Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	3980
Gene name	DNA ligase 3
Gene symbol	LIG3
Synonyms (NCBI Gene)	LIG2LIG3alphaMTDPS20
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

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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

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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

MIM	HGNC	e!Ensembl
600940	6600	ENSG00000005156

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
PF04675	DNA_ligase_A_N	263 → 434	DNA ligase N terminus	Family
PF01068	DNA_ligase_A_M	483 → 677	ATP dependent DNA ligase domain	Domain
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

Interactions

View interactions

	KEGG		Reactome
	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

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)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Mitochondrial DNA depletion syndrome 20 (mngie type)	Pathogenic; Likely pathogenic	rs2142263659, rs199702205, rs2142294288, rs566713386, rs1192808191, rs771267651, rs2090759946, rs750089034, rs2142286963	RCV001847480 RCV001847481 RCV001847482 RCV001847483 RCV001847484 View all (4 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (13)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
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 DNA DEPLETION SYNDROME 20	—	CTD, ClinVar, Disgenet, HPO CTD, ClinVar, Disgenet, HPO CTD, ClinVar, Disgenet, HPO	★★★★★ ★★☆☆☆ 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	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★★★★ ★★☆☆☆ 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

LIG3 (DNA ligase 3)