CTCF

Summary

CTCF (CCCTC-binding factor, HGNC:13723) is a protein-coding gene on chromosome 16q22.1, encoding Transcriptional repressor CTCF (P49711). Chromatin binding factor that binds to DNA sequence specific sites and regulates the 3D structure of chromatin. It is a common-essential gene (DepMap: required in 99.8% of cancer cell lines) and haploinsufficient (ClinGen: sufficient evidence).

This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. Depending upon the context of the site, the protein can bind a histone acetyltransferase (HAT)-containing complex and function as a transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as a transcriptional repressor. If the protein is bound to a transcriptional insulator element, it can block communication between enhancers and upstream promoters, thereby regulating imprinted expression. Mutations in this gene have been associated with invasive breast cancers, prostate cancers, and Wilms’ tumors. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 10664 — RefSeq curated summary.

At a glance

• Gene–disease (curated): syndromic intellectual disability (Definitive, ClinGen) — +1 more curated relationship
• GWAS associations: 5
• Clinical variants (ClinVar): 388 total — 41 pathogenic, 45 likely-pathogenic
• Phenotypes (HPO): 153
• Druggable target: yes
• Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 4 cancer types
• Cancer dependency (DepMap): dependent in 99.8% of screened cell lines (common-essential)
• Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
• Transcription factor: yes — 185 downstream targets (CollecTRI)
• MANE Select transcript: NM_006565

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13723
Approved symbol	CTCF
Name	CCCTC-binding factor
Location	16q22.1
Locus type	gene with protein product
Status	Approved
Aliases	FAP108, CFAP108
Ensembl gene	ENSG00000102974
Ensembl biotype	protein_coding
OMIM	604167
Entrez	10664

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 20 protein_coding, 6 retained_intron, 1 nonsense_mediated_decay

ENST00000264010, ENST00000401394, ENST00000566078, ENST00000642420, ENST00000642819, ENST00000642847, ENST00000642943, ENST00000643892, ENST00000644753, ENST00000644852, ENST00000644950, ENST00000645306, ENST00000645409, ENST00000645699, ENST00000646076, ENST00000646566, ENST00000646771, ENST00000885126, ENST00000885127, ENST00000921455, ENST00000921456, ENST00000921457, ENST00000921458, ENST00000921459, ENST00000921460, ENST00000961391, ENST00000961392

RefSeq mRNA: 3 — MANE Select: NM_006565 NM_001191022, NM_001363916, NM_006565

CCDS: CCDS10841, CCDS54029, CCDS86536

Canonical transcript exons

ENST00000264010 — 12 exons

Exon	Start	End
ENSE00000690280	67620697	67620817
ENSE00000690296	67621442	67621591
ENSE00000690297	67626555	67626715
ENSE00000690303	67629398	67629533
ENSE00000690304	67636690	67636851
ENSE00001251143	67628370	67628552
ENSE00001558712	67562526	67562724
ENSE00001645353	67611951	67612121
ENSE00001664803	67571148	67571264
ENSE00002242686	67610824	67611613
ENSE00003589627	67616745	67616878
ENSE00003822538	67637688	67639177

Expression profiles

Bgee: expression breadth ubiquitous, 297 present calls, max score 97.27.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 45.0806 / max 462.5095, expressed in 1820 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
154662	38.1538	1818
154663	3.2324	1382
154661	1.6494	1026
154659	0.6968	459
154664	0.5179	228
154660	0.5003	260
154665	0.3300	138

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	97.27	gold quality
ganglionic eminence	UBERON:0004023	96.56	gold quality
endometrium epithelium	UBERON:0004811	96.48	gold quality
cortical plate	UBERON:0005343	96.45	gold quality
thymus	UBERON:0002370	96.39	gold quality
embryo	UBERON:0000922	95.60	gold quality
cerebellar vermis	UBERON:0004720	93.66	gold quality
paraflocculus	UBERON:0005351	92.94	gold quality
lymph node	UBERON:0000029	92.48	gold quality
trabecular bone tissue	UBERON:0002483	92.27	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	92.05	gold quality
bone marrow	UBERON:0002371	91.73	gold quality
upper leg skin	UBERON:0004262	91.53	gold quality
gluteal muscle	UBERON:0002000	91.50	gold quality
mucosa of sigmoid colon	UBERON:0004993	91.34	gold quality
ileal mucosa	UBERON:0000331	91.33	gold quality
granulocyte	CL:0000094	91.31	gold quality
biceps brachii	UBERON:0001507	91.31	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	91.31	gold quality
islet of Langerhans	UBERON:0000006	91.25	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.22	gold quality
bone marrow cell	CL:0002092	91.19	gold quality
colonic mucosa	UBERON:0000317	91.11	gold quality
penis	UBERON:0000989	91.05	gold quality
skeletal muscle tissue	UBERON:0001134	91.01	gold quality
tonsil	UBERON:0002372	91.01	gold quality
deltoid	UBERON:0001476	90.69	gold quality
amniotic fluid	UBERON:0000173	90.65	gold quality
blood	UBERON:0000178	90.64	gold quality
buccal mucosa cell	CL:0002336	90.60	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.40
E-CURD-88	yes	4.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

185 targets.

Target	Regulation
ABCA2	Unknown
ACKR3	Unknown
ACTR3	Repression
ACVR1C	Unknown
AFM
AHCYL1	Unknown
AKT1	Repression
ALDH1A3	Repression
ANG	Unknown
ANKRD46	Unknown
APP	Activation
ARL2	Repression
ARSI
ASAP2	Unknown
ATN1	Unknown
ATXN7	Unknown
B4GALNT1	Unknown
BATF2	Unknown
BAX
BBC3	Unknown
BCL2L14	Repression
BCL6	Repression
BICD2	Unknown
BRCA1	Unknown
C1R	Unknown
C4B
CCL16	Unknown
CCND1	Unknown
CD34
CD74

JASPAR motifs

Motif	Name	Family
MA0139.1	CTCF	More than 3 adjacent zinc fingers
MA0139.2	CTCF	More than 3 adjacent zinc fingers
MA1929.1	CTCF	More than 3 adjacent zinc fingers
MA1929.2	CTCF	More than 3 adjacent zinc fingers
MA1930.1	CTCF	More than 3 adjacent zinc fingers
MA1930.2	CTCF	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:17512414, PMID:34326481

Upstream regulators (CollecTRI, top): BCL3, CTCF, EPAS1, FOXH1, NFKB1, PAX6, USF1, WT1, YY1

miRNA regulators (miRDB)

121 targeting CTCF, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-1305	99.91	71.43	3443

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 99.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 40)

• It’s proposed that Tsix and CTCF together establish a regulatable epigenetic switch for X-inactivation. (PMID:11743158)
• observations suggest that CTCF may represent a novel tumor suppressor gene that displays tumor-specific “change of function” rather than complete “loss of function” (PMID:11782357)
• Insertional mutagenesis identified nucleosome positioning sequences (NPSs) allow the remarkably precise distribution of target sites for the chromatin insulator protein CTCF to nucleosome linker sequences in the H19 ICR. (PMID:11971967)
• Conserved CTCF insulator elements flank the mouse and human beta-globin loci. (PMID:11997516)
• Transforming growth factor-beta-induced transcription of the Alzheimer beta-amyloid precursor protein gene involves interaction between the CTCF-complex and Smads (PMID:12099698)
• Loss of CTCF mRNA or protein in Wilms tumors does not predispose to de novo methylation of the maternal allele of H19 but leaves open the possibility that post-transcriptional loss of CTCF protein may account for some instances of loss of imprinting. (PMID:12203779)
• CTCF is a common determinant to different pathways of death signaling in immature B cells. (PMID:12524457)
• the insulator activity of CTCF apparently involves an HDAC-independent association with the nuclear matrix (PMID:12878173)
• CTCF binding at the human IGF2/H19 imprinting control region(ICR). CTCF binding at the IGF2/H19 ICR is insufficient to regulate expression of IGF2/H19 in many human tissues. (PMID:12960026)
• CTCF can be inactivated by somatic mutation and genetic or epigenetic silencing of the wild-type allele in individual cases of invasivene ductal breast cancer; loss of CTCF protein function may contribute to tumor heterogeneity (PMID:14503807)
• beta-globin locus control region HS5 contains enhancer-blocking (insulator) activity that is both CTCF and developmental stage dependent (PMID:14645507)
• CTCF has a role in tethering an insulator to subnuclear sites (PMID:14759373)
• CTCF regulates Pax6 transcription by binding to its repressor element, which in turn blocks the effect of the ectoderm enhancer resulting in the inhibition of P0 promoter activity. (PMID:15096508)
• The terminal domain is active in HeLa, HEK293 and COS-7 cell lines where it is both sufficient and necessary for silencing an SV40 core promoter. (PMID:15304340)
• novel mechanism for IGF2 imprinting regulation, that is, the reduction of CTCF expression in the control of IGF2 imprinting (PMID:15471867)
• CTCF plays a major role in IRAK2 transcription; EMSA revealed a CTCF-binding site within the mouse Irak2 promoter (PMID:15670593)
• point mutations in the XIST promoter reveal a correlation between CTCF binding and pre-emptive choices of X chromosome inactivation (PMID:15731119)
• CTCF is involved in the control of myeloid cell growth and differentiation (PMID:15941718)
• CTCF overexpression may have evolved as a compensatory mechanism to protect breast cancer cells from apoptosis, thus providing selective survival advantages to these cells. (PMID:15958555)
• chromatin loop organized by the CTCF-bound, differentially methylated region at the Igf2/H19 locus can be detected in mitosis (PMID:16107875)
• Data indicate that reciprocal binding of CTCF and BORIS to the NY-ESO-1 promoter mediates epigenetic regulation of this CT gene in lung cancer cells. (PMID:16140944)
• the Kaiso-CTCF interaction negatively regulates CTCF insulator activity (PMID:16230345)
• increased CTCF can repress EBNA2 transcription (PMID:16731911)
• CTCF is a multifunctional epigenetic regulator with a role in carcinogenesis (review) (PMID:16989720)
• this study reports the identification and characterization of an insulator from the herpes simplex virus-1 LAT intron region that functions via CTCF (PMID:17267480)
• Study describes 13,804 CTCF-binding sites in potential insulators of the human genome in primary human fibroblasts; most of these sequences are located far from the transcriptional start sites, with their distribution strongly correlated with genes (PMID:17382889)
• Results reveal that CTCF is a down stream target of stress-induced signaling cascades and it plays a significant anti-apoptotic role in regulation of stress-induced cellular responses in HCE and hematopoietic myeloid cells. (PMID:17583694)
• a small number of zinc fingers mediate strong binding of CTCF to DNA, and a single finger-DNA interaction controls binding at imprinted loci (PMID:17827499)
• CTCF is indeed a protein with multifunctional activity that plays a significant role in modulating signalling pathways to mediate insulin-induced ML-1 cell proliferation. (PMID:18021171)
• Band-shift analysis upon the nuclear fractions from HIV-1 resistant cells showed that CTCF protein bound to HIV-1 promoter and this binding prevented the formation of NF-kappaB/LTR complex. (PMID:18207574)
• description of cohesin-binding sites in the human genome; most of these are associated with the CCCTC-binding factor (CTCF), a zinc-finger protein required for transcriptional insulation (PMID:18235444)
• Study shows that the distribution of cohesins on mammalian chromosome arms is not driven by transcriptional activity, instead, cohesins are found at most CTCF sites and CTCF is required for cohesin localization to these sites. (PMID:18237772)
• The results suggest a model whereby both HLA-DRB1 and HLA-DQA1 loci can interact simultaneously with XL9, and describe a regulatory mechanism involving the alteration of the general chromatin conformation and their regulation by CTCF. (PMID:18347100)
• STAG1 (Scc3/SA1) subunit of cohesin interacts with the CCTC-binding factor CTCF bound to the c-myc insulator element. (PMID:18550811)
• Results decribethe loss IGF2/H19 imprinting,loss of heterozygosity of IGF2R and CTCF, and incidental H. pylori infections in laryngeal squamous cell carcinoma. (PMID:18604514)
• CTCF positions 20 nucleosomes around its binding sites across the human genome. (PMID:18654629)
• CTCF is required in a dose-dependent manner and is involved in cell cycle progression of alphabeta T cells in the thymus. (PMID:18923423)
• CTCF binding-site mutation promotes triplet repeat instability both in the germ line and in somatic tissues. (PMID:19008940)
• mapped the genome-wide binding sites of CTCF in three cell types and identified significant binding of CTCF to the boundaries of repressive chromatin domains marked by H3K27me3 (PMID:19056695)
• intrinsic looping activity of CTCF sites can nullify locus control region function. (PMID:19074263)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ctcf	ENSDARG00000056621
mus_musculus	Ctcf	ENSMUSG00000005698
rattus_norvegicus	Ctcf	ENSRNOG00000017674

Paralogs (36): ZNF302 (ENSG00000089335), ZNF184 (ENSG00000096654), ZNF574 (ENSG00000105732), ZBTB24 (ENSG00000112365), ZNF142 (ENSG00000115568), CTCFL (ENSG00000124092), ZNF473 (ENSG00000142528), ZNF827 (ENSG00000151612), ZNF689 (ENSG00000156853), ZNF208 (ENSG00000160321), ZNF91 (ENSG00000167232), ZNF526 (ENSG00000167625), ZNF764 (ENSG00000169951), ZNF747 (ENSG00000169955), ZNF282 (ENSG00000170265), ZNF160 (ENSG00000170949), ZNF497 (ENSG00000174586), ZBTB34 (ENSG00000177125), ZNF771 (ENSG00000179965), ZNF48 (ENSG00000180035), ZNF594 (ENSG00000180626), ZBTB37 (ENSG00000185278), ZFP92 (ENSG00000189420), ZNF107 (ENSG00000196247), ZNF729 (ENSG00000196350), ZNF569 (ENSG00000196437), ZNF420 (ENSG00000197050), ZNF785 (ENSG00000197162), ZNF665 (ENSG00000197497), ZNF181 (ENSG00000197841), ZNF347 (ENSG00000197937), ZNF84 (ENSG00000198040), ZBTB48 (ENSG00000204859), ZNF845 (ENSG00000213799), ZNF99 (ENSG00000213973), ZNF688 (ENSG00000229809)

Protein

Protein identifiers

Transcriptional repressor CTCF — P49711 (reviewed: P49711)

Alternative names: 11-zinc finger protein, CCCTC-binding factor, CTCFL paralog

All UniProt accessions (5): P49711, A0A2R8Y595, A0A2R8Y6C1, A0A2R8Y6Z6, A0A2R8YFL0

UniProt curated annotations — full annotation on UniProt →

Function. Chromatin binding factor that binds to DNA sequence specific sites and regulates the 3D structure of chromatin. Binds together strands of DNA, thus forming chromatin loops, and anchors DNA to cellular structures, such as the nuclear lamina. Defines the boundaries between active and heterochromatic DNA via binding to chromatin insulators, thereby preventing interaction between promoter and nearby enhancers and silencers. Participates in the allele-specific gene expression at the imprinted IGF2/H19 gene locus. On the maternal allele, binding within the H19 imprinting control region (ICR) mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to IGF2. Mediates interchromosomal association between IGF2/H19 and WSB1/NF1 and may direct distant DNA segments to a common transcription factory. Regulates asynchronous replication of IGF2/H19. Plays a critical role in gene silencing over considerable distances in the genome. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation and maintaining methylation-free zones. Inversely, binding to target sites is prevented by CpG methylation. Plays an important role in chromatin remodeling. Can dimerize when it is bound to different DNA sequences, mediating long-range chromatin looping. Causes local loss of histone acetylation and gain of histone methylation in the beta-globin locus, without affecting transcription. When bound to chromatin, it provides an anchor point for nucleosomes positioning. Seems to be essential for homologous X-chromosome pairing. May participate with Tsix in establishing a regulatable epigenetic switch for X chromosome inactivation. May play a role in preventing the propagation of stable methylation at the escape genes from X-inactivation. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. Plays a role in the recruitment of CENPE to the pericentromeric/centromeric regions of the chromosome during mitosis. Acts as a transcriptional repressor binding to promoters of vertebrate MYC gene and BAG1 gene. Also binds to the PLK and PIM1 promoters. Acts as a transcriptional activator of APP. Regulates APOA1/C3/A4/A5 gene cluster and controls MHC class II gene expression. Plays an essential role in oocyte and preimplantation embryo development by activating or repressing transcription. Seems to act as tumor suppressor.

Subunit / interactions. Interacts with CHD8. Interacts with LLPH. Interacts with CENPE. Interacts with BRD2; promoting BRD2 recruitment to chromatin.

Subcellular location. Nucleus. Nucleoplasm. Chromosome. Centromere.

Tissue specificity. Ubiquitous. Absent in primary spermatocytes.

Post-translational modifications. Sumoylated on Lys-74 and Lys-689; sumoylation of CTCF contributes to the repressive function of CTCF on the MYC P2 promoter.

Disease relevance. Intellectual developmental disorder, autosomal dominant 21 (MRD21) [MIM:615502] A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Additional MRD21 features include short stature, microcephaly, and developmental delay. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The 11 zinc fingers are highly conserved among vertebrates, exhibiting almost identical amino acid sequences. Different subsets or combination of individual zinc fingers gives the ability to CTCF to recognize multiple DNA target sites.

Miscellaneous. More than 13'00 CTCF-binding sites in potential insulators were identified in the human genome.

Similarity. Belongs to the CTCF zinc-finger protein family.

Isoforms (2)

UniProt ID	Names	Canonical?
P49711-1	1	yes
P49711-2	2

RefSeq proteins (3): NP_001177951, NP_001350845, NP_006556* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050331	Zinc_finger_PRDM4/PRDM1/PRDM14	Family
IPR056438	Znf-C2H2_CTCF	Domain

Pfam: PF00096, PF23611

UniProt features (84 total): strand 24, helix 14, zinc finger region 11, sequence variant 9, modified residue 8, compositionally biased region 6, cross-link 4, region of interest 3, turn 3, chain 1, splice variant 1

Structure

Experimental structures (PDB)

21 structures.

PDB	Method	Resolution (Å)
5KKQ	X-RAY DIFFRACTION	1.74
5YEG	X-RAY DIFFRACTION	2
5K5I	X-RAY DIFFRACTION	2.19
5T00	X-RAY DIFFRACTION	2.19
8SST	X-RAY DIFFRACTION	2.19
5K5J	X-RAY DIFFRACTION	2.29
8SSS	X-RAY DIFFRACTION	2.3
5YEH	X-RAY DIFFRACTION	2.33
5UND	X-RAY DIFFRACTION	2.55
6QNX	X-RAY DIFFRACTION	2.7
5YEF	X-RAY DIFFRACTION	2.81
8SSU	X-RAY DIFFRACTION	2.89
5YEL	X-RAY DIFFRACTION	2.96
5K5H	X-RAY DIFFRACTION	3.11
8SSQ	X-RAY DIFFRACTION	3.12
5K5L	X-RAY DIFFRACTION	3.12
8SSR	X-RAY DIFFRACTION	3.14
5T0U	X-RAY DIFFRACTION	3.2
7W1M	ELECTRON MICROSCOPY	6.5
1X6H	SOLUTION NMR
2CT1	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P49711-F1	59.45	0.01

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 (12): 1, 289, 317, 374, 402, 609, 610, 612, 18, 74, 219, 689

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-5617472	Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-9943962	CHD6, CHD7, CHD8, CHD9 subfamily

MSigDB gene sets: 715 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, E2F_Q4, GOBP_CHROMOSOME_ORGANIZATION, E2F_Q4_01, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_MUSCLE_TISSUE_DEVELOPMENT, MORF_MBD4, MORF_SMC1L1, chr16q22, TTTGTAG_MIR520D, GEORGES_CELL_CYCLE_MIR192_TARGETS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, MORF_UBE2N, MORF_RAD21, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION

GO Biological Process (26): negative regulation of transcription by RNA polymerase II (GO:0000122), in utero embryonic development (GO:0001701), DNA methylation-dependent constitutive heterochromatin formation (GO:0006346), regulation of transcription by RNA polymerase II (GO:0006357), mitochondrion organization (GO:0007005), chromosome segregation (GO:0007059), negative regulation of cell population proliferation (GO:0008285), gene expression (GO:0010467), positive regulation of gene expression (GO:0010628), epigenetic regulation of gene expression (GO:0040029), negative regulation of gene expression via chromosomal CpG island methylation (GO:0044027), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of DNA-templated transcription (GO:0045893), positive regulation of transcription by RNA polymerase II (GO:0045944), cardiac muscle cell development (GO:0055013), regulation of centromeric sister chromatid cohesion (GO:0070602), protein localization to chromosome, centromeric region (GO:0071459), genomic imprinting (GO:0071514), chromatin looping (GO:0140588), chromatin organization (GO:0006325), regulation of DNA-templated transcription (GO:0006355), heart development (GO:0007507), positive regulation of macromolecule biosynthetic process (GO:0010557), negative regulation of gene expression (GO:0010629), protein localization to chromosome (GO:0034502), cardiac muscle cell differentiation (GO:0055007)

GO Molecular Function (15): transcription cis-regulatory region binding (GO:0000976), RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), transcription coregulator binding (GO:0001221), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), chromatin insulator sequence binding (GO:0043035), sequence-specific DNA binding (GO:0043565), cis-regulatory region sequence-specific DNA binding (GO:0000987), DNA binding (GO:0003677), chromatin binding (GO:0003682), protein binding (GO:0005515), metal ion binding (GO:0046872), chromatin loop anchoring activity (GO:0140587), sequence-specific double-stranded DNA binding (GO:1990837)

GO Cellular Component (7): chromosome, centromeric region (GO:0000775), condensed chromosome (GO:0000793), male germ cell nucleus (GO:0001673), nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), chromosome (GO:0005694)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Activation of HOX genes during differentiation	1
CHD chromatin remodelers	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	4
transcription by RNA polymerase II	3
regulation of transcription by RNA polymerase II	2
regulation of gene expression	2
DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
transcription cis-regulatory region binding	2
chromatin DNA binding	2
binding	2
nuclear lumen	2
intracellular membraneless organelle	2
negative regulation of DNA-templated transcription	1
chordate embryonic development	1
constitutive heterochromatin formation	1
organelle organization	1
cell cycle process	1
cell population proliferation	1
regulation of cell population proliferation	1
negative regulation of cellular process	1
macromolecule biosynthetic process	1
gene expression	1
positive regulation of macromolecule biosynthetic process	1
chromatin remodeling	1
negative regulation of gene expression, epigenetic	1
negative regulation of RNA biosynthetic process	1
positive regulation of RNA biosynthetic process	1
positive regulation of DNA-templated transcription	1
striated muscle cell development	1
cardiac cell development	1
cardiac muscle cell differentiation	1
regulation of sister chromatid cohesion	1
centromeric sister chromatid cohesion	1
protein localization to chromosome	1
germ cell development	1
epigenetic programming of gene expression	1
chromatin organization	1
cellular component organization	1
transcription regulatory region nucleic acid binding	1
sequence-specific double-stranded DNA binding	1
cis-regulatory region sequence-specific DNA binding	1

Protein interactions and networks

STRING

4884 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CTCF	RAD21	O60216	997
CTCF	YY1	P25490	985
CTCF	SMC3	Q9UQE7	984
CTCF	STAG2	Q8N3U4	953
CTCF	POU5F1	P31359	939
CTCF	IGF2	P01344	935
CTCF	NPM1	P06748	914
CTCF	SMC1A	Q14683	914
CTCF	SUZ12	Q15022	912
CTCF	CHD8	Q9HCK8	904
CTCF	SIN3A	Q96ST3	887
CTCF	NIPBL	Q6KC79	852
CTCF	TAF3	Q5VWG9	847
CTCF	SIX5	Q8N196	839
CTCF	TP53	P04637	824

IntAct

240 interactions, top by confidence:

A	B	Type	Score
LARP7	CCNT1	psi-mi:“MI:0914”(association)	0.850
H2AX	PPM1G	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
NOP53	RRP8	psi-mi:“MI:0914”(association)	0.640
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
NPM1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.610
ZMYM4	CTCF	psi-mi:“MI:0915”(physical association)	0.560
CTCF	TRAF2	psi-mi:“MI:0915”(physical association)	0.560
ZMYM6	CTCF	psi-mi:“MI:0915”(physical association)	0.560
APP	CTCF	psi-mi:“MI:0915”(physical association)	0.560
PCGF1	CBX4	psi-mi:“MI:0914”(association)	0.530
KSR2	POLR3A	psi-mi:“MI:0914”(association)	0.530
H1-4	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
ZNF2	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
PRR11	NVL	psi-mi:“MI:0914”(association)	0.530
PUM3	RRP8	psi-mi:“MI:0914”(association)	0.530
ZBTB48	ZBTB24	psi-mi:“MI:0914”(association)	0.530
ZCRB1	DKC1	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
H2AC20	PPM1G	psi-mi:“MI:0914”(association)	0.530
H1-4	RRP8	psi-mi:“MI:0914”(association)	0.530

BioGRID (589): CTCF (Two-hybrid), CTCF (Affinity Capture-MS), CTCF (Affinity Capture-MS), TOP2B (Affinity Capture-Western), NPM1 (Affinity Capture-Western), PARP1 (Affinity Capture-Western), NCL (Affinity Capture-Western), PARP1 (Reconstituted Complex), CTCF (Affinity Capture-MS), CTCF (Affinity Capture-MS), CTCF (Affinity Capture-MS), CTCF (Affinity Capture-MS), SET (Affinity Capture-MS), CTCF (Affinity Capture-MS), CTCF (Affinity Capture-MS)

ESM2 similar proteins: A1L1J6, A1L1R6, A2APF3, D3ZUU2, E9Q8T2, G5E8B9, O08961, O15060, O43167, O95625, P07665, P10074, P14404, P49711, P57071, Q08705, Q13105, Q1H9T6, Q2M1K9, Q3B725, Q3MHQ4, Q3U288, Q4VBD9, Q5DU09, Q5R633, Q5SVQ8, Q60821, Q61164, Q6GL52, Q6KAS7, Q6NS86, Q6NUD7, Q6P2A1, Q6YND2, Q7TS63, Q7ZVR6, Q80TS5, Q80X44, Q811F1, Q8N1W2

Diamond homologs: A2APF3, P49711, Q08705, Q61164, Q8NI51, Q9R1D1

SIGNOR signaling

10 interactions.

A	Effect	B	Mechanism
BCL3	“down-regulates quantity by repression”	CTCF	“transcriptional regulation”
CTCF	“up-regulates quantity by expression”	APP	“transcriptional regulation”
CTCF	“down-regulates quantity by repression”	BCL6	“transcriptional regulation”
CTCF	“down-regulates quantity by repression”	MYC	“transcriptional regulation”
CTCF	“up-regulates quantity by expression”	RARRES1	“transcriptional regulation”
CTCF	“down-regulates quantity by repression”	TERT	“transcriptional regulation”
NFKB1	“down-regulates quantity by repression”	CTCF	“transcriptional regulation”
HDLBP	“up-regulates activity”	CTCF	binding
CTCF	“up-regulates quantity by expression”	MGAT5B	“transcriptional regulation”
ADNP	“down-regulates activity”	CTCF	relocalization

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 192 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:

Pathway	Partners	Fold	FDR
Peptide chain elongation	27	28.3×	2e-30
Viral mRNA Translation	27	28.3×	2e-30
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	27	28.0×	2e-30
Selenocysteine synthesis	27	26.8×	5e-30
Eukaryotic Translation Termination	27	26.8×	5e-30
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	27	26.3×	7e-30
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	27	26.3×	7e-30
Formation of a pool of free 40S subunits	27	25.0×	3e-29

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	28	29.1×	7e-31
negative regulation of mRNA splicing, via spliceosome	5	21.5×	3e-04
ribosomal large subunit biogenesis	7	17.4×	2e-05
translation	27	15.6×	6e-22
ribosomal small subunit biogenesis	11	14.1×	8e-08
rRNA processing	16	12.7×	5e-11
regulation of alternative mRNA splicing, via spliceosome	9	12.3×	9e-06
mitochondrial translation	7	6.8×	4e-03

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 4 cancer types — ALL, BRCA, HNSC, UCEC.

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	41
Likely pathogenic	45
Uncertain significance	169
Likely benign	64
Benign	21

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1203833	NM_006565.4(CTCF):c.1343G>A (p.Arg448Gln)	Pathogenic
1214237	NM_006565.4(CTCF):c.1129C>T (p.Arg377Cys)	Pathogenic
1254810	NM_006565.4(CTCF):c.677A>G (p.Tyr226Cys)	Pathogenic
1301472	NM_006565.4(CTCF):c.1580dup (p.His527fs)	Pathogenic
1325769	NM_006565.4(CTCF):c.148dup (p.Val50fs)	Pathogenic
1325770	NM_006565.4(CTCF):c.688del (p.Glu230fs)	Pathogenic
1325772	NM_006565.4(CTCF):c.804_805del (p.Cys268_Glu269delinsTer)	Pathogenic
1325777	NM_006565.4(CTCF):c.1102C>T (p.Arg368Cys)	Pathogenic
1325778	NM_006565.4(CTCF):c.1103G>A (p.Arg368His)	Pathogenic
1325779	NM_006565.4(CTCF):c.1117C>G (p.His373Asp)	Pathogenic
1325788	NM_006565.4(CTCF):c.292_293del (p.Leu98fs)	Pathogenic
1343232	NM_006565.4(CTCF):c.1223_1226del (p.Glu408fs)	Pathogenic
2104020	NM_006565.4(CTCF):c.1369C>T (p.Arg457Ter)	Pathogenic
2446041	NM_006565.4(CTCF):c.1485dup (p.Lys496Ter)	Pathogenic
280753	NM_006565.4(CTCF):c.1670_1674del (p.Val556_Cys557insTer)	Pathogenic
280869	NM_006565.4(CTCF):c.610dup (p.Thr204fs)	Pathogenic
3256301	NM_006565.4(CTCF):c.1785dup (p.Arg596fs)	Pathogenic
3342873	NM_006565.4(CTCF):c.1034A>G (p.His345Arg)	Pathogenic
3378409	NM_006565.4(CTCF):c.782-2A>T	Pathogenic
3571458	GRCh38/hg38 16q22.1(chr16:67623831-67627229)x1	Pathogenic
3602939	NM_006565.4(CTCF):c.1015C>T (p.Arg339Trp)	Pathogenic
3900669	NM_006565.4(CTCF):c.1633del (p.Tyr545fs)	Pathogenic
4007875	NM_006565.4(CTCF):c.1568dup (p.Tyr523Ter)	Pathogenic
4075848	GRCh37/hg19 16q22.1(chr16:67627057-67675865)x1	Pathogenic
4081928	NM_006565.4(CTCF):c.633del (p.Lys211fs)	Pathogenic
422876	NM_006565.4(CTCF):c.1814del (p.Lys605fs)	Pathogenic
4536285	NM_006565.4(CTCF):c.2000-1G>A	Pathogenic
4813883	NM_006565.4(CTCF):c.1999+1G>A	Pathogenic
504066	NM_006565.4(CTCF):c.313_314dup (p.Gln106fs)	Pathogenic
521287	NM_006565.4(CTCF):c.615_618del (p.Lys206fs)	Pathogenic

SpliceAI

1830 predictions. Top by Δscore:

Variant	Effect	Δscore
16:67571144:TTAG:T	acceptor_loss	1.0000
16:67571145:TAG:T	acceptor_loss	1.0000
16:67571146:A:AG	acceptor_gain	1.0000
16:67571146:AG:A	acceptor_loss	1.0000
16:67571146:AGAAT:A	acceptor_gain	1.0000
16:67571147:G:GC	acceptor_gain	1.0000
16:67571147:GA:G	acceptor_gain	1.0000
16:67571147:GAA:G	acceptor_gain	1.0000
16:67571147:GAAT:G	acceptor_gain	1.0000
16:67571147:GAATG:G	acceptor_gain	1.0000
16:67571260:GAGAG:G	donor_gain	1.0000
16:67571261:AGAG:A	donor_gain	1.0000
16:67571262:GAG:G	donor_gain	1.0000
16:67571262:GAGG:G	donor_gain	1.0000
16:67571263:AG:A	donor_gain	1.0000
16:67571264:GG:G	donor_gain	1.0000
16:67571264:GGT:G	donor_loss	1.0000
16:67571265:G:GG	donor_gain	1.0000
16:67610817:A:AG	acceptor_gain	1.0000
16:67610820:AAAG:A	acceptor_gain	1.0000
16:67610822:A:AC	acceptor_loss	1.0000
16:67610823:GGCA:G	acceptor_gain	1.0000
16:67612214:G:GT	donor_gain	1.0000
16:67616743:A:T	acceptor_loss	1.0000
16:67616744:GGT:G	acceptor_gain	1.0000
16:67616874:TAG:T	donor_gain	1.0000
16:67616874:TAGAA:T	donor_gain	1.0000
16:67616875:AGA:A	donor_gain	1.0000
16:67616875:AGAAG:A	donor_loss	1.0000
16:67616876:GAA:G	donor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000014428 (16:67571535 G>A,C), RS1000058287 (16:67568481 C>A,T), RS1000063864 (16:67639134 T>G), RS1000082664 (16:67563233 G>A,T), RS1000116705 (16:67633113 A>G), RS1000125798 (16:67613084 G>A,T), RS1000163312 (16:67561443 AG>A), RS1000218226 (16:67564399 C>T), RS1000252555 (16:67600521 T>C), RS1000262090 (16:67610020 A>C), RS1000270894 (16:67600172 G>A,C,T), RS1000287506 (16:67638616 C>G,T), RS1000289256 (16:67563417 C>G,T), RS1000308102 (16:67621907 T>G), RS1000337554 (16:67575218 C>G)

Disease associations

OMIM: gene MIM:604167 | disease phenotypes: MIM:615502, MIM:300238

GenCC curated gene-disease

Disease	Classification	Inheritance
CTCF-related neurodevelopmental disorder	Definitive	Autosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
syndromic intellectual disability	Definitive	AD

Mondo (6): CTCF-related neurodevelopmental disorder (MONDO:0014213), desmoplastic/nodular medulloblastoma (MONDO:0016711), cleft palate (MONDO:0016064), syndromic X-linked intellectual disability Shashi type (MONDO:0010277), intellectual disability (MONDO:0001071), acute megakaryoblastic leukemia in down syndrome (MONDO:0020526)

Orphanet (6): CTCF-related neurodevelopmental disorder (Orphanet:363611), Desmoplastic/nodular medulloblastoma (Orphanet:251863), Cleft palate (Orphanet:2014), X-linked intellectual disability, Shashi type (Orphanet:85286), Acute megakaryoblastic leukemia in children with Down syndrome (Orphanet:99887), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

153 total (30 of 153 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000023	Inguinal hernia
HP:0000028	Cryptorchidism
HP:0000059	Hypoplastic labia majora
HP:0000160	Narrow mouth
HP:0000164	Abnormality of the dentition
HP:0000175	Cleft palate
HP:0000194	Open mouth
HP:0000219	Thin upper lip vermilion
HP:0000233	Thin vermilion border
HP:0000248	Brachycephaly
HP:0000252	Microcephaly
HP:0000275	Narrow face
HP:0000276	Long face
HP:0000280	Coarse facial features
HP:0000286	Epicanthus
HP:0000303	Mandibular prognathia
HP:0000307	Pointed chin
HP:0000308	Microretrognathia
HP:0000316	Hypertelorism
HP:0000322	Short philtrum
HP:0000325	Triangular face
HP:0000331	Short chin
HP:0000336	Prominent supraorbital ridges
HP:0000341	Narrow forehead
HP:0000343	Long philtrum
HP:0000347	Micrognathia
HP:0000348	High forehead
HP:0000358	Posteriorly rotated ears
HP:0000365	Hearing impairment

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST000288_10	HDL cholesterol	8.000000e-16
GCST006257_4	Elevated fasting plasma glucose	5.000000e-06
GCST010002_113	Refractive error	2.000000e-14
GCST010083_158	Hemoglobin levels	1.000000e-10
GCST90002382_443	Eosinophil percentage of white cells	1.000000e-13

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004509	hemoglobin measurement
EFO:0007991	eosinophil percentage of leukocytes

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
D002972	Cleft Palate	C05.500.460.185; C05.660.207.540.460.185; C07.320.440.185; C07.465.525.185; C07.650.500.460.185; C07.650.525.185; C16.131.621.207.540.460.185; C16.131.850.500.460.185; C16.131.850.525.185
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
C537135	Orofaciodigital syndrome, Shashi type (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4523233 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.70	Kd	1988	nM	CHEMBL3752910
5.70	ED50	1988	nM	CHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149848: Binding affinity to human CTCF incubated for 45 mins by Kinobead based pull down assay	kd	1.9881	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects binding, affects reaction, affects cotreatment, decreases expression	4
Valproic Acid	decreases expression, affects expression, affects cotreatment	3
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	3
Air Pollutants	affects cotreatment, decreases expression, increases abundance, affects expression	2
Ozone	affects expression, affects cotreatment, decreases expression, increases abundance	2
Tretinoin	affects cotreatment, decreases expression, affects expression	2
aristolochic acid I	decreases expression	1
TAK-243	decreases sumoylation	1
triphenyl phosphate	affects expression	1
alpha-pinene	increases abundance, affects cotreatment, decreases expression	1
uranyl acetate	affects expression	1
bisphenol A	affects cotreatment, increases expression	1
arsenite	decreases reaction, affects binding	1
cobaltous chloride	decreases expression	1
methacrylaldehyde	increases abundance, affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
Resveratrol	affects cotreatment, increases expression	1
Decitabine	affects binding, affects reaction, affects expression	1
Arsenic Trioxide	affects methylation	1
Acrolein	affects cotreatment, decreases expression, increases abundance	1
Butyrates	decreases response to substance	1
Caffeine	increases phosphorylation	1
Formaldehyde	decreases expression	1
Hydralazine	affects cotreatment, decreases expression	1
Phenolsulfonphthalein	affects cotreatment, increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Ribonucleotides	affects binding	1
Rotenone	decreases expression	1
Tunicamycin	decreases expression	1
Uranium	affects expression	1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL4421277	Binding	Inhibition of CTCF in HUVEC assessed as reduction of CTCF transcriptional activity by genome-wide RNA-seq and ChlP-seq analysis	Inhibitors of sox18 protein activity for treating angiogenesis- and/or lymphangiogenesis-related diseases

Cellosaurus cell lines

4 cell lines: 3 embryonic stem cell, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A0U1	SEES3-1V human CTCF, clone1	Embryonic stem cell	Male
CVCL_A0U2	SEES3-1V human CTCF, clone2	Embryonic stem cell	Male
CVCL_A0U3	SEES3-1V human CTCF, clone3	Embryonic stem cell	Male
CVCL_HC72	HEK293 eGFP-CTCF	Transformed cell line	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT02422056	PHASE4	COMPLETED	Acid Tranexamic Effectiveness in Reducing the Intraoperative Bleeding in Palatoplasty
NCT02915042	PHASE4	WITHDRAWN	Dexmedetomidine vs Placebo for Pediatric Cleft Palate Repair
NCT02953145	PHASE4	WITHDRAWN	The Use of Fibrin Sealant to Reduce Post Operative Pain in Cleft Palate Surgery
NCT03632044	PHASE4	ACTIVE_NOT_RECRUITING	Evaluation of Trigeminal Nerve Blockade
NCT06962306	PHASE4	RECRUITING	Optimizing Perioperative Analgesia to Lower Pain Following Cleft Palate Surgery
NCT05657860	PHASE4	COMPLETED	Guanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479	PHASE4	RECRUITING	Metformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829	PHASE4	WITHDRAWN	Valbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198	PHASE4	NOT_YET_RECRUITING	Deutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT00098319	PHASE3	COMPLETED	Oral Cleft Prevention Trial in Brazil
NCT00397917	PHASE3	COMPLETED	Oral Cleft Prevention Program
NCT04928352	PHASE3	RECRUITING	Nebulized Bupivacaine Analgesia for Cleft Palate Repair
NCT04928391	PHASE3	COMPLETED	A Single Bolus of Dexmedetomidine Versus Normal Saline in Postoperative Agitation
NCT02270736	PHASE3	COMPLETED	Clinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02017964	PHASE2	COMPLETED	Combination Chemotherapy in Treating Younger Patients With Newly Diagnosed, Non-metastatic Desmoplastic Medulloblastoma
NCT00004639	PHASE2	COMPLETED	Cleft Palate Surgery and Speech Development
NCT00760006	PHASE2	COMPLETED	Preventing Complications in Cleft Palate Repair With Antibiotics
NCT01760330	PHASE2	WITHDRAWN	IV Acetaminophen in Children Undergoing Palatoplasty
NCT02350803	PHASE2	COMPLETED	Does Use of Rigid Fixation After Removing Distraction Osteogenesis Device Reduce the Relapse?
NCT03412474	PHASE2	COMPLETED	Suprazygomatic Block in Cleft Palate Surgery in Children
NCT02304302	PHASE2	COMPLETED	Down Syndrome Memantine Follow-up Study
NCT03862950	PHASE2	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226	PHASE2	UNKNOWN	Study to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856	PHASE2	COMPLETED	Evaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320	PHASE1	COMPLETED	Clinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361	PHASE1	ENROLLING_BY_INVITATION	Sensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764	PHASE1	COMPLETED	Use of MRI and cTBS for Catatonia in Autism
NCT06586827	PHASE1	COMPLETED	Impact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940	PHASE1	NOT_YET_RECRUITING	Escalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT01616953	PHASE1/PHASE2	COMPLETED	Cell Therapy for Craniofacial Bone Defects
NCT02247193	PHASE1/PHASE2	COMPLETED	Botulinum Toxin to Improve Cosmesis of Primary Cleft Lip Repair
NCT00097149	Not specified	COMPLETED	Systematic Pediatric Care for Oral Clefts - South America
NCT00285714	Not specified	UNKNOWN	3D Imaging of Hard and Soft Tissue in Orthognathic Surgery
NCT00340977	Not specified	COMPLETED	Svangerskap, Arv, Og Miljo (Pregnancy, Heredity and Environment)
NCT00423072	Not specified	COMPLETED	Middle Ear Pressure Disregulation in Cleft Palate Patients
NCT00584272	Not specified	COMPLETED	Retrospective Study on the Outcome of Cleft Palate Repair: Comparing US Surgical and Ethicon Suture Materials
NCT00773994	Not specified	COMPLETED	Pilot Study Evaluating Characteristic Closure Patterns of the Normal Velopharyngeal Portal
NCT00779961	Not specified	UNKNOWN	An Investigation for the Optimal Timing of a Cleft Palate Repair
NCT00829101	Not specified	COMPLETED	Articulation and Phonology in Children With Unilateral Cleft Lip and Palate
NCT00993551	Not specified	COMPLETED	Timing of Primary Surgery for Cleft Palate