Gene
|
Entrez ID
Entrez Gene ID - the GENE ID in NCBI Gene database.
|
3981 |
Gene nameGene Name - the full gene name approved by the HGNC.
|
DNA ligase 4 |
Gene symbolGene Symbol - the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name.
|
LIG4 |
SynonymsGene synonyms aliases
|
LIG4S |
ChromosomeChromosome number
|
13 |
Chromosome locationChromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
|
13q33.3 |
SummarySummary of gene provided in NCBI Entrez Gene.
|
The protein encoded by this gene is a DNA ligase that joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. This protein is essential for V(D)J recombination and DNA double-strand break (DSB) repair through nonhomologous end joining (NHEJ). This protein forms a complex with the X-ray repair cross complementing protein 4 (XRCC4), and further interacts with the DNA-dependent protein kinase (DNA-PK). Both XRCC4 and DNA-PK are known to be required for NHEJ. The crystal structure of the complex formed by this protein and XRCC4 has been resolved. Defects in this gene are the cause of LIG4 syndrome. Alternatively spliced transcript variants encoding the same protein have been observed. [provided by RefSeq, Jul 2008] |
SNPsSNP information provided by dbSNP.
|
SNP ID |
Visualize variation |
Clinical significance |
Consequence |
rs72660870 |
G>C,T |
Conflicting-interpretations-of-pathogenicity, uncertain-significance |
Missense variant, coding sequence variant |
rs104894418 |
G>A,C |
Pathogenic |
Stop gained, missense variant, coding sequence variant |
rs104894419 |
G>A |
Pathogenic-likely-pathogenic, pathogenic |
Stop gained, coding sequence variant |
rs104894420 |
C>T |
Pathogenic |
Missense variant, coding sequence variant |
rs104894421 |
C>A,T |
Pathogenic |
Missense variant, coding sequence variant |
rs142957638 |
T>C |
Conflicting-interpretations-of-pathogenicity, uncertain-significance |
Missense variant, coding sequence variant |
rs201176444 |
G>A |
Likely-pathogenic |
Coding sequence variant, missense variant |
rs375554612 |
T>- |
Pathogenic |
Coding sequence variant, frameshift variant |
rs587776663 |
GTT>- |
Pathogenic |
Inframe deletion, coding sequence variant |
rs748385144 |
C>T |
Uncertain-significance, likely-pathogenic |
Missense variant, coding sequence variant |
rs751070095 |
ATTTC>- |
Likely-pathogenic |
Frameshift variant, coding sequence variant |
rs751409106 |
T>C,G |
Likely-pathogenic |
Missense variant, coding sequence variant |
rs759838407 |
AG>-,AGAG |
Pathogenic |
Frameshift variant, coding sequence variant |
rs770128720 |
ATCTT>- |
Pathogenic |
Frameshift variant, coding sequence variant |
rs772226399 |
CTTTT>- |
Pathogenic |
Frameshift variant, coding sequence variant |
rs780504243 |
C>A |
Pathogenic |
Coding sequence variant, missense variant |
rs780879476 |
A>- |
Pathogenic |
Coding sequence variant, frameshift variant |
rs886037777 |
A>G |
Likely-pathogenic |
Coding sequence variant, missense variant |
rs1060499662 |
A>G |
Likely-pathogenic |
Coding sequence variant, missense variant |
rs1131691430 |
C>G |
Likely-pathogenic |
Coding sequence variant, missense variant |
rs1246940345 |
AG>- |
Likely-pathogenic |
Frameshift variant, coding sequence variant |
rs1555305016 |
CTCTT>- |
Likely-pathogenic |
Coding sequence variant, frameshift variant |
rs1566366148 |
CT>- |
Pathogenic |
Coding sequence variant, frameshift variant |
rs1594458526 |
TA>- |
Pathogenic |
Frameshift variant, coding sequence variant |
rs1594462950 |
T>C |
Likely-pathogenic |
Missense variant, coding sequence variant |
|
miRNAmiRNA information provided by mirtarbase database.
|
|
Gene ontology (GO)Gene ontology information of associated ontologies with gene provided by GO database.
|
GO ID |
Ontology |
Definition |
Evidence |
Reference |
GO:0000012 |
Process |
Single strand break repair |
IDA |
8798671 |
GO:0000781 |
Component |
Chromosome, telomeric region |
IC |
23275564 |
GO:0000793 |
Component |
Condensed chromosome |
IDA |
12589063 |
GO:0001701 |
Process |
In utero embryonic development |
ISS |
|
GO:0002328 |
Process |
Pro-B cell differentiation |
ISS |
|
GO:0003677 |
Function |
DNA binding |
IBA |
21873635 |
GO:0003677 |
Function |
DNA binding |
IDA |
8798671 |
GO:0003909 |
Function |
DNA ligase activity |
IDA |
12517771 |
GO:0003909 |
Function |
DNA ligase activity |
TAS |
|
GO:0003910 |
Function |
DNA ligase (ATP) activity |
IBA |
21873635 |
GO:0003910 |
Function |
DNA ligase (ATP) activity |
IDA |
8798671, 22192310 |
GO:0005515 |
Function |
Protein binding |
IPI |
9242410, 9259561, 9809069, 11702069, 16439205, 17389648, 17396150, 21070942, 22529269, 22658747, 23178593, 23219551, 25416956, 25910212, 28514442, 32296183 |
GO:0005524 |
Function |
ATP binding |
IBA |
21873635 |
GO:0005634 |
Component |
Nucleus |
IDA |
8798671, 12589063 |
GO:0005654 |
Component |
Nucleoplasm |
IDA |
|
GO:0005654 |
Component |
Nucleoplasm |
TAS |
|
GO:0005958 |
Component |
DNA-dependent protein kinase-DNA ligase 4 complex |
IBA |
21873635 |
GO:0005958 |
Component |
DNA-dependent protein kinase-DNA ligase 4 complex |
IDA |
15194694 |
GO:0005958 |
Component |
DNA-dependent protein kinase-DNA ligase 4 complex |
ISS |
|
GO:0006260 |
Process |
DNA replication |
IEA |
|
GO:0006266 |
Process |
DNA ligation |
IDA |
12517771 |
GO:0006297 |
Process |
Nucleotide-excision repair, DNA gap filling |
IBA |
21873635 |
GO:0006297 |
Process |
Nucleotide-excision repair, DNA gap filling |
IDA |
12517771 |
GO:0006302 |
Process |
Double-strand break repair |
IDA |
9242410, 19589734 |
GO:0006302 |
Process |
Double-strand break repair |
ISS |
|
GO:0006303 |
Process |
Double-strand break repair via nonhomologous end joining |
IBA |
21873635 |
GO:0006303 |
Process |
Double-strand break repair via nonhomologous end joining |
IDA |
12517771 |
GO:0006303 |
Process |
Double-strand break repair via nonhomologous end joining |
IGI |
23275564 |
GO:0006303 |
Process |
Double-strand break repair via nonhomologous end joining |
IMP |
9809069 |
GO:0006303 |
Process |
Double-strand break repair via nonhomologous end joining |
ISS |
|
GO:0006303 |
Process |
Double-strand break repair via nonhomologous end joining |
TAS |
|
GO:0007049 |
Process |
Cell cycle |
IEA |
|
GO:0007417 |
Process |
Central nervous system development |
ISS |
|
GO:0008022 |
Function |
Protein C-terminus binding |
IPI |
12589063 |
GO:0008283 |
Process |
Cell population proliferation |
ISS |
|
GO:0010165 |
Process |
Response to X-ray |
IMP |
9809069 |
GO:0010332 |
Process |
Response to gamma radiation |
ISS |
|
GO:0016874 |
Function |
Ligase activity |
IDA |
9242410 |
GO:0032807 |
Component |
DNA ligase IV complex |
IBA |
21873635 |
GO:0032807 |
Component |
DNA ligase IV complex |
IMP |
9809069 |
GO:0033077 |
Process |
T cell differentiation in thymus |
ISS |
|
GO:0033151 |
Process |
V(D)J recombination |
IDA |
9809069 |
GO:0033152 |
Process |
Immunoglobulin V(D)J recombination |
IBA |
21873635 |
GO:0033153 |
Process |
T cell receptor V(D)J recombination |
ISS |
|
GO:0035019 |
Process |
Somatic stem cell population maintenance |
ISS |
|
GO:0036464 |
Component |
Cytoplasmic ribonucleoprotein granule |
IDA |
|
GO:0043524 |
Process |
Negative regulation of neuron apoptotic process |
ISS |
|
GO:0045190 |
Process |
Isotype switching |
ISS |
|
GO:0046872 |
Function |
Metal ion binding |
IEA |
|
GO:0048146 |
Process |
Positive regulation of fibroblast proliferation |
ISS |
|
GO:0050769 |
Process |
Positive regulation of neurogenesis |
ISS |
|
GO:0051102 |
Process |
DNA ligation involved in DNA recombination |
ISS |
|
GO:0051103 |
Process |
DNA ligation involved in DNA repair |
IBA |
21873635 |
GO:0051103 |
Process |
DNA ligation involved in DNA repair |
IDA |
12517771 |
GO:0051103 |
Process |
DNA ligation involved in DNA repair |
ISS |
|
GO:0051276 |
Process |
Chromosome organization |
ISS |
|
GO:0051301 |
Process |
Cell division |
IEA |
|
GO:0051402 |
Process |
Neuron apoptotic process |
ISS |
|
GO:0070419 |
Component |
Nonhomologous end joining complex |
IDA |
20383123, 25941166 |
GO:0071285 |
Process |
Cellular response to lithium ion |
IEA |
|
GO:0071479 |
Process |
Cellular response to ionizing radiation |
IGI |
29463814 |
GO:0071897 |
Process |
DNA biosynthetic process |
IEA |
|
GO:0075713 |
Process |
Establishment of integrated proviral latency |
TAS |
|
GO:0097680 |
Process |
Double-strand break repair via classical nonhomologous end joining |
IMP |
24837021 |
GO:2001252 |
Process |
Positive regulation of chromosome organization |
IMP |
23275564 |
|
Other IDsOther ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
|
|
Protein
|
UniProt ID |
P49917 |
Protein name |
DNA ligase 4 (EC 6.5.1.1) (DNA ligase IV) (Polydeoxyribonucleotide synthase [ATP] 4) |
Protein function |
Efficiently joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. |
PDB |
1IK9
,
2E2W
,
3II6
,
3VNN
,
3W1B
,
3W1G
,
3W5O
,
4HTO
,
4HTP
,
6BKF
,
6BKG
,
7D9K
,
7D9Y
|
Family and domains |
Pfam
Accession |
ID |
Position in sequence |
Description |
Type |
PF04675 |
DNA_ligase_A_N |
15 → 208 |
DNA ligase N terminus |
Family |
PF01068 |
DNA_ligase_A_M |
248 → 451 |
ATP dependent DNA ligase domain |
Domain |
PF04679 |
DNA_ligase_A_C |
476 → 588 |
|
Family |
PF00533 |
BRCT |
654 → 730 |
BRCA1 C Terminus (BRCT) domain |
Family |
PF11411 |
DNA_ligase_IV |
750 → 783 |
DNA ligase IV |
Family |
PF00533 |
BRCT |
813 → 898 |
BRCA1 C Terminus (BRCT) domain |
Family |
|
Sequence |
|
Sequence length |
911 |
Interactions |
View interactions |
|
|
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