LIPT2

Chr 11AR

lipoyl(octanoyl) transferase 2

NCBI Gene: 387787 ENSG00000175536 UniProt: A6NK58 OMIM: 617659

The protein catalyzes the transfer of octanoic acid to lipoate-dependent enzymes in mitochondria, which is essential for proper mitochondrial metabolism. Autosomal recessive mutations cause neonatal severe encephalopathy with lactic acidosis and brain abnormalities due to impaired mitochondrial function.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a mitochondrial protein that catalyzes the transfer of octanoic acid to lipoate-dependent enzymes such as octanoyl-ACP. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2016]

OMIM ResearchGenerating clinical summary…

ARLOEUF 0.941 OMIM phenotype

Clinical Summary— LIPT2

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Gene-Disease Validity (ClinGen)

mitochondrial disease · ARLimited

Limited evidence — not for standalone diagnostic reporting

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.63) — some intolerance to loss-of-function variants.

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ClinVar Variants

2 unique Pathogenic / Likely Pathogenic· 97 VUS of 148 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.94LOEUF

pLI 0.626

Z-score 1.64

OE 0.00 (0.00–0.94)

Moderately constrained

Typical tolerance to LoF variation

Missense Constraint?

-0.12Z-score

OE missense 1.04 (0.87–1.24)

85 obs / 81.9 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.94)

0≤0.351.4

Missense OE?1.04 (0.87–1.24)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 0 / 3.1Missense obs/exp: 85 / 81.9Syn Z: 0.08

ClinVar Variant Classifications

148 submitted variants in ClinVar

ClinVar

Classification Summary

Likely Pathogenic2

VUS97

Likely Benign31

Benign10

Conflicting6

Likely Pathogenic

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	2	0	0	2
VUS	1	94	1	1	97
Likely Benign	0	6	3	22	31
Benign	0	3	4	3	10
Conflicting	—				6
Total	1	105	8	26	146

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

9 pathogenic / likely-pathogenic (of 11) ClinVar copy-number / structural variants overlap LIPT2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →