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	3978
Gene name	DNA ligase 1
Gene symbol	LIG1
Synonyms (NCBI Gene)	IMD96LIGIhLig1
Chromosome	19
Chromosome location	19q13.33
Summary	This gene encodes a member of the ATP-dependent DNA ligase protein family. The encoded protein functions in DNA replication, recombination, and the base excision repair process. Mutations in this gene that lead to DNA ligase I deficiency result in immunod

Show/Hide all (13)

miRTarBase ID	miRNA	Experiments	Reference
MIRT030288	hsa-miR-26b-5p	Microarray	19088304
MIRT045653	hsa-miR-149-5p	CLASH	23622248
MIRT040334	hsa-miR-615-3p	CLASH	23622248
MIRT2030323	hsa-miR-3064-3p	CLIP-seq
MIRT2030324	hsa-miR-4639-5p	CLIP-seq
MIRT2030325	hsa-miR-922	CLIP-seq
MIRT2261053	hsa-miR-1203	CLIP-seq
MIRT2261054	hsa-miR-342-3p	CLIP-seq
MIRT2261055	hsa-miR-4640-3p	CLIP-seq
MIRT2390142	hsa-miR-329	CLIP-seq
MIRT2261054	hsa-miR-342-3p	CLIP-seq
MIRT2390143	hsa-miR-362-3p	CLIP-seq
MIRT2390144	hsa-miR-377	CLIP-seq

Show/Hide all (32)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003677	Function	DNA binding	TAS	8696349
GO:0003909	Function	DNA ligase activity	IDA	9809069, 19589734
GO:0003909	Function	DNA ligase activity	IEA
GO:0003909	Function	DNA ligase activity	IMP	15871698
GO:0003909	Function	DNA ligase activity	TAS
GO:0003910	Function	DNA ligase (ATP) activity	IBA
GO:0003910	Function	DNA ligase (ATP) activity	IEA
GO:0005515	Function	Protein binding	IPI	19336415
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	8696349
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0006260	Process	DNA replication	IEA
GO:0006273	Process	Lagging strand elongation	IBA
GO:0006281	Process	DNA repair	IEA
GO:0006281	Process	DNA repair	TAS	8696349
GO:0006284	Process	Base-excision repair	IDA	19589734
GO:0006287	Process	Base-excision repair, gap-filling	TAS
GO:0006298	Process	Mismatch repair	TAS
GO:0006310	Process	DNA recombination	IEA
GO:0006974	Process	DNA damage response	IEA
GO:0009653	Process	Anatomical structure morphogenesis	TAS	8696349
GO:0016874	Function	Ligase activity	IEA
GO:0033151	Process	V(D)J recombination	IDA	9809069
GO:0046872	Function	Metal ion binding	IEA
GO:0051301	Process	Cell division	IEA
GO:0071897	Process	DNA biosynthetic process	IEA
GO:1903461	Process	Okazaki fragment processing involved in mitotic DNA replication	IBA

MIM	HGNC	e!Ensembl
126391	6598	ENSG00000105486

P18858

Protein name

DNA ligase 1 (EC 6.5.1.1) (DNA ligase I) (Polydeoxyribonucleotide synthase [ATP] 1)

Protein function

DNA ligase that seals nicks in double-stranded during DNA repair (PubMed:30395541). Also involved in DNA replication and DNA recombination.

PDB

1X9N , 5YY9 , 6P09 , 6P0A , 6P0B , 6P0C , 6P0D , 6P0E , 6Q1V , 7KR3 , 7KR4 , 7L34 , 7L35 , 7QNZ , 7QO1 , 7SUM , 7SX5 , 7SXE , 8B8T , 8VDN , 8VDS , 8VDT , 8VZL , 8VZM , 9BS3 , 9BS4

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF04675	DNA_ligase_A_N	288 → 464	DNA ligase N terminus	Family
PF01068	DNA_ligase_A_M	542 → 746	ATP dependent DNA ligase domain	Domain
PF04679	DNA_ligase_A_C	771 → 882		Family

Sequence

MQRSIMSFFHPKKEGKAKKPEKEASNSSRETEPPPKAALKEWNGVVSESDSPVKRPGRKA
ARVLGSEGEEEDEALSPAKGQKPALDCSQVSPPRPATSPENNASLSDTSPMDSSPSGIPK
RRTARKQLPKRTIQEVLEEQSEDEDREAKRKKEEEEEETPKESLTEAEVATEKEGEDGDQ
PTTPPKPLKTSKAETPTESVSEPEVATKQELQEEEEQTKPPRRAPKTLSSFFTPRKPAVK
KEVKEEEPGAPGKEGAAEGPLDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIE
EVSARLRMVETLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLELGVGDGVLLKAVAQ
ATGRQLESVRAEAAEKGDVGLVAENSRSTQRLMLPPPPLTASGVFSKFRDIARLTGSAST
AKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAM
VDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCKLSPGIPL
KPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQEDNTGKYPD
IISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAF
DLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVKDSCE
GLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAYLGRGKRAGRYGGFLL
ASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVLPSPRPYVRIDGAVIPDHWLDPSA
VWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQ
SQIQNQQGEDSGSDPEDTY

Sequence length

919

Interactions

View interactions

	KEGG		Reactome
	DNA replication Base excision repair Nucleotide excision repair Mismatch repair		POLB-Dependent Long Patch Base Excision Repair Early Phase of HIV Life Cycle Processive synthesis on the C-strand of the telomere Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) PCNA-Dependent Long Patch Base Excision Repair Gap-filling DNA repair synthesis and ligation in GG-NER Gap-filling DNA repair synthesis and ligation in TC-NER Processive synthesis on the lagging strand

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
Immunodeficiency 96	Pathogenic; Likely pathogenic	rs778319960, rs2513978101, rs121434560	RCV001843697 RCV003232054 RCV001843457	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (20)

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.
Acute myeloid leukemia	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DNA Ligase I Deficiency	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIG1-related disorder	Benign; Uncertain significance; Likely benign; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Uncertain significance; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Conflicting classifications of pathogenicity; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Conflicting classifications of pathogenicity; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
URINARY BLADDER NEOPLASMS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

LIG1 (DNA ligase 1)