Gene Gene information from NCBI Gene database.
Entrez ID 1203
Gene name CLN5 lysosomal BMP synthase
Gene symbol CLN5
Synonyms (NCBI Gene)
-
Chromosome 13
Chromosome location 13q22.3
Summary This gene is one of eight which have been associated with neuronal ceroid lipofuscinoses (NCL). Also referred to as Batten disease, NCL comprises a class of autosomal recessive, neurodegenerative disorders affecting children. The genes responsible likely
SNPs SNP information provided by dbSNP.
4
SNP ID Visualize variation Clinical significance Consequence
rs61504484 C>A,G,T Pathogenic, likely-benign Upstream transcript variant
rs200353554 C>T Conflicting-interpretations-of-pathogenicity, likely-benign Upstream transcript variant
rs201615354 T>A,C,G Conflicting-interpretations-of-pathogenicity, uncertain-significance Upstream transcript variant
rs765323914 G>- Pathogenic Upstream transcript variant
miRNA miRNA information provided by mirtarbase database.
199
miRTarBase ID miRNA Experiments Reference
MIRT022416 hsa-miR-124-3p Microarray 18668037
MIRT897034 hsa-miR-1207-5p CLIP-seq
MIRT897035 hsa-miR-1238 CLIP-seq
MIRT897036 hsa-miR-3663-5p CLIP-seq
MIRT897037 hsa-miR-4269 CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
33
GO ID Ontology Definition Evidence Reference
GO:0005515 Function Protein binding IPI 12134079, 14699076, 22431521, 32296183
GO:0005537 Function D-mannose binding IDA 16399764
GO:0005764 Component Lysosome IDA 11971870, 19941651, 22431521, 37708259
GO:0005764 Component Lysosome IEA
GO:0005765 Component Lysosomal membrane IBA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
608102 2076 ENSG00000102805
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O75503
Protein name Bis(monoacylglycero)phosphate synthase CLN5 (BMP synthase CLN5) (EC 2.3.1.-) (Ceroid-lipofuscinosis neuronal protein 5) (Protein CLN5) (Palmitoyl protein thioesterase CLN5) (EC 3.1.2.22) (S-depalmitoylase CLN5) [Cleaved into: Bis(monoacylglycero)phosphate
Protein function [Bis(monoacylglycero)phosphate synthase CLN5, secreted form]: Catalyzes the synthesis of bis(monoacylglycero)phosphate (BMP) via transacylation of 2 molecules of lysophosphatidylglycerol (LPG) (PubMed:37708259). BMP also known as lysobisphosphat
PDB 6R99
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF15014 CLN5 51 349 Ceroid-lipofuscinosis neuronal protein 5 Family
Tissue specificity TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:9662406}.
Sequence
Sequence length 358
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG 
  Lysosome  
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
926
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Abnormality of metabolism/homeostasis Pathogenic rs2154034622 RCV001814483
CLN5-related disorder Pathogenic rs546989392 RCV003927734
Neuronal ceroid lipofuscinosis Pathogenic; Likely pathogenic rs1271064370, rs2034242246, rs2154035107, rs2154035159, rs2154035166, rs386833968, rs587780315, rs2034349886, rs2154035111, rs2154035183, rs2154035204, rs2154034636, rs2154034716, rs2154035196, rs2154035131
View all (66 more)
RCV001381766
RCV001389542
RCV001389234
RCV001386240
RCV001383792
RCV001385483
RCV001036078
RCV001960560
RCV001939433
RCV001970142
RCV001963063
RCV002051530
RCV001926582
RCV002007442
RCV001994504
RCV001968769
RCV001949633
RCV001914211
RCV003647863
RCV000684967
RCV000689128
RCV000698933
RCV002512684
RCV001039257
RCV000468638
RCV002635835
RCV000989150
RCV000556663
RCV002828257
RCV002908504
RCV002877424
RCV002899282
RCV003012522
RCV003020738
RCV003029629
RCV003037953
RCV003044214
RCV002282043
RCV005102475
RCV003533863
RCV003779162
RCV003533899
RCV003534098
RCV003531673
RCV003531679
RCV003648098
RCV003648196
RCV003648274
RCV003648291
RCV003648418
RCV003648628
RCV003833240
RCV003114526
RCV003532090
RCV001850973
RCV003766127
RCV001858008
RCV001868156
RCV000632674
RCV000632695
RCV001861846
RCV001861806
RCV001855490
RCV002544673
RCV001049322
RCV001389657
RCV000803462
RCV000632714
RCV001527017
RCV001058589
RCV002265586
RCV000989151
RCV000690321
RCV000818212
RCV003531948
RCV001853062
RCV001390094
RCV001070707
RCV001064628
RCV001036090
RCV001217019
RCV001222281
RCV001243960
Neuronal ceroid lipofuscinosis 5 Likely pathogenic; Pathogenic rs2034242246, rs2154035107, rs2154035159, rs386833968, rs2154035202, rs587780315, rs2034349886, rs2154035183, rs2154035204, rs2154034716, rs2034339711, rs386833969, rs104894385, rs104894386, rs121908292
View all (77 more)
RCV003469757
RCV001729913
RCV001729912
RCV001729909
RCV001580667
RCV000116757
RCV003471150
RCV005008298
RCV005008311
RCV004571628
RCV005008494
RCV000002673
RCV000002674
RCV000002676
RCV000002677
RCV000002678
RCV000002680
RCV002306665
RCV000169429
RCV002510732
RCV000613275
RCV004571810
RCV000210062
RCV003136483
RCV003338187
RCV003388909
RCV003388910
RCV003388911
RCV003388912
RCV003468468
RCV003468469
RCV003468470
RCV003468471
RCV003468473
RCV003468475
RCV003468476
RCV003468477
RCV003468478
RCV003468479
RCV004573228
RCV003993536
RCV004575663
RCV004575664
RCV004575665
RCV004577969
RCV000410812
RCV000409209
RCV000410399
RCV000409719
RCV000412162
RCV000411598
RCV000501228
RCV000984156
RCV000625737
RCV001729667
RCV000668838
RCV000674631
RCV000672807
RCV000664744
RCV000671450
RCV000672485
RCV000667867
RCV000674729
RCV000668417
RCV000674770
RCV000674313
RCV000670302
RCV000675014
RCV000761545
RCV000790375
RCV000049938
RCV000049939
RCV000049940
RCV000049941
RCV000049942
RCV000049945
RCV000049947
RCV000049949
RCV000049950
RCV000049951
RCV000049952
RCV000049955
RCV000049956
RCV000049957
RCV000049958
RCV000049959
RCV000049960
RCV001729791
RCV001336970
RCV001194250
RCV001729815
RCV001729819
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Intellectual disability Uncertain significance rs2034339472 RCV001251943
Lymphoma Benign; Likely benign rs9573974 RCV005893242
Melanoma Benign; Likely benign rs9573974 RCV005893244
Neuronal Ceroid-Lipofuscinosis, Dominant/Recessive Benign; Likely benign; Uncertain significance; Conflicting classifications of pathogenicity rs138037471, rs7987664, rs1800209, rs36038805, rs41287036, rs9565308, rs77416795, rs34481987, rs587780896, rs202118652, rs146993892, rs376454715, rs144656959, rs9573974, rs700365
View all (13 more)
RCV000365818
RCV000305280
RCV000372934
RCV000259654
RCV000319549
RCV000271170
RCV000337559
RCV000312256
RCV000360042
RCV000405110
RCV000395302
RCV000306509
RCV000367115
RCV000374238
RCV000283336
RCV000378855
RCV000286703
RCV000396698
RCV000277190
RCV000332312
RCV000308848
RCV000312250
RCV000369306
RCV000340633
RCV000344084
RCV000347500
RCV000403374
RCV000276913
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Alzheimer Disease Associate 30037983, 35427157, 40037332
Ataxia Associate 33507209
Brain Diseases Associate 8661106
Cerebellar Diseases Associate 33507209, 39525553
Ceroid lipofuscinosis neuronal 5 Associate 28468312, 30655561, 34680045, 35427157, 8661106
Ceroid Lipofuscinosis Neuronal 6 Associate 8644710
Cognition Disorders Associate 28542837, 34680045
Cognitive Dysfunction Associate 34680045
Death Associate 33507209
Dizziness Associate 33507209