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Gene

CTCF

CCCTC-binding factor

Summary

Cytogenetic location
16q22.1
Coordinates
Chromosome 16: 67,562,526–67,639,177 (GRCh38)
Exons
12 exons across 76.7 kb
Protein
727 amino acids
Also known as
FAP108, CFAP108
MANE Select transcript
ENST00000264010.10NM_006565.4
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

    • Intellectual Disability

      • One of 233 genes linked to it

        • ClinGen rates the link definitive
        • 4 GenCC submitters rate it definitive or strong

    How CTCF is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 16, with a bracket where CTCF sits. CTCF and 49 genes near it on chromosome 16, from 67,100,852 to 68,100,851.Chromosome 1616q22.1p13.3p13.2p13.13p13.12p13.11p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q13q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.367.2 Mb67.4 Mb67.6 Mb67.8 Mb68 MbCBFB: 67,028,984–67,101,058, forward strandCBFBPHAF1: 67,109,941–67,148,544, forward strandPHAF1B3GNT9: 67,142,023–67,151,260, reverse strandTRADD: 67,153,969–67,163,760, reverse strandFBXL8: 67,159,932–67,164,570, forward strand: 67,163,385–67,165,815, forward strandHSF4: 67,164,681–67,169,945, forward strandHSF4NOL3: 67,170,154–67,176,189, forward strandMATCAP1: 67,175,599–67,184,228, reverse strandEXOC3L1: 67,184,313–67,190,242, reverse strandE2F4: 67,192,117–67,198,919, forward strandE2F4ELMO3: 67,199,105–67,204,029, forward strandELMO3TMEM208: 67,227,103–67,229,281, forward strandTMEM208FHOD1: 67,229,387–67,247,539, reverse strandFHOD1SLC9A5: 67,237,683–67,272,191, forward strandSLC9A5PLEKHG4: 67,277,510–67,289,499, forward strandPLEKHG4KCTD19: 67,289,428–67,326,766, reverse strandKCTD19LRRC36: 67,326,798–67,385,221, forward strandLRRC36TPPP3: 67,389,027–67,393,518, reverse strandTPPP3ZDHHC1: 67,394,152–67,416,833, reverse strandZDHHC1HSD11B2: 67,430,652–67,437,553, forward strandHSD11B2ATP6V0D1: 67,437,523–67,481,227, reverse strandATP6V0D1AGRP: 67,482,571–67,483,552, reverse strandAGRPRIPOR1: 67,518,418–67,546,788, forward strandRIPOR1CTCF: 67,562,526–67,639,177, forward strandCTCFCARMIL2: 67,644,988–67,657,569, forward strandCARMIL2ACD: 67,657,512–67,660,810, reverse strandACDPARD6A: 67,660,350–67,664,266, forward strandPARD6AENKD1: 67,662,945–67,667,954, reverse strandC16orf86: 67,666,802–67,668,757, forward strandGFOD2: 67,674,527–67,719,352, reverse strandRANBP10: 67,723,070–67,806,563, reverse strandRANBP10TSNAXIP1: 67,806,765–67,832,148, forward strandTSNAXIP1CENPT: 67,828,157–67,847,811, reverse strandCENPTTHAP11: 67,842,320–67,844,195, forward strandTHAP11NUTF2: 67,844,369–67,872,569, forward strandNUTF2EDC4: 67,873,049–67,884,520, forward strandNRN1L: 67,884,868–67,888,855, forward strandPSKH1: 67,893,244–67,929,676, forward strandPSKH1CTRL: 67,927,640–67,932,365, reverse strandCTRL: 67,929,614–67,936,017, reverse strandPSMB10: 67,934,504–67,936,865, reverse strandPSMB10LCAT: 67,939,150–67,944,681, reverse strandSLC12A4: 67,943,474–67,969,601, reverse strandDPEP3: 67,975,661–67,980,554, reverse strandDPEP3DPEP2: 67,987,392–68,000,624, reverse strandDPEP2DUS2: 67,987,746–68,079,344, forward strandDPEP2NB: 68,013,436–68,015,911, reverse strandDPEP2NBDDX28: 68,020,916–68,023,232, reverse strandDDX28NFATC3: 68,084,751–68,229,259, forward strandNFATC3Diagram of CTCF: 12 exons on the forward strand of chromosome 16Exon 3: 19 known disease-causing sitesExon 4: 4 known disease-causing sitesExon 5: 8 known disease-causing sitesExon 6: 13 known disease-causing sitesExon 7: 3 known disease-causing sitesExon 8: 2 known disease-causing sitesExon 9: 2 known disease-causing sitesExon 11: 2 known disease-causing sitesExon 1: 67,562,526–67,562,724, 199 basesExon 2: 67,571,148–67,571,264, 117 basesExon 3: 67,610,824–67,611,613, 790 basesExon 4: 67,611,951–67,612,121, 171 basesExon 5: 67,616,745–67,616,878, 134 basesExon 6: 67,620,697–67,620,817, 121 basesExon 7: 67,621,442–67,621,591, 150 basesExon 8: 67,626,555–67,626,715, 161 basesExon 9: 67,628,370–67,628,552, 183 basesExon 10: 67,629,398–67,629,533, 136 basesExon 11: 67,636,690–67,636,851, 162 basesExon 12: 67,637,688–67,639,177, 1,490 bases1246810125′3′

    Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

    Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

    Nearby genes from Ensembl release 116, on GRCh38.

    Exons make up 3.8 kb of the gene's 76.7 kb; 2,184 of those bases code for the protein.

    Sequencing CTCF

    1Low

    How hard CTCF is to sequence with short reads, out of 100

    • Mappability0%
    • Homology0%
    • Repeats5.4%
    • GC content5.2%
    • Reference coverage0%

    57

    positions in CTCF where ClinVar classes a change as pathogenic or likely pathogenic

    None of them falls in a region short reads find hard.

    A whole genome covers all 76.7 kb of CTCF, introns included, not only the 3.8 kb of exons.

    Genes linked to the same conditions

    Traits linked to CTCF

    The Human Phenotype Ontology lists these as features of the rare conditions CTCF can cause. Each trait's page lists the other genes linked to it.

    Abnormality of head or neck

    Show 45 more traits

    External links

    Where this comes from

    • HGNC: the gene's symbol, name, other symbols and location.
    • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
    • GenCC and ClinGen, released 2026-10-17: which conditions the gene is linked to, and how strongly.
    • The ACMG secondary findings list, SF v3.2.
    • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
    • The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
    • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
    • Data release 2026.10.17-8666dff2.

    Cite this page

    APA

    Dante Labs. (n.d.). CTCF gene: CCCTC-binding factor. Retrieved 17 October 2026, from https://dantelabs.com/genes/ctcf

    Vancouver

    Dante Labs. CTCF gene: CCCTC-binding factor [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/ctcf

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