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Intellectual disability

Gene: LIPT1

Amber List (moderate evidence)

LIPT1 (lipoyltransferase 1)
EnsemblGeneIds (GRCh38): ENSG00000144182
EnsemblGeneIds (GRCh37): ENSG00000144182
OMIM: 610284, Gene2Phenotype
LIPT1 is in 11 panels

2 reviews

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review - cognitive impairment has been reported in more than 3 unrelated surviving patients.
Created: 24 Jul 2020, 12:33 p.m. | Last Modified: 24 Jul 2020, 12:33 p.m.
Panel Version: 3.196
Associated with phenotype in OMIM and probable for Leigh syndrome with secondary deficiency for pyruvate and alpha-ketoglutarate dehydrogenase in G2P.

LIPT1 deficiency, resulting from biallelic variants, is associated with developmental delay, epilepsy, and broad metabolic abnormalities. To date, five unrelated families have been reported with at least one affected child.

PMID: 24341803 (2013) - In a boy with LIPT1 deficiency, exome sequencing revealed two compound heterozygous variants (c.875C>G and c.535A>G). Psychomotor development was delayed from birth, but sudden further regression occurred at 18 months. He could not speak but understood simple orders. He was otherwise fully conscious, alert, and he could smile, laugh and follow with eyes. Supporting functional data, including a yeast model.

PMID: 29681092 (2018) – Compound heterozygous variants (c.212C>T and c.539T>C) identified in a male with seizures, severe lactic acidosis, and failure to thrive. Initially he was reportedly developmentally normal; however, due to subsequent neurodevelopmental regression, he had global developmental delays by 21-months-of-age.

PMID 31042466 (2019) – In an 8-year-old female with developmental delay, seizures, and lactic acidosis, WES revealed two compound heterozygous variants (c.875C>G, c.131A>G). Two older sibs died of a similar condition at 7 months and 3 years. Sequencing was not possible in these individuals; however, a healthy sibling did not carry either variant. Functional analysis in patient-derived fibroblasts and mice confirmed LIPT1 deficiency.

In two unrelated families, the phenotype resulted in early infant death, and therefore ID could not be assessed:
PMID: 24256811 (2014) – compound heterozygous missense variants (c.212C>T and c.292C>G) were identified in a female that died on the ninth day of life.
PMID: 27247813 (2016) – compound heterozygous nonsense variants (c.806G>A and c.980T>G) detected in two sibs who both died on the first day of life. A third sibling, who did not harbour these variants, was healthy and thriving at 12 months of life.
Created: 24 Jul 2020, 11:08 a.m. | Last Modified: 24 Jul 2020, 12:31 p.m.
Panel Version: 3.195

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Lipoyltransferase 1 deficiency, 616299


Zornitza Stark (Australian Genomics)

Green List (high evidence)

Cognitive development is affected in this metabolic condition.
Sources: Expert list
Created: 8 Feb 2020, 10:59 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Lipoyltransferase 1 deficiency, MIM#616299


Variants in this GENE are reported as part of current diagnostic practice

History Filter Activity

24 Jul 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: lipt1 has been classified as Amber List (Moderate Evidence).

24 Jul 2020, Gel status: 0

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag for-review tag was added to gene: LIPT1.

8 Feb 2020, Gel status: 0

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

Zornitza Stark (Australian Genomics)

gene: LIPT1 was added gene: LIPT1 was added to Intellectual disability. Sources: Expert list Mode of inheritance for gene: LIPT1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LIPT1 were set to 24341803; 24256811; 29681092 Phenotypes for gene: LIPT1 were set to Lipoyltransferase 1 deficiency, MIM#616299 Review for gene: LIPT1 was set to GREEN gene: LIPT1 was marked as current diagnostic