Seroatlas · Human Serome Atlas

CTCF

Transcriptional repressor CTCF

Also known as: CFAP108, CTCF_HUMAN, FAP108

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: P49711
Gene: CTCF
Ensembl: ENSG00000102974
Chromosome: 16
Canonical length: 727 aa
Protein class: Cancer-related genes, Disease related genes, Human disease related genes, Predicted intracellular proteins, Transcription factors
Subcellular location: Nucleoplasm

OverviewNCBI Gene

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. [provided by RefSeq, Jul 2010]

Canonical amino-acid sequenceUniProt

727 residues, UniProt reviewed canonical sequence.

>P49711|CTCF
     1  MEGDAVEAIV EESETFIKGK ERKTYQRRRE GGQEEDACHL PQNQTDGGEV VQDVNSSVQM
    61  VMMEQLDPTL LQMKTEVMEG TVAPEAEAAV DDTQIITLQV VNMEEQPINI GELQLVQVPV
   121  PVTVPVATTS VEELQGAYEN EVSKEGLAES EPMICHTLPL PEGFQVVKVG ANGEVETLEQ
   181  GELPPQEDPS WQKDPDYQPP AKKTKKTKKS KLRYTEEGKD VDVSVYDFEE EQQEGLLSEV
   241  NAEKVVGNMK PPKPTKIKKK GVKKTFQCEL CSYTCPRRSN LDRHMKSHTD ERPHKCHLCG
   301  RAFRTVTLLR NHLNTHTGTR PHKCPDCDMA FVTSGELVRH RRYKHTHEKP FKCSMCDYAS
   361  VEVSKLKRHI RSHTGERPFQ CSLCSYASRD TYKLKRHMRT HSGEKPYECY ICHARFTQSG
   421  TMKMHILQKH TENVAKFHCP HCDTVIARKS DLGVHLRKQH SYIEQGKKCR YCDAVFHERY
   481  ALIQHQKSHK NEKRFKCDQC DYACRQERHM IMHKRTHTGE KPYACSHCDK TFRQKQLLDM
   541  HFKRYHDPNF VPAAFVCSKC GKTFTRRNTM ARHADNCAGP DGVEGENGGE TKKSKRGRKR
   601  KMRSKKEDSS DSENAEPDLD DNEDEEEPAV EIEPEPEPQP VTPAPPPAKK RRGRPPGRTN
   661  QPKQNQPTAI IQVEDQNTGA IENIIVEVKK EPDAEPAEGE EEEAQPAATD APNGDLTPEM
   721  ILSMMDR

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CTCF can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.57
Highest tissue expression: 65 nTPM

Expression across tissuesHPA

Tissue

thymus: 65 nTPM
tonsil: 33 nTPM
bone marrow: 33 nTPM
skeletal muscle: 29 nTPM
lymph node: 27 nTPM
parathyroid gland: 27 nTPM

Single-cell type

erythrocyte progenitors: 206 nCPM
monocyte progenitors: 189 nCPM
neutrophil progenitors: 133 nCPM
megakaryocyte progenitors: 125 nCPM
neutrophils: 104 nCPM
myonuclei: 98 nCPM

Immune cell

naive B-cell: 7.4 nTPM
basophil: 6.8 nTPM
neutrophil: 6.8 nTPM
memory B-cell: 5.6 nTPM
plasmacytoid DC: 5.6 nTPM
memory CD4 T-cell: 4.8 nTPM

Brain region

cerebellum: 49 nTPM
white matter: 44 nTPM
cerebral cortex: 39 nTPM
basal ganglia: 37 nTPM
hypothalamus: 37 nTPM
hippocampal formation: 35 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about CTCF.

Disease | AllUniProt

Conditions CTCF is implicated in, by any mechanism.

Intellectual developmental disorder, autosomal dominant 21 (MRD21) MIM:615502

Disease | GeneticClinVar

95 pathogenic / likely-pathogenic of 392 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

CTCF-related neurodevelopmental disorder
Inborn genetic diseases
CTCF-related disorder
Intellectual disability
Melanoma

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.15
gnomAD pLI: 1
gnomAD missense Z: 4.44
DepMap mean gene effect: -1.63
DepMap dependency class: pan

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of CTCF in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads CTCF as an antibody target. Whether an autoantibody or antibody against CTCF could matter depends on whether native CTCF is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CTCF is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label CTCF as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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