LIG3 (DNA ligase 3)

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Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 3980
• Gene name: DNA ligase 3
• Gene symbol: LIG3
• Synonyms (NCBI Gene): LIG2, LIG3alpha, MTDPS20
• Chromosome: 17
• Chromosome location: 17q12
• Summary: This gene is a member of the DNA ligase family. Each member of this family encodes a protein that catalyzes the joining of DNA ends but they each have a distinct role in DNA metabolism. The protein encoded by this gene is involved in excision repair and i

miRNA Show/Hide all (68)

miRTarBase ID	miRNA	Experiments	Reference
MIRT028636	hsa-miR-30a-5p	Proteomics	18668040
MIRT045688	hsa-miR-149-5p	CLASH	23622248
MIRT1109235	hsa-miR-199a-3p	CLIP-seq
MIRT1109236	hsa-miR-199b-3p	CLIP-seq
MIRT1109237	hsa-miR-3129-5p	CLIP-seq
MIRT1109238	hsa-miR-4293	CLIP-seq
MIRT1109239	hsa-miR-455-3p	CLIP-seq
MIRT1109240	hsa-miR-4712-5p	CLIP-seq
MIRT1109241	hsa-miR-770-5p	CLIP-seq
MIRT2030326	hsa-miR-1343	CLIP-seq
MIRT2030327	hsa-miR-198	CLIP-seq
MIRT2030328	hsa-miR-23a	CLIP-seq
MIRT2030329	hsa-miR-23b	CLIP-seq
MIRT2030330	hsa-miR-23c	CLIP-seq
MIRT2030331	hsa-miR-3128	CLIP-seq
MIRT2030332	hsa-miR-3155	CLIP-seq
MIRT2030333	hsa-miR-3155b	CLIP-seq
MIRT2030334	hsa-miR-3662	CLIP-seq
MIRT2030335	hsa-miR-375	CLIP-seq
MIRT2030336	hsa-miR-4326	CLIP-seq
MIRT2030337	hsa-miR-4434	CLIP-seq
MIRT2030338	hsa-miR-4464	CLIP-seq
MIRT2030339	hsa-miR-4470	CLIP-seq
MIRT2030340	hsa-miR-4516	CLIP-seq
MIRT2030341	hsa-miR-4531	CLIP-seq
MIRT2030342	hsa-miR-4696	CLIP-seq
MIRT2030343	hsa-miR-4717-3p	CLIP-seq
MIRT2030344	hsa-miR-4748	CLIP-seq
MIRT2030345	hsa-miR-484	CLIP-seq
MIRT2261056	hsa-miR-1207-3p	CLIP-seq
MIRT2030326	hsa-miR-1343	CLIP-seq
MIRT2261057	hsa-miR-1910	CLIP-seq
MIRT2261058	hsa-miR-2392	CLIP-seq
MIRT2030328	hsa-miR-23a	CLIP-seq
MIRT2030329	hsa-miR-23b	CLIP-seq
MIRT2030330	hsa-miR-23c	CLIP-seq
MIRT2261059	hsa-miR-300	CLIP-seq
MIRT2030331	hsa-miR-3128	CLIP-seq
MIRT2030332	hsa-miR-3155	CLIP-seq
MIRT2030333	hsa-miR-3155b	CLIP-seq
MIRT2261060	hsa-miR-3156-5p	CLIP-seq
MIRT2261061	hsa-miR-3616-3p	CLIP-seq
MIRT2261062	hsa-miR-3688-5p	CLIP-seq
MIRT2030335	hsa-miR-375	CLIP-seq
MIRT2261063	hsa-miR-381	CLIP-seq
MIRT2261064	hsa-miR-3929	CLIP-seq
MIRT2030336	hsa-miR-4326	CLIP-seq
MIRT2261065	hsa-miR-4419b	CLIP-seq
MIRT2261066	hsa-miR-4427	CLIP-seq
MIRT2261067	hsa-miR-4436b-3p	CLIP-seq
MIRT2030338	hsa-miR-4464	CLIP-seq
MIRT2030339	hsa-miR-4470	CLIP-seq
MIRT2261068	hsa-miR-4478	CLIP-seq
MIRT2261069	hsa-miR-451b	CLIP-seq
MIRT2030342	hsa-miR-4696	CLIP-seq
MIRT2030343	hsa-miR-4717-3p	CLIP-seq
MIRT2030344	hsa-miR-4748	CLIP-seq
MIRT2030345	hsa-miR-484	CLIP-seq
MIRT2261070	hsa-miR-572	CLIP-seq
MIRT2261071	hsa-miR-617	CLIP-seq
MIRT2261072	hsa-miR-634	CLIP-seq
MIRT1109235	hsa-miR-199a-3p	CLIP-seq
MIRT1109236	hsa-miR-199b-3p	CLIP-seq
MIRT1109237	hsa-miR-3129-5p	CLIP-seq
MIRT1109238	hsa-miR-4293	CLIP-seq
MIRT1109239	hsa-miR-455-3p	CLIP-seq
MIRT1109240	hsa-miR-4712-5p	CLIP-seq
MIRT1109241	hsa-miR-770-5p	CLIP-seq

Gene ontology (GO) Show/Hide all (48)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000724	Process	Double-strand break repair via homologous recombination	TAS
GO:0003677	Function	DNA binding	IEA
GO:0003909	Function	DNA ligase activity	IDA	9809069, 19589734, 24674627
GO:0003909	Function	DNA ligase activity	IEA
GO:0003909	Function	DNA ligase activity	TAS
GO:0003910	Function	DNA ligase (ATP) activity	IBA
GO:0003910	Function	DNA ligase (ATP) activity	IDA	7565692
GO:0003910	Function	DNA ligase (ATP) activity	IEA
GO:0003910	Function	DNA ligase (ATP) activity	IMP	10207110
GO:0005515	Function	Protein binding	IPI	8532526, 15744309, 19336415, 19589734, 24407287, 25609649, 33855352
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	10207110, 24837021
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IDA	24674627
GO:0005739	Component	Mitochondrion	IDA	10207110, 24837021
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006260	Process	DNA replication	IEA
GO:0006273	Process	Lagging strand elongation	IBA
GO:0006281	Process	DNA repair	IEA
GO:0006284	Process	Base-excision repair	IDA	19589734
GO:0006284	Process	Base-excision repair	IMP	24674627
GO:0006287	Process	Base-excision repair, gap-filling	TAS
GO:0006302	Process	Double-strand break repair	IBA
GO:0006302	Process	Double-strand break repair	IDA	19589734
GO:0006310	Process	DNA recombination	IEA
GO:0006974	Process	DNA damage response	IEA
GO:0007005	Process	Mitochondrion organization	IDA	24837021
GO:0008270	Function	Zinc ion binding	IEA
GO:0016874	Function	Ligase activity	IEA
GO:0033151	Process	V(D)J recombination	IDA	9809069
GO:0043504	Process	Mitochondrial DNA repair	IDA	24674627
GO:0043504	Process	Mitochondrial DNA repair	IEA
GO:0043504	Process	Mitochondrial DNA repair	IMP	21390132
GO:0046872	Function	Metal ion binding	IEA
GO:0051053	Process	Negative regulation of DNA metabolic process	IEA
GO:0051301	Process	Cell division	IEA
GO:0070421	Component	DNA ligase III-XRCC1 complex	IDA	8532526
GO:0071897	Process	DNA biosynthetic process	IEA
GO:0090298	Process	Negative regulation of mitochondrial DNA replication	IMP	21878356
GO:0097681	Process	Double-strand break repair via alternative nonhomologous end joining	IEA
GO:0097681	Process	Double-strand break repair via alternative nonhomologous end joining	IGI	24837021

Other IDs

• MIM: 600940
• HGNC: 6600
• e!Ensembl: ENSG00000005156

Protein

• UniProt ID: P49916
• Protein name: DNA ligase 3 (EC 6.5.1.1) (DNA ligase III) (Polydeoxyribonucleotide synthase [ATP] 3)
• Protein function: Isoform 3 functions as a heterodimer with DNA-repair protein XRCC1 in the nucleus and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. Isoform 1 is tar
• PDB: 1IMO , 1IN1 , 1UW0 , 3L2P , 3PC7 , 3PC8 , 3QVG , 6WH1
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00645	zf-PARP	96 → 181	Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region	Domain
  PF01068	DNA_ligase_A_M	483 → 677	ATP dependent DNA ligase domain	Domain
  PF04675	DNA_ligase_A_N	263 → 434	DNA ligase N terminus	Family
  PF04679	DNA_ligase_A_C	704 → 814		Family
  PF16759	LIG3_BRCT	933 → 1005	DNA ligase 3 BRCT domain	Family

• Tissue specificity: TISSUE SPECIFICITY: Testis, thymus, prostate and heart.
• Sequence:

  MSLAFKIFFPQTLRALSRKELCLFRKHHWRDVRQFSQWSETDLLHGHPLFLRRKPVLSFQ
  GSHLRSRATYLVFLPGLHVGLCSGPCEMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIG
  KVVPNPFSESGGDMKEWYHIKCMFEKLERARATTKKIEDLTELEGWEELEDNEKEQITQH
  IADLSSKAAGTPKKKAVVQAKLTTTGQVTSPVKGASFVTSTNPRKFSGFSAKPNNSGEAP
  SSPTPKRSLSSSKCDPRHKDCLLREFRKLCAMVADNPSYNTKTQIIQDFLRKGSAGDGFH
  GDVYLTVKLLLPGVIKTVYNLNDKQIVKLFSRIFNCNPDDMARDLEQGDVSETIRVFFEQ
  SKSFPPAAKSLLTIQEVDEFLLRLSKLTKEDEQQQALQDIASRCTANDLKCIIRLIKHDL
  KMNSGAKHVLDALDPNAYEAFKASRNLQDVVERVLHNAQEVEKEPGQRRALSVQASLMTP
  VQPMLAEACKSVEYAMKKCPNGMFSEIKYDGERVQVHKNGDHFSYFSRSLKPVLPHKVAH
  FKDYIPQAFPGGHSMILDSEVLLIDNKTGKPLPFGTLGVHKKAAFQDANVCLFVFDCIYF
  NDVSLMDRPLCERRKFLHDNMVEIPNRIMFSEMKRVTKALDLADMITRVIQEGLEGLVLK
  DVKGTYEPGKRHWLKVKKDYLNEGAMADTADLVVLGAFYGQGSKGGMMSIFLMGCYDPGS
  QKWCTVTKCAGGHDDATLARLQNELDMVKISKDPSKIPSWLKVNKIYYPDFIVPDPKKAA
  VWEITGAEFSKSEAHTADGISIRFPRCTRIRDDKDWKSATNLPQLKELYQLSKEKADFTV
  VAGDEGSSTTGGSSEENKGPSGSAVSRKAPSKPSASTKKAEGKLSNSNSKDGNMQTAKPS
  AMKVGEKLATKSSPVKVGEKRKAADETLCQTKVLLDIFTGVRLYLPPSTPDFSRLRRYFV
  AFDGDLVQEFDMTSATHVLGSRDKNPAAQQVSPEWIWACIRKRRLVAPC

• Sequence length: 1009

Pathways

KEGG Pathway	Reactome Pathway
Base excision repair	Resolution of AP sites via the single-nucleotide replacement pathway
	APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway
	HDR through MMEJ (alt-NHEJ)
	Gap-filling DNA repair synthesis and ligation in GG-NER
	Gap-filling DNA repair synthesis and ligation in TC-NER

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Mitochondrial DNA depletion syndrome 20 (mngie type)	Pathogenic; Likely pathogenic	rs2142263659, rs199702205, rs2142294288, rs566713386, rs1192808191, rs771267651, rs2090759946, rs750089034, rs2142286963	RCV001847480 RCV001847481 RCV001847482 RCV001847483 RCV001847484 RCV001847485 RCV001847486 RCV001847487 RCV002273039	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations Show/Hide Unknown Diseases (14)
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
Cardiac arrhythmia	Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIG3-related disorder	Uncertain significance; Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
mitochondrial disease	—	ClinGen	ClinGen report	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MITOCHONDRIAL DNA DEPLETION SYNDROME 20	—	CTD, ClinVar, Disgenet, HPO CTD, ClinVar, Disgenet, HPO CTD, ClinVar, Disgenet, HPO	32107856, 33855352	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RESTLESS LEGS SYNDROME	—	GWAS catalog	38839884	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	30019117	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign; Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Related Genes

Sort by: Blended Diseases Pathways Evidence source

MGME1 2 shared diseasesMitochondrial dna depletion syndrome, Mitochondrial disease 5 shared evidence sourcesDisgenet (Mitochondrial dna depletion syndrome), ClinGen (Mitochondrial disease), ClinVar (Mitochondrial dna depletion syndrome), CTD (Mitochondrial dna depletion syndrome), HPO (Mitochondrial dna depletion syndrome) Related via 2 shared diseases including Mitochondrial dna depletion syndrome, Mitochondrial disease — evidence mostly Disgenet. GUK1 2 shared diseasesMitochondrial dna depletion syndrome, Mitochondrial disease 2 shared evidence sourcesClinVar (Mitochondrial dna depletion syndrome), HPO (Mitochondrial dna depletion syndrome) Related via 2 shared diseases including Mitochondrial dna depletion syndrome, Mitochondrial disease — evidence mostly ClinVar. SUCLA2 2 shared diseasesMitochondrial dna depletion syndrome, Mitochondrial disease 5 shared evidence sourcesDisgenet (Mitochondrial dna depletion syndrome), ClinGen (Mitochondrial disease), ClinVar (Mitochondrial dna depletion syndrome), CTD (Mitochondrial dna depletion syndrome), HPO (Mitochondrial dna depletion syndrome) Related via 2 shared diseases including Mitochondrial dna depletion syndrome, Mitochondrial disease — evidence mostly Disgenet. FBXL4 2 shared diseasesMitochondrial dna depletion syndrome, Mitochondrial disease 5 shared evidence sourcesDisgenet (Mitochondrial dna depletion syndrome), ClinGen (Mitochondrial disease), ClinVar (Mitochondrial dna depletion syndrome), CTD (Mitochondrial dna depletion syndrome), HPO (Mitochondrial dna depletion syndrome) Related via 2 shared diseases including Mitochondrial dna depletion syndrome, Mitochondrial disease — evidence mostly Disgenet. TK2 2 shared diseasesMitochondrial dna depletion syndrome, Mitochondrial disease 5 shared evidence sourcesDisgenet (Mitochondrial dna depletion syndrome), ClinGen (Mitochondrial disease), ClinVar (Mitochondrial dna depletion syndrome), CTD (Mitochondrial dna depletion syndrome), HPO (Mitochondrial dna depletion syndrome) Related via 2 shared diseases including Mitochondrial dna depletion syndrome, Mitochondrial disease — evidence mostly Disgenet.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
MGME1	2	["Mitochondrial dna depletion syndrome","Mitochondrial disease"]	0	[]	5	["Disgenet (Mitochondrial dna depletion syndrome)","ClinGen (Mitochondrial disease)","ClinVar (Mitochondrial dna depletion syndrome)","CTD (Mitochondrial dna depletion syndrome)","HPO (Mitochondrial dna depletion syndrome)"]
GUK1	2	["Mitochondrial dna depletion syndrome","Mitochondrial disease"]	0	[]	2	["ClinVar (Mitochondrial dna depletion syndrome)","HPO (Mitochondrial dna depletion syndrome)"]
SUCLA2	2	["Mitochondrial dna depletion syndrome","Mitochondrial disease"]	0	[]	5	["Disgenet (Mitochondrial dna depletion syndrome)","ClinGen (Mitochondrial disease)","ClinVar (Mitochondrial dna depletion syndrome)","CTD (Mitochondrial dna depletion syndrome)","HPO (Mitochondrial dna depletion syndrome)"]
FBXL4	2	["Mitochondrial dna depletion syndrome","Mitochondrial disease"]	0	[]	5	["Disgenet (Mitochondrial dna depletion syndrome)","ClinGen (Mitochondrial disease)","ClinVar (Mitochondrial dna depletion syndrome)","CTD (Mitochondrial dna depletion syndrome)","HPO (Mitochondrial dna depletion syndrome)"]
TK2	2	["Mitochondrial dna depletion syndrome","Mitochondrial disease"]	0	[]	5	["Disgenet (Mitochondrial dna depletion syndrome)","ClinGen (Mitochondrial disease)","ClinVar (Mitochondrial dna depletion syndrome)","CTD (Mitochondrial dna depletion syndrome)","HPO (Mitochondrial dna depletion syndrome)"]

Diseases Linked via Similar Genes

Global developmental delay Linked via 2 of 5 related genesSUCLA2, FBXL4 Leigh syndrome Linked via 2 of 5 related genesSUCLA2, FBXL4 Alzheimer disease Linked via 1 of 5 related genesMGME1 Ophthalmoplegia Linked via 1 of 5 related genesMGME1 Coronary artery disease Linked via 1 of 5 related genesGUK1

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Global developmental delay	2	["SUCLA2","FBXL4"]
Leigh syndrome	2	["SUCLA2","FBXL4"]
Alzheimer disease	1	["MGME1"]
Ophthalmoplegia	1	["MGME1"]
Coronary artery disease	1	["GUK1"]