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Gene

LIG3

DNA ligase 3

Summary

Cytogenetic location
17q12
Coordinates
Chromosome 17: 34,980,512–35,009,743 (GRCh38)
Exons
20 exons across 29.2 kb
Protein
1,009 amino acids
Also known as
LIG3alpha
Previous symbols
LIG2
MANE Select transcript
ENST00000378526.9NM_013975.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Primary Mitochondrial Disease

    • Mitochondrial DNA Depletion Syndrome

      Caused by variants in nuclear genes such as POLG, TWNK, TK2, DGUOK, MPV17, RRM2B and SUCLA2, which reduce the amount of mitochondrial DNA and can cause muscle, liver or brain disease.

      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing is directly actionable: valproate must be avoided in POLG disease because of the risk of fatal liver failure, and TK2 deficiency has a nucleoside therapy.

How LIG3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 17, with a bracket where LIG3 sits. LIG3 and 15 genes near it on chromosome 17, from 34,495,128 to 35,495,127.Chromosome 1717q12p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.334.6 Mb34.8 Mb35 Mb35.2 Mb35.4 MbTMEM132E: 34,579,487–34,639,318, forward strandTMEM132ECCT6B: 34,927,842–34,981,078, reverse strandCCT6BZNF830: 34,961,540–34,963,777, forward strandZNF830LIG3: 34,980,512–35,009,743, forward strandLIG3RFFL: 35,005,990–35,089,899, reverse strandRFFL: 35,011,349–35,121,493, reverse strandRAD51D: 35,092,221–35,121,522, reverse strandRAD51DFNDC8: 35,121,615–35,130,732, forward strandFNDC8NLE1: 35,125,556–35,142,313, reverse strandNLE1UNC45B: 35,146,495–35,189,346, forward strandUNC45BSLC35G3: 35,192,520–35,194,393, reverse strandSLC35G3SLFN5: 35,243,043–35,273,655, forward strandSLFN5SLFN11: 35,350,305–35,373,701, reverse strandSLFN11SLFN12: 35,409,339–35,433,475, reverse strandSLFN12SLFN13: 35,435,096–35,449,766, reverse strandSLFN13SLFN12L: 35,464,249–35,537,770, reverse strandSLFN12LDiagram of LIG3: 20 exons on the forward strand of chromosome 17Exon 2: 1 known disease-causing siteExon 10: 1 known disease-causing siteExon 17: 1 known disease-causing siteExon 18: 1 known disease-causing siteExon 19: 1 known disease-causing siteExon 1: 34,980,512–34,980,622, 111 basesExon 2: 34,983,002–34,983,552, 551 basesExon 3: 34,985,988–34,986,131, 144 basesExon 4: 34,989,466–34,989,663, 198 basesExon 5: 34,990,963–34,991,114, 152 basesExon 6: 34,991,671–34,991,837, 167 basesExon 7: 34,991,958–34,992,035, 78 basesExon 8: 34,992,524–34,992,692, 169 basesExon 9: 34,994,276–34,994,431, 156 basesExon 10: 34,996,064–34,996,195, 132 basesExon 11: 34,996,574–34,996,653, 80 basesExon 12: 34,997,738–34,997,825, 88 basesExon 13: 34,998,219–34,998,296, 78 basesExon 14: 34,998,604–34,998,727, 124 basesExon 15: 34,999,307–34,999,449, 143 basesExon 16: 34,999,782–34,999,856, 75 basesExon 17: 35,001,257–35,001,403, 147 basesExon 18: 35,001,909–35,002,104, 196 basesExon 19: 35,002,668–35,002,789, 122 basesExon 20: 35,004,273–35,009,743, 5,471 bases124681012141618205′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 8.4 kb of the gene's 29.2 kb; 3,030 of those bases code for the protein.

How a genome test reads LIG3

6

positions in LIG3 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 29.2 kb of LIG3, introns included, not only the 8.4 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). LIG3 gene: DNA ligase 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/lig3

Vancouver

Dante Labs. LIG3 gene: DNA ligase 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/lig3

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