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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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CLN5
CLN5 lysosomal BMP synthase
Chromosome 13 Β· 13q22.3
NCBI Gene: 1203Ensembl: ENSG00000102805.16HGNC: HGNC:2076UniProt: A0A1B0GTR6
59PubMed Papers
21Diseases
0Drugs
153Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingD-mannose bindingprotein maturationpositive regulation of GTP bindingneuronal ceroid lipofuscinosis 5CLN5 diseaseneuronal ceroid lipofuscinosisintellectual disability, short stature, facial anomalies, and joint dislocations
✦AI Summary

CLN5 is a lysosomal bis(monoacylglycero)phosphate (BMP) synthase essential for lysosomal function and neuronal health 1. The protein catalyzes BMP synthesis through an energy-independent base exchange reaction between two lysophosphatidylglycerol molecules, with increased activity on BMP-laden vesicles 1. BMP is a critical phospholipid constituent of late endosomes/lysosomes that stimulates lipid catabolism, cholesterol homeostasis, and lysosomal organization 1. CLN5 deficiency causes variant late-infantile neuronal ceroid lipofuscinosis (Batten disease), with disease onset between 4-7 years, characterized by progressive neuronal loss, visual failure, motor and mental decline, epilepsy, and premature death 23. Loss of CLN5 function leads to massive accumulation of its precursor lysophosphatidylglycerol, BMP depletion, and dysfunctional lipid metabolism 1. Recent evidence reveals that CLN5 deficiency impairs glucose uptake and calcium homeostasis, with PHGDH identified as a potential biomarker 4. Genetically, CLN5 is implicated in Alzheimer's disease pathogenesis through lysosomal dysfunction pathways 5. Gene therapy approaches using adeno-associated viral vectors encoding CLN5 show promise in preclinical models, slowing disease progression and preserving visual and neurological function 6.

Sources cited
1
CLN5 is the BMP synthase; mediates BMP synthesis through base exchange reaction; BMP stimulates lipid catabolism and lysosomal function
PMID: 37708259
2
CLN5 mutations cause late infantile variant NCL with variable age of onset, motor/mental decline, epilepsy, visual loss, premature death
PMID: 21990111
3
CLN5 mutations cause variant late-infantile NCL (Batten disease) with onset 4-7 years; CLN5 is ubiquitously expressed and lysosomal-resident
PMID: 33792748
4
CLN5 deficiency impairs glucose uptake and calcium homeostasis; PHGDH identified as biomarker; metformin improves outcomes in patient cells
PMID: 40346285
5
CLN5 abundance is causally associated with Alzheimer's disease through lysosomal involvement
PMID: 40037332
6
AAV9-mediated CLN5 gene therapy slows disease progression and preserves vision and neurological function in preclinical models
PMID: 37942487
Disease Associationsβ“˜21
neuronal ceroid lipofuscinosis 5Open Targets
0.81Strong
CLN5 diseaseOpen Targets
0.78Strong
neuronal ceroid lipofuscinosisOpen Targets
0.71Strong
intellectual disability, short stature, facial anomalies, and joint dislocationsOpen Targets
0.48Moderate
genetic disorderOpen Targets
0.47Moderate
Retinal dystrophyOpen Targets
0.34Weak
Abnormality of metabolism/homeostasisOpen Targets
0.34Weak
pontocerebellar hypoplasia type 2DOpen Targets
0.27Weak
neuronal ceroid-lipofuscinosis, dominant/recessiveOpen Targets
0.19Weak
experimental autoimmune encephalomyelitisOpen Targets
0.10Suggestive
neoplasmOpen Targets
0.09Suggestive
glioblastoma multiformeOpen Targets
0.08Suggestive
breast cancerOpen Targets
0.07Suggestive
juvenile neuronal ceroid lipofuscinosisOpen Targets
0.07Suggestive
polycystic ovary syndromeOpen Targets
0.05Suggestive
gliomaOpen Targets
0.05Suggestive
cancerOpen Targets
0.04Suggestive
lung adenocarcinomaOpen Targets
0.04Suggestive
HirsutismOpen Targets
0.03Suggestive
inflammatory bowel diseaseOpen Targets
0.03Suggestive
Ceroid lipofuscinosis, neuronal, 5UniProt
Pathogenic Variants153
NM_006493.4(CLN5):c.626A>G (p.Tyr209Cys)Likely pathogenic
Neuronal ceroid lipofuscinosis 5|Neuronal ceroid lipofuscinosis
β˜…β˜…β˜†β˜†2026β†’ Residue 209
NM_006493.4(CLN5):c.625T>G (p.Tyr209Asp)Pathogenic
Neuronal ceroid lipofuscinosis 5|Neuronal ceroid lipofuscinosis
β˜…β˜…β˜†β˜†2026β†’ Residue 209
NM_006493.4(CLN5):c.84G>A (p.Trp28Ter)Pathogenic
not provided|Neuronal ceroid lipofuscinosis 5|Neuronal ceroid lipofuscinosis
β˜…β˜…β˜†β˜†2026β†’ Residue 28
NM_006493.4(CLN5):c.524G>A (p.Trp175Ter)Pathogenic
Neuronal ceroid lipofuscinosis 5|not provided|Neuronal ceroid lipofuscinosis
β˜…β˜…β˜†β˜†2025β†’ Residue 175
NM_006493.4(CLN5):c.428A>G (p.Asn143Ser)Pathogenic
Neuronal ceroid lipofuscinosis 5|Neuronal ceroid lipofuscinosis|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 143
NM_006493.4(CLN5):c.448C>T (p.Arg150Ter)Pathogenic
not provided|Neuronal ceroid lipofuscinosis|Neuronal ceroid lipofuscinosis 5|CLN5-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 150
NM_006493.4(CLN5):c.717dup (p.Asn240Ter)Pathogenic
Neuronal ceroid lipofuscinosis 5|Neuronal ceroid lipofuscinosis
β˜…β˜…β˜†β˜†2025β†’ Residue 240
NM_006493.4(CLN5):c.525del (p.His174_Trp175insTer)Pathogenic
Neuronal ceroid lipofuscinosis 5|Neuronal ceroid lipofuscinosis|not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 174
NM_006493.4(CLN5):c.907G>T (p.Glu303Ter)Pathogenic
Neuronal ceroid lipofuscinosis 5|Neuronal ceroid lipofuscinosis
β˜…β˜…β˜†β˜†2025β†’ Residue 303
NM_006493.4(CLN5):c.174-2A>GLikely pathogenic
Neuronal ceroid lipofuscinosis 5|Neuronal ceroid lipofuscinosis
β˜…β˜…β˜†β˜†2025
NM_006493.4(CLN5):c.441_442dup (p.His148fs)Pathogenic
Neuronal ceroid lipofuscinosis|Neuronal ceroid lipofuscinosis 5
β˜…β˜…β˜†β˜†2025β†’ Residue 148
NM_006493.4(CLN5):c.112del (p.Val38fs)Pathogenic
Neuronal ceroid lipofuscinosis|Neuronal ceroid lipofuscinosis 5
β˜…β˜…β˜†β˜†2025β†’ Residue 38
NM_006493.4(CLN5):c.838G>T (p.Gly280Ter)Pathogenic
Neuronal ceroid lipofuscinosis|Neuronal ceroid lipofuscinosis 5
β˜…β˜…β˜†β˜†2025β†’ Residue 280
NM_006493.4(CLN5):c.188G>A (p.Arg63His)Pathogenic
Neuronal ceroid lipofuscinosis 5|Neuronal ceroid lipofuscinosis|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 63
NM_006493.4(CLN5):c.808_823del (p.Gly270fs)Pathogenic
Neuronal ceroid lipofuscinosis 5|not provided|Neuronal ceroid lipofuscinosis
β˜…β˜…β˜†β˜†2025β†’ Residue 270
NM_006493.4(CLN5):c.956_959del (p.Lys319fs)Pathogenic
Neuronal ceroid lipofuscinosis 5|Neuronal ceroid lipofuscinosis|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 319
NM_006493.4(CLN5):c.286C>T (p.Arg96Ter)Pathogenic
Neuronal ceroid lipofuscinosis 5|Neuronal ceroid lipofuscinosis
β˜…β˜…β˜†β˜†2025β†’ Residue 96
NM_006493.4(CLN5):c.777_778del (p.Phe260fs)Pathogenic
Neuronal ceroid lipofuscinosis 5|not provided|Neuronal ceroid lipofuscinosis|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 260
NM_006493.4(CLN5):c.522dup (p.Trp175fs)Pathogenic
Neuronal ceroid lipofuscinosis 5|Neuronal ceroid lipofuscinosis
β˜…β˜…β˜†β˜†2025β†’ Residue 175
NM_006493.4(CLN5):c.594G>A (p.Trp198Ter)Pathogenic
not provided|Neuronal ceroid lipofuscinosis|Neuronal ceroid lipofuscinosis 5
β˜…β˜…β˜†β˜†2025β†’ Residue 198
View on ClinVar β†—
Related Genes
CTSDProtein interaction80%KCTD7Protein interaction80%MFSD8Protein interaction79%PPT2Protein interaction71%DNAJC5Protein interaction70%TPP1Protein interaction63%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
76%
Ovary
69%
Liver
46%
Heart
45%
Lung
42%
Gene Interaction Network
Click a node to explore
CLN5CTSDKCTD7MFSD8PPT2DNAJC5TPP1
PROTEIN STRUCTURE
Preparing viewer…
PDB6R99 Β· 2.70 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.20LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.89 [0.67–1.20]
RankingsWhere CLN5 stands among ~20K protein-coding genes
  • #7,749of 20,598
    Most Researched59
  • #498of 5,498
    Most Pathogenic Variants153 Β· top 10%
  • #12,572of 17,882
    Most Constrained (LOEUF)1.20
Genes detectedCLN5
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
The Batten disease gene product CLN5 is the lysosomal bis(monoacylglycero)phosphate synthase.
PMID: 37708259
Science Β· 2023
1.00
2
PMID: 39637217
0.90
3
Mendelian randomization identifies proteins involved in neurodegenerative diseases.
PMID: 40037332
Brain Β· 2025
0.80
4
Update of the mutation spectrum and clinical correlations of over 360 mutations in eight genes that underlie the neuronal ceroid lipofuscinoses.
PMID: 21990111
Hum Mutat Β· 2012
0.70
5
Alcohol activates ATF4/LPLA2-mediated BMP metabolism to enhance HBV-induced hepatocellular carcinogenesis.
PMID: 40885211
J Hepatol Β· 2026
0.60