Gene Gene information from NCBI Gene database.
Entrez ID 3981
Gene name DNA ligase 4
Gene symbol LIG4
Synonyms (NCBI Gene)
LIG4S
Chromosome 13
Chromosome location 13q33.3
Summary 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 nonh
SNPs SNP information provided by dbSNP.
25
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
miRNA miRNA information provided by mirtarbase database.
20
miRTarBase ID miRNA Experiments Reference
MIRT021742 hsa-miR-132-3p Microarray 17612493
MIRT028768 hsa-miR-26b-5p Microarray 19088304
MIRT051082 hsa-miR-16-5p CLASH 23622248
MIRT2030346 hsa-miR-1279 CLIP-seq
MIRT2561080 hsa-miR-1 CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
97
GO ID Ontology Definition Evidence Reference
GO:0000012 Process Single strand break repair IDA 8798671
GO:0000166 Function Nucleotide binding IEA
GO:0000287 Function Magnesium ion binding IDA 29980672
GO:0000781 Component Chromosome, telomeric region IC 23275564
GO:0000793 Component Condensed chromosome IDA 12589063
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
601837 6601 ENSG00000174405
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P49917
Protein name DNA ligase 4 (EC 6.5.1.1) (DNA ligase IV) (Polydeoxyribonucleotide synthase [ATP] 4)
Protein function DNA ligase involved in DNA non-homologous end joining (NHEJ); required for double-strand break (DSB) repair and V(D)J recombination (PubMed:12517771, PubMed:17290226, PubMed:23523427, PubMed:29980672, PubMed:33586762, PubMed:8798671, PubMed:9242
PDB 1IK9 , 2E2W , 3II6 , 3VNN , 3W1B , 3W1G , 3W5O , 4HTO , 4HTP , 6BKF , 6BKG , 7D9K , 7D9Y , 7LSY , 7LT3 , 7NFC , 7NFE , 8BH3 , 8BHV , 8BHY , 8BOT , 8EZA , 8EZB
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
Tissue specificity TISSUE SPECIFICITY: Testis, thymus, prostate and heart. {ECO:0000269|PubMed:7760816}.
Sequence
MAASQTSQTVASHVPFADLCSTLERIQKSKGRAEKIRHFREFLDSWRKFHDALHKNHKDV
TDSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPTGTHG
DAGDFAMIAYFVLKPRCLQKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQLITQSSA
LEQKWLIRMIIKDLKLGVSQQTIFSVFH
NDAAELHNVTTDLEKVCRQLHDPSVGLSDISI
TLFSAFKPMLAAIADIEHIEKDMKHQSFYIETKLDGERMQMHKDGDVYKYFSRNGYNYTD
QFGASPTEGSLTPFIHNAFKADIQICILDGEMMAYNPNTQTFMQKGTKFDIKRMVEDSDL
QTCYCVFDVLMVNNKKLGHETLRKRYEILSSIFTPIPGRIEIVQKTQAHTKNEVIDALNE
AIDKREEGIMVKQPLSIYKPDKRGEGWLKIK
PEYVSGLMDELDILIVGGYWGKGSRGGMM
SHFLCAVAEKPPPGEKPSVFHTLSRVGSGCTMKELYDLGLKLAKYWKPFHRKAPPSSILC
GTEKPEVYIEPCNSVIVQIKAAEIVPSDMYKTGCTLRFPRIEKIRDDK
EWHECMTLDDLE
QLRGKASGKLASKHLYIGGDDEPQEKKRKAAPKMKKVIGIIEHLKAPNLTNVNKISNIFE
DVEFCVMSGTDSQPKPDLENRIAEFGGYIVQNPGPDTYCVIAGSENIRVKNIILSNKHDV
VKPAWLLECF
KTKSFVPWQPRFMIHMCPSTKEHFAREYDCYGDSYFIDTDLNQLKEVFSG
IKN
SNEQTPEEMASLIADLEYRYSWDCSPLSMFRRHTVYLDSYAVINDLSTKNEGTRLAI
KALELRFHGAKVVSCLAEGVSHVIIGEDHSRVADFKAFRRTFKRKFKILKESWVTDSI
DK
CELQEENQYLI
Sequence length 911
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
29
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 Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
DNA ligase IV deficiency Pathogenic; Likely pathogenic rs750080610, rs759838407, rs759829934, rs2138967445, rs2138974645, rs373938258, rs752339466, rs2138974907, rs2138978299, rs767195999, rs753883369, rs1286797317, rs2138978193, rs777008519, rs1386691031
View all (66 more)
RCV001320593
RCV001885359
RCV001389935
RCV001533455
RCV001824262
View all (81 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
LIG4-related disorder Likely pathogenic; Pathogenic rs104894419, rs772226399, rs2501600808, rs375554612, rs765317127 RCV004532308
RCV000267680
RCV004540864
RCV004535497
RCV001535528
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Multiple myeloma Likely pathogenic; Pathogenic rs759829934, rs752339466, rs2138978299, rs104894418, rs104894419, rs772226399, rs104894421, rs1317409403, rs948441067, rs375554612, rs759838407, rs751070095, rs780879476 RCV005005244
RCV005005322
RCV005002677
RCV005007834
RCV000763320
View all (8 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Papillary thyroid carcinoma Likely pathogenic rs751409106 RCV000761169
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Actinic keratosis Actinic keratosis BEFREE 29036257
★☆☆☆☆
Found in Text Mining only
Acute leukemia Leukemia HPO_DG
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia GENOMICS_ENGLAND_DG 28297620
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 23752193
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Of Esophagus Esophageal Cancer BEFREE 23137018
★☆☆☆☆
Found in Text Mining only
Adenoma Adenoma BEFREE 23752193
★☆☆☆☆
Found in Text Mining only
Adult Diffuse Large B-Cell Lymphoma B-cell Lymphoma BEFREE 11773279, 26774591
★☆☆☆☆
Found in Text Mining only
Adult Medulloblastoma Medulloblastoma BEFREE 14500378
★☆☆☆☆
Found in Text Mining only
Agammaglobulinemia Agammaglobulinemia Pubtator 27063650, 35592332, 37004747 Associate
★☆☆☆☆
Found in Text Mining only
AICARDI-GOUTIERES SYNDROME Aicardi Goutieres Syndrome BEFREE 29016854
★☆☆☆☆
Found in Text Mining only