Base Excision Repair (Homo sapiens)

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1, 2Gap fillingShort patch BERRecognition by glycosylasesand removal of damaged base5'AP siteOHOxidized or ring-saturated baseAPEX1PNKPPARP1OGG1NTHL1NTHL1NEIL2NEIL3APEX25'3'3'3' hydroxyl adjacent to5' deoxyribosephosphate (dRP)XRCC1LIG3LIG1End processingPOLBXRCC1Ligation5'5'3'3'5'5'3'3'5'5'3'3'5'5'3'3'Long patch BER5'5'3'3'Deaminated, alkylatedor mismatched baseUNGSMUG1MUTYHMPGMBD4TDG5'5'3'3'APEX1APEX2OH5'5'3'3'POLBPOLLHMGB1POLBPOLEPOLD1POLD2POLE2POLE3POLE4POLD3POLD4PCNA5'5'3'3'PCNAFEN15'5'3'3'5'5'3'3'PCNALigationGap filling andstrand displacementAP sitePARP2PARP1PARP2Native DNANative DNA


Base excision repair is a cellular mechanism that repairs damaged DNA throughout the cell cycle. It is primarily responsible for removing small, non-helix-distorting base lesions from the genome.

Base excision repair is important for removing damaged bases that could otherwise cause mutations by mispairing, or could lead to breaks in DNA during replication.

BER is initiated by DNA glycosylases, which recognize and remove specific damaged or inappropriate bases, forming AP sites. These are then cleaved by an AP endonuclease. The resulting single-strand break can then be processed by either short-patch (where a single nucleotide is replaced) or long-patch BER (where 2-10 new nucleotides are synthesized). The choice between short- and long-patch repair is currently under investigation. Various factors are thought to influence this decision, including the type of lesion, the cell cycle stage, and whether the cell is terminally differentiated or actively dividing. Some lesions, such as oxidized or reduced AP sites, are resistant to pol β lyase activity and therefore must be processed by long-patch BER.

This pathway is based on information from REPAIRtoire, Wikipedia and KEGG. The description was adapted from REPAIRtoire, layout is based on KEGG.

Quality Tags

Ontology Terms



  1. ''REPAIRtoire'';,
  2. ''KEGG'';,


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110588view21:08, 19 May 2020Khanspersminor update
108597view23:49, 9 January 2020KhanspersModified description
108050view00:41, 27 November 2019Khanspersadded references
108049view00:39, 27 November 2019KhanspersModified description
108032view22:37, 23 November 2019KhanspersOntology Term : 'DNA repair pathway' added !
108031view22:37, 23 November 2019KhanspersOntology Term : 'base excision repair pathway' added !
108030view22:36, 23 November 2019KhanspersModified description
108029view22:26, 23 November 2019Khanspersfixed interaction
108028view22:25, 23 November 2019Khanspersupdated complexes
108027view22:24, 23 November 2019KhanspersAdded PARPs
108026view01:16, 23 November 2019KhanspersNew pathway

External references


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NameTypeDatabase referenceComment
APEX1GeneProductENSG00000100823 (Ensembl)
APEX2GeneProductENSG00000169188 (Ensembl)
FEN1GeneProductENSG00000168496 (Ensembl)
HMGB1GeneProductENSG00000189403 (Ensembl)
LIG1GeneProductENSG00000105486 (Ensembl)
LIG3GeneProductENSG00000005156 (Ensembl)
MBD4GeneProductENSG00000129071 (Ensembl)
MPGGeneProductENSG00000103152 (Ensembl)
MUTYHGeneProductENSG00000132781 (Ensembl)
NEIL2GeneProductENSG00000154328 (Ensembl)
NEIL3GeneProductENSG00000109674 (Ensembl)
NTHL1GeneProductENSG00000065057 (Ensembl)
OGG1GeneProductENSG00000114026 (Ensembl)
PARP1GeneProductENSG00000143799 (Ensembl)
PARP2GeneProductENSG00000129484 (Ensembl)
PCNAGeneProductENSG00000132646 (Ensembl)
PNKPGeneProductENSG00000039650 (Ensembl) PKNP has a kinase domain which phosphorylates 5' hydroxyl ends, and a phosphatase domain, which removes phosphates from 3' ends.
POLBGeneProductENSG00000070501 (Ensembl)
POLD1GeneProductENSG00000062822 (Ensembl)
POLD2GeneProductENSG00000106628 (Ensembl)
POLD3GeneProductENSG00000077514 (Ensembl)
POLD4GeneProductENSG00000175482 (Ensembl)
POLE2GeneProductENSG00000100479 (Ensembl)
POLE3GeneProductENSG00000148229 (Ensembl)
POLE4GeneProductENSG00000115350 (Ensembl)
POLEGeneProductENSG00000177084 (Ensembl)
POLLGeneProductENSG00000166169 (Ensembl)
SMUG1GeneProductENSG00000123415 (Ensembl)
TDGGeneProductENSG00000139372 (Ensembl)
UNGGeneProductENSG00000076248 (Ensembl)
XRCC1GeneProductENSG00000073050 (Ensembl)

Annotated Interactions

No annotated interactions

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