LIAS

lipoic acid synthetase, the group of Radical S-adenosylmethionine domain containing

Basic information

Region (hg38): 4:39459003-39485109

Links

ENSG00000121897 ∙ NCBI:11019 ∙ OMIM:607031 ∙ HGNC:16429 ∙ Uniprot:O43766 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• lipoic acid synthetase deficiency (Strong), mode of inheritance: AR
• lipoic acid synthetase deficiency (Moderate), mode of inheritance: AR
• lipoic acid synthetase deficiency (Strong), mode of inheritance: AR
• lipoic acid synthetase deficiency (Supportive), mode of inheritance: AR
• Leigh syndrome (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hyperglycinemia, lactic acidosis, and seizures	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Neurologic	22152680; 24334290

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LIAS gene.

• Lipoic acid synthetase deficiency (310 variants)
• not provided (93 variants)
• not specified (15 variants)
• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIAS gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	53	2	56
missense		1	158	6	1	166
nonsense	2	2				4
start loss			1			1
frameshift	11	1	1			13
inframe indel			2			2
splice donor/acceptor (+/-2bp)		3				3
splice region			10	15		25
non coding				62	38	100
Total	13	7	163	121	41

Highest pathogenic variant AF is 0.0000198

Variants in LIAS

This is a list of pathogenic ClinVar variants found in the LIAS region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-39459073-T-C		not specified	Likely benign (Feb 03, 2016)
4-39459083-C-T		not specified	Benign (Feb 20, 2014)
4-39459086-A-T		not specified	Benign (Oct 15, 2013)
4-39459089-C-T		not specified	Likely benign (Oct 08, 2015)
4-39459106-C-T		not specified	Likely benign (Jul 10, 2017)
4-39459117-A-G		LIAS-related disorder	Conflicting classifications of pathogenicity (Dec 16, 2019)
4-39459118-A-C		Lipoic acid synthetase deficiency	Uncertain significance (Nov 22, 2022)
4-39459121-T-C		Lipoic acid synthetase deficiency	Uncertain significance (Jun 22, 2022)
4-39459122-C-G		Lipoic acid synthetase deficiency	Uncertain significance (Aug 24, 2021)
4-39459122-C-T		Lipoic acid synthetase deficiency	Uncertain significance (Mar 07, 2022)
4-39459124-C-T		Lipoic acid synthetase deficiency	Likely benign (Aug 15, 2022)
4-39459127-C-T		Lipoic acid synthetase deficiency	Uncertain significance (Feb 04, 2022)
4-39459128-G-T		Lipoic acid synthetase deficiency	Uncertain significance (Sep 12, 2022)
4-39459131-G-C		Lipoic acid synthetase deficiency	Uncertain significance (Sep 04, 2019)
4-39459132-C-G		Lipoic acid synthetase deficiency	Uncertain significance (May 20, 2020)
4-39459134-G-A		Lipoic acid synthetase deficiency	Uncertain significance (May 27, 2022)
4-39459135-G-A		Lipoic acid synthetase deficiency • LIAS-related disorder	Likely benign (Jun 05, 2023)
4-39459136-G-A		Lipoic acid synthetase deficiency	Uncertain significance (Mar 03, 2021)
4-39459137-A-T		Lipoic acid synthetase deficiency	Uncertain significance (Oct 14, 2022)
4-39459140-C-T		Lipoic acid synthetase deficiency	Uncertain significance (Aug 16, 2022)
4-39459141-A-G		Lipoic acid synthetase deficiency	Likely benign (Mar 22, 2023)
4-39459142-G-T		Lipoic acid synthetase deficiency	Uncertain significance (Jul 19, 2022)
4-39459143-C-T		Lipoic acid synthetase deficiency	Uncertain significance (Jan 28, 2022)
4-39459144-C-A		Lipoic acid synthetase deficiency	Likely benign (Dec 07, 2023)
4-39459145-C-T		Lipoic acid synthetase deficiency	Uncertain significance (Jul 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIAS	protein_coding	protein_coding	ENST00000261434	11	18654

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000231	0.981	125715	0	30	125745	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	153	203	0.753	0.0000106	2406
Missense in Polyphen		33	68.225	0.48369		767
Synonymous	0.618	64	70.6	0.906	0.00000353	716
Loss of Function	2.11	11	21.6	0.510	0.00000108	277

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000178
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000118	0.000114
Middle Eastern	0.0000546	0.0000544
South Asian	0.000369	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives. {ECO:0000255|HAMAP-Rule:MF_03123}.
• Disease: DISEASE: Hyperglycinemia, lactic acidosis, and seizures (HGCLAS) [MIM:614462]: An enzymatic defect resulting in an autosomal recessive disorder of mitochondrial metabolism. It is characterized by early-onset lactic acidosis, severe encephalomyopathy, and a pyruvate oxidation defect. Affected individuals have neonatal-onset epilepsy, poor growth, psychomotor retardation, muscular hypotonia, lactic acidosis, and elevated glycine concentration in plasma and urine. {ECO:0000269|PubMed:22152680}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Lipoic acid metabolism - Homo sapiens (human);Metabolism of amino acids and derivatives;Metabolism;Glyoxylate metabolism and glycine degradation;lipoate biosynthesis and incorporation (Consensus)

Recessive Scores

• pRec: 0.358

Intolerance Scores

• loftool: 0.576
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.101
• hipred: Y
• hipred_score: 0.554
• ghis: 0.587

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.983

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lias
• Phenotype: embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: neural tube closure;inflammatory response;response to oxidative stress;lipoate biosynthetic process;protein lipoylation;response to lipopolysaccharide;cellular nitrogen compound metabolic process
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: lipoate synthase activity;metal ion binding;4 iron, 4 sulfur cluster binding