIP2UTP11Q9Y3A2692
DNTTIP2FBLP22087520
DNTTIP2ESR2Q92731515
DNTTIP2DNTTIP1Q9H147503
DNTTIP2UTP15Q8TED0477
DNTTIP2KRR1Q13601457
DNTTIP2UTP20O75691453
DNTTIP2UTP23Q9BRU9447
DNTTIP2ESR1P03372438
DNTTIP2HEATR1Q9H583426

IntAct

105 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
DNTTIP2CAVIN1psi-mi:“MI:0915”(physical association)0.680
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
DNTTIP2CEP70psi-mi:“MI:0915”(physical association)0.560
DNTTIP2PICK1psi-mi:“MI:0915”(physical association)0.560
RNF8DNTTIP2psi-mi:“MI:0915”(physical association)0.560
FGF3GTPBP10psi-mi:“MI:0914”(association)0.530
ZNF2MPHOSPH10psi-mi:“MI:0914”(association)0.530
MAGEB2POLRMTpsi-mi:“MI:0914”(association)0.530
ABT1ZNF316psi-mi:“MI:0914”(association)0.530
EXOSC4ZFC3H1psi-mi:“MI:0914”(association)0.530
NPM1WDR46psi-mi:“MI:0914”(association)0.480
RBM6DNTTIP2psi-mi:“MI:0915”(physical association)0.400
RPF2DNTTIP2psi-mi:“MI:0915”(physical association)0.400
IFIT2DNTTIP2psi-mi:“MI:0915”(physical association)0.400
FAM50ADNTTIP2psi-mi:“MI:0915”(physical association)0.400
NELL1DNTTIP2psi-mi:“MI:0915”(physical association)0.400
DNTTIP2psi-mi:“MI:0915”(physical association)0.370
DNTTIP2psi-mi:“MI:0915”(physical association)0.370
PHF8MACROH2A1psi-mi:“MI:0914”(association)0.350
Kif20bSHTN1psi-mi:“MI:0914”(association)0.350
RRP1BZNF785psi-mi:“MI:0914”(association)0.350
MKI67ARHGAP10psi-mi:“MI:0914”(association)0.350
MecomESYT2psi-mi:“MI:0914”(association)0.350
DGCR8MPHOSPH10psi-mi:“MI:0914”(association)0.350
RBM4NOP56psi-mi:“MI:0914”(association)0.350
NIFKRRP8psi-mi:“MI:0914”(association)0.350
HNRNPA1HNRNPRpsi-mi:“MI:0914”(association)0.350

BioGRID (174): DNTTIP2 (Affinity Capture-MS), DNTTIP2 (Affinity Capture-MS), DNTTIP2 (Affinity Capture-MS), DNTTIP2 (Affinity Capture-MS), DNTTIP2 (Affinity Capture-MS), DNTTIP2 (Affinity Capture-MS), DNTTIP2 (Affinity Capture-MS), DNTTIP2 (Affinity Capture-MS), DNTTIP2 (Affinity Capture-MS), DNTTIP2 (Affinity Capture-MS), DNTTIP2 (Affinity Capture-MS), DNTTIP2 (Affinity Capture-MS), DNTTIP2 (Affinity Capture-MS), DNTTIP2 (Affinity Capture-MS), DNTTIP2 (Positive Genetic)

ESM2 similar proteins: A0A3Q2UEI8, A0JNH9, A2BIL8, A8PUI7, B1H1S4, B2GUZ2, E7FAP1, E9Q309, F1R983, O60284, P49452, P51960, P86345, Q0P5H2, Q3T0A6, Q3T8J9, Q4KLP8, Q4QY64, Q4R731, Q535K8, Q563C3, Q58EL7, Q5FBB7, Q5QJE6, Q5VT06, Q5XG21, Q65Z40, Q6KAQ7, Q6NWJ0, Q6P0N0, Q6P6I6, Q76FK4, Q7YQM1, Q7YQM2, Q80WQ8, Q8C263, Q8C551, Q8IYH5, Q8NA57, Q8R2M2

Diamond homologs: O42877, Q0P5H2, Q12035, Q5QJE6, Q8R2M2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 128 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
Major pathway of rRNA processing in the nucleolus and cytosol1610.8×5e-10
rRNA modification in the nucleus and cytosol510.3×4e-03
Formation of a pool of free 40S subunits89.8×3e-04
Peptide chain elongation79.8×5e-04
Viral mRNA Translation79.8×5e-04
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA79.7×5e-04
SARS-CoV-1-host interactions59.7×5e-03
Selenocysteine synthesis79.2×5e-04

GO biological processes:

GO termPartnersFoldFDR
ribosomal small subunit biogenesis713.6×2e-04
RNA processing713.1×2e-04
cytoplasmic translation812.7×2e-04
regulation of alternative mRNA splicing, via spliceosome612.5×8e-04
heterochromatin formation510.9×7e-03
rRNA processing89.7×2e-04
RNA splicing107.5×2e-04
mRNA processing106.7×3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance95
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

774 predictions. Top by Δscore:

VariantEffectΔscore
1:93869853:A:ACdonor_gain1.0000
1:93869854:A:Cdonor_gain1.0000
1:93869868:T:TAdonor_gain1.0000
1:93869940:TGTAT:Tacceptor_gain1.0000
1:93869941:GTAT:Gacceptor_gain1.0000
1:93869942:TAT:Tacceptor_gain1.0000
1:93869943:ATCTG:Aacceptor_loss1.0000
1:93869944:TC:Tacceptor_loss1.0000
1:93869945:C:CCacceptor_gain1.0000
1:93869945:C:CGacceptor_loss1.0000
1:93869946:T:Cacceptor_loss1.0000
1:93870675:T:TAdonor_gain1.0000
1:93870680:TACC:Tdonor_loss1.0000
1:93870681:A:ACdonor_gain1.0000
1:93870682:C:CCdonor_gain1.0000
1:93870682:C:CGdonor_loss1.0000
1:93870682:CCTT:Cdonor_gain1.0000
1:93870788:CCAAT:Cacceptor_gain1.0000
1:93870789:CAAT:Cacceptor_gain1.0000
1:93870789:CAATC:Cacceptor_gain1.0000
1:93870792:TC:Tacceptor_loss1.0000
1:93870793:C:CCacceptor_gain1.0000
1:93870793:CTGT:Cacceptor_loss1.0000
1:93870800:C:CTacceptor_gain1.0000
1:93872067:CATAC:Cdonor_loss1.0000
1:93872068:ATACC:Adonor_loss1.0000
1:93872069:TACCT:Tdonor_loss1.0000
1:93872070:A:Cdonor_loss1.0000
1:93872071:C:CTdonor_loss1.0000
1:93872233:CTTT:Cacceptor_gain1.0000

AlphaMissense

5044 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:93870707:A:GL718P1.000
1:93870760:G:CF700L0.999
1:93870760:G:TF700L0.999
1:93870762:A:GF700L0.999
1:93872108:C:AK677N0.999
1:93872108:C:GK677N0.999
1:93872114:A:CF675L0.999
1:93872114:A:TF675L0.999
1:93872116:A:GF675L0.999
1:93872138:T:AR667S0.999
1:93872138:T:GR667S0.999
1:93872148:A:GL664P0.999
1:93872157:A:GL661P0.999
1:93872206:A:GW645R0.999
1:93872206:A:TW645R0.999
1:93869913:C:GA737P0.998
1:93870704:A:GL719P0.998
1:93870730:C:AR710S0.998
1:93870730:C:GR710S0.998
1:93870788:C:TG691E0.998
1:93870789:C:GG691R0.998
1:93870789:C:TG691R0.998
1:93872110:T:CK677E0.998
1:93872139:C:GR667T0.998
1:93872169:A:GL657P0.998
1:93872204:C:AW645C0.998
1:93872204:C:GW645C0.998
1:93869928:A:CY732D0.997
1:93870688:G:CF724L0.997
1:93870688:G:TF724L0.997

dbSNP variants (sampled 300 via entrez): RS1000148046 (1:93871982 C>T), RS1000148458 (1:93866941 C>G), RS1000285851 (1:93878789 CAGTA>C), RS1000287791 (1:93871812 A>T), RS1000642110 (1:93877206 T>C,G), RS1000830720 (1:93867838 AACAG>A), RS1000975096 (1:93865919 G>C), RS1001075127 (1:93867464 G>A), RS1001491318 (1:93878346 C>T), RS1001791780 (1:93871546 G>T), RS1002536006 (1:93880147 A>C,G), RS1002980585 (1:93868309 G>A), RS1003007550 (1:93880375 A>T), RS1003193162 (1:93874926 G>A), RS1003315973 (1:93869567 A>G)

Disease associations

OMIM: gene MIM:611199 | 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
GCST010313_2Serum polyunsaturated fatty acid concentration x sex interaction in metabolic syndrome1.000000e-08
GCST010313_3Serum polyunsaturated fatty acid concentration x sex interaction in metabolic syndrome1.000000e-07
GCST010313_5Serum polyunsaturated fatty acid concentration x sex interaction in metabolic syndrome1.000000e-07
GCST010818_3Gut microbiota alpha diversity (PD_whole_tree index)5.000000e-06

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0008343sex interaction measurement
EFO:0010733polyunsaturated fatty acid measurement
EFO:0006807linoleic acid measurement
EFO:0005680omega-6 polyunsaturated fatty acid measurement
EFO:0007874gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneincreases expression, increases methylation5
bisphenol Aaffects expression, decreases expression3
deoxynivalenolincreases expression2
sodium arsenitedecreases expression2
Tobacco Smoke Pollutionincreases expression2
Cyclosporineincreases expression2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
bisphenol Fdecreases methylation1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
sodium arsenatedecreases expression1
kojic aciddecreases expression1
sulforaphaneincreases expression1
cobaltous chlorideincreases expression1
potassium chromate(VI)affects cotreatment, increases expression1
coumarinaffects phosphorylation1
nivalenolincreases expression1
epigallocatechin gallateincreases expression, affects cotreatment1
azoxystrobindecreases expression1
CGP 52608affects binding, increases reaction1
K 7174increases expression1
fenpyroximatedecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrineincreases expression1
pyrachlostrobindecreases expression1
jinfukangdecreases expression1
LDN 193189affects cotreatment, decreases expression1
MT19c compoundincreases expression1
Air Pollutantsdecreases expression, increases abundance1

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.