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Retinal disorders

Gene: LIG3

Amber List (moderate evidence)

LIG3 (DNA ligase 3)
EnsemblGeneIds (GRCh38): ENSG00000005156
EnsemblGeneIds (GRCh37): ENSG00000005156
OMIM: 600940, Gene2Phenotype
LIG3 is in 9 panels

2 reviews

Ivone Leong (Genomics England Curator)

I don't know

As only 2 affected families have macular degeneration this gene has been given an Amber rating until more evidence is available.
Created: 19 May 2021, 12:51 p.m. | Last Modified: 19 May 2021, 12:51 p.m.
Panel Version: 2.186
Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype.

PMID:33855352. 3 unrelated families with 7 affected individuals. Clinical features of affected individuals resemble mitochondrial neurogastrointestinal encephalomyopathy (MNGIE). All had severe dysmotility of the gut, leukoencephalopathy and/or progressive cortical atrophy. Cerebella atrophy was only seen in patients in family 3. Other neurological features were epilepsy, stroke-like episodes, migraine and developmental delay. 4 members from families 1 and 2 had macular degeneration, 1 member from family 3 had cataracts and hearing loss. Age of onset and disease severity differed, ranging from paediatric severe disease with premature death to adult cases. All affected members from the 3 families were compound heterozygous for different LIG3 variants.

LIG3 variants cause impared ligase activity, mtDNA depletion and mitochondrial dysfunction.

The authors also created a zebrafish model, which recapitulated the cerebellar phenotype (seen in mice) and eye defects and gut propulsion impairment (seen in patients). Knockdown of lig3 in zf also led to decrease in expression of mitochondrial markers.

Knocking out Lig3 in mice led to early embryonic lethality with mitochondrial dysfunction due to reduced mtDNA in the nervous system (PMID: 21390131); however, gut motility was not investigated in these mice.

There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Created: 19 May 2021, 12:38 p.m. | Last Modified: 19 May 2021, 12:38 p.m.
Panel Version: 1.99

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Seven individuals from three unrelated families and functional data, variable ages of onset from early childhood to late adolescence.
Sources: Literature
Created: 10 May 2021, 10:06 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

gut dysmotility; spasticity; ataxia; repetitive behaviours; neurogenic bladder; macular degeneration; leukoencephalopathy; cerebellar atrophy



Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
  • Literature
  • Expert Review Amber
  • gut dysmotility
  • spasticity
  • ataxia
  • repetitive behaviours
  • neurogenic bladder
  • macular degeneration
  • leukoencephalopathy
  • cerebellar atrophy
  • mitochondrial DNA depletion
Clinvar variants
Variants in LIG3
Panels with this gene

History Filter Activity

19 May 2021, Gel status: 2

Removed Tag, Added Tag

Ivone Leong (Genomics England Curator)

Tag Q2_21_rating was removed from gene: LIG3. Tag watchlist tag was added to gene: LIG3.

19 May 2021, Gel status: 2

Created, Added New Source, Added Tag, Set mode of inheritance, Set publications, Set Phenotypes

Ivone Leong (Genomics England Curator)

gene: LIG3 was added gene: LIG3 was added to Retinal disorders. Sources: Expert Review Amber,Literature Q2_21_rating tags were added to gene: LIG3. Mode of inheritance for gene: LIG3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LIG3 were set to 33855352 Phenotypes for gene: LIG3 were set to gut dysmotility; spasticity; ataxia; repetitive behaviours; neurogenic bladder; macular degeneration; leukoencephalopathy; cerebellar atrophy; mitochondrial DNA depletion