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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PNPLA6
patatin like domain 6, lysophospholipase
Chromosome 19 Β· 19p13.2
NCBI Gene: 10908Ensembl: ENSG00000032444.17HGNC: HGNC:16268UniProt: A0A384DVU0
116PubMed Papers
24Diseases
0Drugs
122Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
phosphatidylcholine lysophospholipase A1 activityB-type glycerophospholipase activitymembraneendoplasmic reticulumataxia-hypogonadism-choroidal dystrophy syndromehereditary spastic paraplegia 39trichomegaly-retina pigmentary degeneration-dwarfism syndromeTrichomegaly - retina pigmentary degeneration - dwarfism
✦AI Summary

PNPLA6 encodes Neuropathy Target Esterase (NTE), a phospholipase B that catalyzes deacylation of phosphatidylcholine (PtdCho) at both sn-2 and sn-1 positions, generating glycerophosphocholine 1. The enzyme hydrolyzes lysophospholipids and monoacylglycerols with preference for 1-acyl isomers, functioning primarily in endoplasmic reticulum membranes to maintain phospholipid homeostasis 2. Recently, mechanistic studies revealed PNPLA6 regulates retinal homeostasis by mobilizing choline from phosphatidylcholine for phospholipid recycling in retinal pigment epithelial cells, which supply choline to adjacent photoreceptors for survival 3. Biallelic pathogenic PNPLA6 variants cause five systemic neurological disorders: spastic paraplegia type 39, Gordon-Holmes, Boucher-NeuhΓ€user, Laurence-Moon, and Oliver-McFarlane syndromes, characterized by gait disturbance, chorioretinal dystrophy, anterior hypopituitarism, and hair anomalies 4. Disease phenotypes exhibit a striking inverse relationship with NTE enzymatic activity; individuals with lower NTE activity develop retinopathy and endocrinopathy, establishing an NTE activity threshold for disease manifestation 5. Animal models demonstrate loss-of-function mechanisms, and delayed therapeutic induction of NTE function can ameliorate neurodegeneration even after symptom onset, suggesting treatment windows may exist 6.

Sources cited
1
PNPLA6 is a phospholipase B that deacylates phosphatidylcholine at sn-2 and sn-1 positions, generating glycerophosphocholine, and hydrolyzes lysophospholipids and monoacylglycerols
PMID: 11927584
2
PNPLA6/NTE is an evolutionarily conserved phospholipase involved in lipid homeostasis and nervous system integrity, located on endoplasmic reticulum membranes
PMID: 35448471
3
PNPLA6 regulates retinal homeostasis by mobilizing choline from phosphatidylcholine for phospholipid recycling, with retinal pigment epithelial cells supplying choline to photoreceptors; choline supplementation rescues PNPLA6-deficiency phenotypes
PMID: 40082403
4
Biallelic PNPLA6 variants cause five neurological disorders (spastic paraplegia 39, Gordon-Holmes, Boucher-NeuhΓ€user, Laurence-Moon, Oliver-McFarlane syndromes) with gait disturbance, visual impairment, anterior hypopituitarism, and hair anomalies
PMID: 37732399
5
NTE activity inversely correlates with presence of retinopathy and endocrinopathy; PNPLA6 disorders form a continuous phenotypic spectrum defined by NTE genotype-activity-phenotype relationships
PMID: 38735647
6
Delayed induction of human NTE rescues neurodegeneration and mobility defects in Drosophila mutants, suggesting late therapeutic intervention may ameliorate symptoms after disease onset
PMID: 26671664
Disease Associationsβ“˜24
ataxia-hypogonadism-choroidal dystrophy syndromeOpen Targets
0.81Strong
hereditary spastic paraplegia 39Open Targets
0.80Strong
trichomegaly-retina pigmentary degeneration-dwarfism syndromeOpen Targets
0.78Strong
Trichomegaly - retina pigmentary degeneration - dwarfismOpen Targets
0.76Strong
Autosomal recessive spastic paraplegia type 39Open Targets
0.76Strong
Laurence-Moon syndromeOpen Targets
0.67Moderate
Ataxia - hypogonadism - choroidal dystrophyOpen Targets
0.66Moderate
Retinal dystrophyOpen Targets
0.49Moderate
hereditary spastic paraplegiaOpen Targets
0.48Moderate
spastic ataxiaOpen Targets
0.47Moderate
genetic disorderOpen Targets
0.47Moderate
Cerebellar ataxia - hypogonadismOpen Targets
0.40Moderate
cerebellar ataxia-hypogonadism syndromeOpen Targets
0.40Weak
PNPLA6-related spastic paraplegia with or without ataxiaOpen Targets
0.40Weak
Rod-cone dystrophyOpen Targets
0.37Weak
DysarthriaOpen Targets
0.35Weak
Kallmann syndromeOpen Targets
0.34Weak
cerebellar ataxiaOpen Targets
0.34Weak
hypogonadotropic hypogonadismOpen Targets
0.34Weak
amyotrophic lateral sclerosisOpen Targets
0.15Weak
Boucher-Neuhauser syndromeUniProt
Laurence-Moon syndromeUniProt
Oliver-McFarlane syndromeUniProt
Spastic paraplegia 39, autosomal recessiveUniProt
Pathogenic Variants122
NM_001166114.2(PNPLA6):c.3304G>A (p.Ala1102Thr)Pathogenic
Hereditary spastic paraplegia 39
β˜…β˜…β˜†β˜†2026β†’ Residue 1102
NM_001166114.2(PNPLA6):c.3816+1G>ALikely pathogenic
not provided|Hereditary spastic paraplegia 39|Sarcoma
β˜…β˜…β˜†β˜†2026
NM_001166114.2(PNPLA6):c.3058_3061dup (p.Arg1021fs)Pathogenic
Hereditary spastic paraplegia 39|Laurence-Moon syndrome|Trichomegaly-retina pigmentary degeneration-dwarfism syndrome|not provided|PNPLA6-related disorder|Inborn genetic diseases|Ataxia-hypogonadism-choroidal dystrophy syndrome|Hereditary spastic paraplegia|Ataxia-hypogonadism-choroidal dystrophy syndrome;Laurence-Moon syndrome;Trichomegaly-retina pigmentary degeneration-dwarfism syndrome;Hereditary spastic paraplegia 39|Retinal dystrophy
β˜…β˜…β˜†β˜†2025β†’ Residue 1021
NM_001166114.2(PNPLA6):c.1211dup (p.Leu405fs)Pathogenic
Hereditary spastic paraplegia 39|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 405
NM_001166114.2(PNPLA6):c.4051C>T (p.Arg1351Ter)Pathogenic
Hereditary spastic paraplegia 39|Ataxia-hypogonadism-choroidal dystrophy syndrome|Hereditary spastic paraplegia|not provided|Laurence-Moon syndrome;Ataxia-hypogonadism-choroidal dystrophy syndrome;Trichomegaly-retina pigmentary degeneration-dwarfism syndrome;Hereditary spastic paraplegia 39
β˜…β˜…β˜†β˜†2025β†’ Residue 1351
NM_001166114.2(PNPLA6):c.3850_3851del (p.Leu1284fs)Pathogenic
not provided|Hereditary spastic paraplegia 39
β˜…β˜…β˜†β˜†2025β†’ Residue 1284
NM_001166114.2(PNPLA6):c.4045C>T (p.Arg1349Trp)Pathogenic
Cerebellar ataxia;Hypogonadotropic hypogonadism 7 with or without anosmia;Dysarthria|Gait ataxia;Dysarthria;Cerebellar atrophy|not provided|Ataxia-hypogonadism-choroidal dystrophy syndrome|Hereditary spastic paraplegia 39|PNPLA6-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 1349
NM_001166114.2(PNPLA6):c.316-2A>TPathogenic
not provided|Hereditary spastic paraplegia 39|Ataxia-hypogonadism-choroidal dystrophy syndrome|Retinal dystrophy
β˜…β˜…β˜†β˜†2025
NM_001166114.2(PNPLA6):c.3266G>A (p.Arg1089Gln)Pathogenic
Trichomegaly-retina pigmentary degeneration-dwarfism syndrome|not provided|Ataxia-hypogonadism-choroidal dystrophy syndrome|Hereditary spastic paraplegia 39
β˜…β˜…β˜†β˜†2025β†’ Residue 1089
NM_001166114.2(PNPLA6):c.3496G>A (p.Gly1166Ser)Likely pathogenic
Trichomegaly-retina pigmentary degeneration-dwarfism syndrome|Hereditary spastic paraplegia 39|not provided|Retinal dystrophy
β˜…β˜…β˜†β˜†2025β†’ Residue 1166
NM_001166114.2(PNPLA6):c.3104C>T (p.Ser1035Leu)Pathogenic
Ataxia-hypogonadism-choroidal dystrophy syndrome|Hereditary spastic paraplegia 39|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1035
NM_001166114.2(PNPLA6):c.2016del (p.Ser673fs)Pathogenic
not provided|Hereditary spastic paraplegia 39
β˜…β˜…β˜†β˜†2024β†’ Residue 673
NM_001166114.2(PNPLA6):c.3361del (p.Leu1121fs)Pathogenic
Hereditary spastic paraplegia 39|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 1121
NM_001166114.2(PNPLA6):c.3298G>A (p.Val1100Met)Pathogenic
Ataxia-hypogonadism-choroidal dystrophy syndrome|Trichomegaly-retina pigmentary degeneration-dwarfism syndrome|Hereditary spastic paraplegia 39
β˜…β˜…β˜†β˜†2024β†’ Residue 1100
NM_001166114.2(PNPLA6):c.2483del (p.Leu828fs)Pathogenic
Hereditary spastic paraplegia 39|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 828
NM_001166114.2(PNPLA6):c.3614T>C (p.Val1205Ala)Likely pathogenic
Hereditary spastic paraplegia 39|Hereditary spastic paraplegia 39;Laurence-Moon syndrome;Trichomegaly-retina pigmentary degeneration-dwarfism syndrome
β˜…β˜…β˜†β˜†2023β†’ Residue 1205
NM_001166114.2(PNPLA6):c.3265C>T (p.Arg1089Ter)Pathogenic
not provided|Hereditary spastic paraplegia 39
β˜…β˜…β˜†β˜†2023β†’ Residue 1089
NM_001166114.2(PNPLA6):c.2936+2T>CLikely pathogenic
Hereditary spastic paraplegia 39|not provided
β˜…β˜…β˜†β˜†2023
NM_001166114.2(PNPLA6):c.1814+3A>GLikely pathogenic
Retinal dystrophy-ataxia-pituitary hormone abnormality-hypogonadism syndrome
β˜…β˜†β˜†β˜†2026
NM_001166114.2(PNPLA6):c.3984del (p.Ser1329fs)Pathogenic
Hereditary spastic paraplegia 39
β˜…β˜†β˜†β˜†2025β†’ Residue 1329
View on ClinVar β†—
Related Genes
SPG11Protein interaction95%LCATProtein interaction95%PLA2G2AProtein interaction95%PLA2G4AProtein interaction95%PLA2G6Protein interaction95%PLA2G4CProtein interaction95%
Tissue Expression6 tissues
Lung
100%
Liver
44%
Brain
43%
Bone Marrow
40%
Ovary
36%
Heart
20%
Gene Interaction Network
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PNPLA6SPG11LCATPLA2G2APLA2G4APLA2G6PLA2G4C
PROTEIN STRUCTURE
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AlphaFoldAI-predicted Β· UniProt Q8IY17
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.87LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.74 [0.63–0.87]
RankingsWhere PNPLA6 stands among ~20K protein-coding genes
  • #4,092of 20,598
    Most Researched116 Β· top quartile
  • #643of 5,498
    Most Pathogenic Variants122 Β· top quartile
  • #7,692of 17,882
    Most Constrained (LOEUF)0.87
Genes detectedPNPLA6
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
PMID: 25299038
1.00
2
PMID: 37732399
Ophthalmic Genet Β· 2023
0.90
3
Neuropathy target esterase activity defines phenotypes among PNPLA6 disorders.
PMID: 38735647
Brain Β· 2024
0.80
4
PNPLA6 regulates retinal homeostasis by choline through phospholipid turnover.
PMID: 40082403
Nat Commun Β· 2025
0.70
5
PNPLA6/NTE, an Evolutionary Conserved Phospholipase Linked to a Group of Complex Human Diseases.
PMID: 35448471
Metabolites Β· 2022
0.60