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Transcription Factor Binding Site Deletion Mutation

MedGen UID:
1662030
•Concept ID:
C4725194
•
Cell or Molecular Dysfunction
Synonym: TFBS Ablation

Definition

A deletion mutation where the deleted sequence includes a transcription factor binding site for a gene. [from NCI]

Term Hierarchy

CClinical test,  RResearch test,  OOMIM,  GGeneReviews,  VClinVar  
  • CROGVTranscription Factor Binding Site Deletion Mutation

Professional guidelines

PubMed

The phenotypic spectrum and genotype-phenotype correlations in 106 patients with variants in major autism gene CHD8.
Dingemans AJM, Truijen KMG, van de Ven S, Bernier R, Bongers EMHF, Bouman A, de Graaff-Herder L, Eichler EE, Gerkes EH, De Geus CM, van Hagen JM, Jansen PR, Kerkhof J, Kievit AJA, Kleefstra T, Maas SM, de Man SA, McConkey H, Patterson WG, Dobson AT, Prijoles EJ, Sadikovic B, Relator R, Stevenson RE, Stumpel CTRM, Heijligers M, Stuurman KE, Löhner K, Zeidler S, Lee JA, Lindy A, Zou F, Tedder ML, Vissers LELM, de Vries BBA
Transl Psychiatry 2022 Oct 1;12(1):421. doi: 10.1038/s41398-022-02189-1. PMID: 36182950Free PMC Article
Chromatin Accessibility of Human Mitral Valves and Functional Assessment of MVP Risk Loci.
Kyryachenko S, Georges A, Yu M, Barrandou T, Guo L, Bruneval P, Rubio T, Gronwald J, Baraki H, Kutschka I, Aras KK, Efimov IR, Norris RA, Voigt N, Bouatia-Naji N
Circ Res 2021 Mar 5;128(5):e84-e101. Epub 2021 Jan 28 doi: 10.1161/CIRCRESAHA.120.317581. PMID: 33508947Free PMC Article
Evaluation of an amplicon-based next-generation sequencing panel for detection of BRCA1 and BRCA2 genetic variants.
Shin S, Hwang IS, Lee ST, Choi JR
Breast Cancer Res Treat 2016 Aug;158(3):433-40. Epub 2016 Jul 6 doi: 10.1007/s10549-016-3891-z. PMID: 27383479

Recent clinical studies

Etiology

Transcriptional downregulation of FAM3C/ILEI in the Alzheimer's brain.
Watanabe N, Nakano M, Mitsuishi Y, Hara N, Mano T, Iwata A, Murayama S, Suzuki T, Ikeuchi T, Nishimura M
Hum Mol Genet 2021 Dec 17;31(1):122-132. doi: 10.1093/hmg/ddab226. PMID: 34378027
Genetic Variability of Long Terminal Repeat Region between HIV-2 Groups Impacts Transcriptional Activity.
Le Hingrat Q, Visseaux B, Bertine M, Chauveau L, Schwartz O, Collin F, Damond F, Matheron S, Descamps D, Charpentier C
J Virol 2020 Mar 17;94(7) doi: 10.1128/JVI.01504-19. PMID: 31915276Free PMC Article
Prospective investigation of FOXP1 syndrome.
Siper PM, De Rubeis S, Trelles MDP, Durkin A, Di Marino D, Muratet F, Frank Y, Lozano R, Eichler EE, Kelly M, Beighley J, Gerdts J, Wallace AS, Mefford HC, Bernier RA, Kolevzon A, Buxbaum JD
Mol Autism 2017;8:57. Epub 2017 Oct 24 doi: 10.1186/s13229-017-0172-6. PMID: 29090079Free PMC Article
Zinc finger proteins RUSH in where others fear to tread.
Chilton BS, Hewetson A
Biol Reprod 1998 Feb;58(2):285-94. doi: 10.1095/biolreprod58.2.285. PMID: 9475378
Blood group polymorphisms: molecular approach and biological significance.
Daniels G
Transfus Clin Biol 1997 Jul;4(4):383-90. doi: 10.1016/s1246-7820(97)80043-2. PMID: 9269718

Diagnosis

Functional filter for whole-genome sequencing data identifies HHT and stress-associated non-coding SMAD4 polyadenylation site variants >5 kb from coding DNA.
Xiao S, Kai Z, Murphy D, Li D, Patel D, Bielowka AM, Bernabeu-Herrero ME, Abdulmogith A, Mumford AD, Westbury SK, Aldred MA, Vargesson N, Caulfield MJ; Genomics England Research Consortium, Shovlin CL
Am J Hum Genet 2023 Nov 2;110(11):1903-1918. Epub 2023 Oct 9 doi: 10.1016/j.ajhg.2023.09.005. PMID: 37816352Free PMC Article
Expanding the genotypic spectrum of TXNL4A variants in Burn-McKeown syndrome.
Wood KA, Ellingford JM, Thomas HB; Genomics UK Research Consortium, Douzgou S, Beaman GM, Hobson E, Prescott K, O'Keefe RT, Newman WG
Clin Genet 2022 Feb;101(2):255-259. Epub 2021 Nov 5 doi: 10.1111/cge.14082. PMID: 34713892
Aberrant super-enhancer-driven oncogene ENC1 promotes the radio-resistance of breast carcinoma.
Li L, Wang N, Zhu M, Xiong Y, Wang F, Guo G, Wang X, Gu Y
Cell Death Dis 2021 Aug 6;12(8):777. doi: 10.1038/s41419-021-04060-5. PMID: 34362881Free PMC Article
Prospective investigation of FOXP1 syndrome.
Siper PM, De Rubeis S, Trelles MDP, Durkin A, Di Marino D, Muratet F, Frank Y, Lozano R, Eichler EE, Kelly M, Beighley J, Gerdts J, Wallace AS, Mefford HC, Bernier RA, Kolevzon A, Buxbaum JD
Mol Autism 2017;8:57. Epub 2017 Oct 24 doi: 10.1186/s13229-017-0172-6. PMID: 29090079Free PMC Article
Sterol response element binding protein and thyroid transcription factor-1 (Nkx2.1) regulate Abca3 gene expression.
Besnard V, Xu Y, Whitsett JA
Am J Physiol Lung Cell Mol Physiol 2007 Dec;293(6):L1395-405. Epub 2007 Sep 21 doi: 10.1152/ajplung.00275.2007. PMID: 17890326

Therapy

Targeting DNA binding proteins for cancer therapy.
Shiroma Y, Takahashi RU, Yamamoto Y, Tahara H
Cancer Sci 2020 Apr;111(4):1058-1064. Epub 2020 Mar 24 doi: 10.1111/cas.14355. PMID: 32073717Free PMC Article
Targeting transcription factors in cancer - from undruggable to reality.
Bushweller JH
Nat Rev Cancer 2019 Nov;19(11):611-624. Epub 2019 Sep 11 doi: 10.1038/s41568-019-0196-7. PMID: 31511663Free PMC Article
Metformin alleviates hyperglycemia-induced endothelial impairment by downregulating autophagy via the Hedgehog pathway.
Niu C, Chen Z, Kim KT, Sun J, Xue M, Chen G, Li S, Shen Y, Zhu Z, Wang X, Liang J, Jiang C, Cong W, Jin L, Li X
Autophagy 2019 May;15(5):843-870. Epub 2019 Jan 27 doi: 10.1080/15548627.2019.1569913. PMID: 30653446Free PMC Article
Loss-of-function mutation in the X-linked TBX22 promoter disrupts an ETS-1 binding site and leads to cleft palate.
Fu X, Cheng Y, Yuan J, Huang C, Cheng H, Zhou R
Hum Genet 2015 Feb;134(2):147-58. Epub 2014 Nov 6 doi: 10.1007/s00439-014-1503-8. PMID: 25373698
DNA binding by the ribosomal DNA transcription factor rrn3 is essential for ribosomal DNA transcription.
Stepanchick A, Zhi H, Cavanaugh AH, Rothblum K, Schneider DA, Rothblum LI
J Biol Chem 2013 Mar 29;288(13):9135-44. Epub 2013 Feb 7 doi: 10.1074/jbc.M112.444265. PMID: 23393135Free PMC Article

Prognosis

DNA Methylation of Human Choline Kinase Alpha Promoter-Associated CpG Islands in MCF-7 Cells.
Mohamed Sa'dom SAF, Raikundalia S, Shamsuddin S, See Too WC, Few LL
Genes (Basel) 2021 Jun 1;12(6) doi: 10.3390/genes12060853. PMID: 34205960Free PMC Article
Loop competition and extrusion model predicts CTCF interaction specificity.
Xi W, Beer MA
Nat Commun 2021 Feb 16;12(1):1046. doi: 10.1038/s41467-021-21368-0. PMID: 33594051Free PMC Article
A new transcription factor ATG10S activates IFNL2 transcription by binding at an IRF1 site in HepG2 cells.
Zhang MQ, Zhao Q, Zhang JP
Autophagy 2020 Dec;16(12):2167-2179. Epub 2020 Jan 29 doi: 10.1080/15548627.2020.1719681. PMID: 31996071Free PMC Article
CD68/macrosialin: not just a histochemical marker.
Chistiakov DA, Killingsworth MC, Myasoedova VA, Orekhov AN, Bobryshev YV
Lab Invest 2017 Jan;97(1):4-13. Epub 2016 Nov 21 doi: 10.1038/labinvest.2016.116. PMID: 27869795
DNA binding by the ribosomal DNA transcription factor rrn3 is essential for ribosomal DNA transcription.
Stepanchick A, Zhi H, Cavanaugh AH, Rothblum K, Schneider DA, Rothblum LI
J Biol Chem 2013 Mar 29;288(13):9135-44. Epub 2013 Feb 7 doi: 10.1074/jbc.M112.444265. PMID: 23393135Free PMC Article

Clinical prediction guides

Linkage analysis identifies an isolated strabismus locus at 14q12 overlapping with FOXG1 syndrome region.
Ye XC, Roslin NM, Paterson AD, Lyons CJ, Pegado V, Richmond P, Shyr C, Fornes O, Han X, Higginson M, Ross CJ, Giaschi D, Gregory-Evans C, Patel MS, Wasserman WW
J Med Genet 2022 Jan;59(1):46-55. Epub 2020 Nov 30 doi: 10.1136/jmedgenet-2020-107226. PMID: 33257509Free PMC Article
Forkhead Box Protein P3 (FOXP3) Represses ATF3 Transcriptional Activity.
Wang CM, Yang WH, Cardoso L, Gutierrez N, Yang RH, Yang WH
Int J Mol Sci 2021 Oct 22;22(21) doi: 10.3390/ijms222111400. PMID: 34768829Free PMC Article
A new transcription factor ATG10S activates IFNL2 transcription by binding at an IRF1 site in HepG2 cells.
Zhang MQ, Zhao Q, Zhang JP
Autophagy 2020 Dec;16(12):2167-2179. Epub 2020 Jan 29 doi: 10.1080/15548627.2020.1719681. PMID: 31996071Free PMC Article
Genetic Variability of Long Terminal Repeat Region between HIV-2 Groups Impacts Transcriptional Activity.
Le Hingrat Q, Visseaux B, Bertine M, Chauveau L, Schwartz O, Collin F, Damond F, Matheron S, Descamps D, Charpentier C
J Virol 2020 Mar 17;94(7) doi: 10.1128/JVI.01504-19. PMID: 31915276Free PMC Article
Regulation of the hypoxanthine phosphoribosyltransferase gene: in vitro and in vivo approaches.
Jiralerspong S, Patel PI
Proc Soc Exp Biol Med 1996 Jun;212(2):116-27. doi: 10.3181/00379727-212-43998. PMID: 8650248

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