Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	1203
Gene name Gene Name - the full gene name approved by the HGNC.	CLN5 lysosomal BMP synthase
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	CLN5
Synonyms (NCBI Gene) Gene synonyms aliases	-
Chromosome Chromosome number	13
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	13q22.3
Summary Summary of gene provided in NCBI Entrez Gene.	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

Show/Hide all(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

Show/Hide all(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
MIRT897038	hsa-miR-4521	CLIP-seq
MIRT897039	hsa-miR-4668-3p	CLIP-seq
MIRT897040	hsa-miR-4719	CLIP-seq
MIRT897041	hsa-miR-4736	CLIP-seq
MIRT897042	hsa-miR-4763-3p	CLIP-seq
MIRT897043	hsa-miR-513b	CLIP-seq
MIRT897044	hsa-miR-548a-5p	CLIP-seq
MIRT897045	hsa-miR-548ab	CLIP-seq
MIRT897046	hsa-miR-548ak	CLIP-seq
MIRT897047	hsa-miR-548b-5p	CLIP-seq
MIRT897048	hsa-miR-548c-5p	CLIP-seq
MIRT897049	hsa-miR-548d-5p	CLIP-seq
MIRT897050	hsa-miR-548h	CLIP-seq
MIRT897051	hsa-miR-548i	CLIP-seq
MIRT897052	hsa-miR-548j	CLIP-seq
MIRT897053	hsa-miR-548n	CLIP-seq
MIRT897054	hsa-miR-548w	CLIP-seq
MIRT897055	hsa-miR-548y	CLIP-seq
MIRT897056	hsa-miR-559	CLIP-seq
MIRT897057	hsa-miR-802	CLIP-seq
MIRT1965989	hsa-miR-31	CLIP-seq
MIRT1965990	hsa-miR-323-3p	CLIP-seq
MIRT1965991	hsa-miR-3647-3p	CLIP-seq
MIRT1965992	hsa-miR-375	CLIP-seq
MIRT1965993	hsa-miR-4273	CLIP-seq
MIRT1965994	hsa-miR-4423-3p	CLIP-seq
MIRT1965995	hsa-miR-4677-5p	CLIP-seq
MIRT1965996	hsa-miR-4790-3p	CLIP-seq
MIRT2201872	hsa-miR-186	CLIP-seq
MIRT2201873	hsa-miR-3133	CLIP-seq
MIRT2201874	hsa-miR-34b	CLIP-seq
MIRT2201875	hsa-miR-4661-5p	CLIP-seq
MIRT2201876	hsa-miR-4676-5p	CLIP-seq
MIRT2201877	hsa-miR-4705	CLIP-seq
MIRT2201878	hsa-miR-4731-3p	CLIP-seq
MIRT2201879	hsa-miR-4801	CLIP-seq
MIRT2201880	hsa-miR-483-3p	CLIP-seq
MIRT2201881	hsa-miR-508-5p	CLIP-seq
MIRT2201882	hsa-miR-575	CLIP-seq
MIRT2201883	hsa-miR-935	CLIP-seq
MIRT2386200	hsa-miR-3160-5p	CLIP-seq
MIRT2386201	hsa-miR-3670	CLIP-seq
MIRT2386202	hsa-miR-4652-3p	CLIP-seq
MIRT2386203	hsa-miR-4677-3p	CLIP-seq
MIRT2386204	hsa-miR-4679	CLIP-seq
MIRT2504899	hsa-miR-103a	CLIP-seq
MIRT2504900	hsa-miR-107	CLIP-seq
MIRT2504901	hsa-miR-1184	CLIP-seq
MIRT2504902	hsa-miR-1200	CLIP-seq
MIRT2504903	hsa-miR-1205	CLIP-seq
MIRT2504904	hsa-miR-1253	CLIP-seq
MIRT2504905	hsa-miR-1273f	CLIP-seq
MIRT2504906	hsa-miR-143	CLIP-seq
MIRT2504907	hsa-miR-145	CLIP-seq
MIRT2504908	hsa-miR-146a	CLIP-seq
MIRT2504909	hsa-miR-146b-5p	CLIP-seq
MIRT2504910	hsa-miR-187	CLIP-seq
MIRT2504911	hsa-miR-18a	CLIP-seq
MIRT2504912	hsa-miR-18b	CLIP-seq
MIRT2504913	hsa-miR-2053	CLIP-seq
MIRT2504914	hsa-miR-2277-3p	CLIP-seq
MIRT2504915	hsa-miR-3064-3p	CLIP-seq
MIRT2504916	hsa-miR-3074-5p	CLIP-seq
MIRT2504917	hsa-miR-3120-3p	CLIP-seq
MIRT2504918	hsa-miR-3158-5p	CLIP-seq
MIRT2504919	hsa-miR-3183	CLIP-seq
MIRT2504920	hsa-miR-3185	CLIP-seq
MIRT2504921	hsa-miR-3187-3p	CLIP-seq
MIRT2504922	hsa-miR-346	CLIP-seq
MIRT2201874	hsa-miR-34b	CLIP-seq
MIRT2504923	hsa-miR-3615	CLIP-seq
MIRT2504924	hsa-miR-3909	CLIP-seq
MIRT2504925	hsa-miR-3917	CLIP-seq
MIRT2504926	hsa-miR-3925-3p	CLIP-seq
MIRT2504927	hsa-miR-3926	CLIP-seq
MIRT2504928	hsa-miR-4261	CLIP-seq
MIRT2504929	hsa-miR-4265	CLIP-seq
MIRT2504930	hsa-miR-4288	CLIP-seq
MIRT2504931	hsa-miR-4296	CLIP-seq
MIRT2504932	hsa-miR-4322	CLIP-seq
MIRT2504933	hsa-miR-4324	CLIP-seq
MIRT2504934	hsa-miR-4326	CLIP-seq
MIRT2504935	hsa-miR-4419a	CLIP-seq
MIRT2504936	hsa-miR-4435	CLIP-seq
MIRT2504937	hsa-miR-4496	CLIP-seq
MIRT2504938	hsa-miR-4510	CLIP-seq
MIRT2504939	hsa-miR-4517	CLIP-seq
MIRT2504940	hsa-miR-4648	CLIP-seq
MIRT2504941	hsa-miR-4654	CLIP-seq
MIRT2504942	hsa-miR-4700-3p	CLIP-seq
MIRT2504943	hsa-miR-4701-5p	CLIP-seq
MIRT2201877	hsa-miR-4705	CLIP-seq
MIRT2504944	hsa-miR-4708-5p	CLIP-seq
MIRT2504945	hsa-miR-4716-5p	CLIP-seq
MIRT2504946	hsa-miR-4723-3p	CLIP-seq
MIRT2504947	hsa-miR-4735-3p	CLIP-seq
MIRT2504948	hsa-miR-4747-5p	CLIP-seq
MIRT2504949	hsa-miR-4769-5p	CLIP-seq
MIRT2504950	hsa-miR-4770	CLIP-seq
MIRT2201880	hsa-miR-483-3p	CLIP-seq
MIRT2504951	hsa-miR-491-3p	CLIP-seq
MIRT2504952	hsa-miR-501-3p	CLIP-seq
MIRT2504953	hsa-miR-502-3p	CLIP-seq
MIRT2201881	hsa-miR-508-5p	CLIP-seq
MIRT2504954	hsa-miR-544b	CLIP-seq
MIRT2504955	hsa-miR-548s	CLIP-seq
MIRT2504956	hsa-miR-550a	CLIP-seq
MIRT2504957	hsa-miR-569	CLIP-seq
MIRT2504958	hsa-miR-584	CLIP-seq
MIRT2504959	hsa-miR-588	CLIP-seq
MIRT2504960	hsa-miR-605	CLIP-seq
MIRT2504961	hsa-miR-632	CLIP-seq
MIRT2504962	hsa-miR-649	CLIP-seq
MIRT2504963	hsa-miR-767-5p	CLIP-seq
MIRT2504964	hsa-miR-889	CLIP-seq
MIRT2504899	hsa-miR-103a	CLIP-seq
MIRT2504900	hsa-miR-107	CLIP-seq
MIRT2504901	hsa-miR-1184	CLIP-seq
MIRT2504902	hsa-miR-1200	CLIP-seq
MIRT2504903	hsa-miR-1205	CLIP-seq
MIRT2678311	hsa-miR-1245	CLIP-seq
MIRT2504904	hsa-miR-1253	CLIP-seq
MIRT2504905	hsa-miR-1273f	CLIP-seq
MIRT2678312	hsa-miR-136	CLIP-seq
MIRT2504906	hsa-miR-143	CLIP-seq
MIRT2504907	hsa-miR-145	CLIP-seq
MIRT2504908	hsa-miR-146a	CLIP-seq
MIRT2504909	hsa-miR-146b-5p	CLIP-seq
MIRT2504910	hsa-miR-187	CLIP-seq
MIRT2504911	hsa-miR-18a	CLIP-seq
MIRT2504912	hsa-miR-18b	CLIP-seq
MIRT2678313	hsa-miR-190	CLIP-seq
MIRT2678314	hsa-miR-190b	CLIP-seq
MIRT2504913	hsa-miR-2053	CLIP-seq
MIRT2504914	hsa-miR-2277-3p	CLIP-seq
MIRT2504915	hsa-miR-3064-3p	CLIP-seq
MIRT2504916	hsa-miR-3074-5p	CLIP-seq
MIRT2504917	hsa-miR-3120-3p	CLIP-seq
MIRT2504918	hsa-miR-3158-5p	CLIP-seq
MIRT2504919	hsa-miR-3183	CLIP-seq
MIRT2504920	hsa-miR-3185	CLIP-seq
MIRT2504921	hsa-miR-3187-3p	CLIP-seq
MIRT2504922	hsa-miR-346	CLIP-seq
MIRT2201874	hsa-miR-34b	CLIP-seq
MIRT2678315	hsa-miR-3591-5p	CLIP-seq
MIRT2678316	hsa-miR-3606	CLIP-seq
MIRT2504923	hsa-miR-3615	CLIP-seq
MIRT2504924	hsa-miR-3909	CLIP-seq
MIRT2504925	hsa-miR-3917	CLIP-seq
MIRT2504926	hsa-miR-3925-3p	CLIP-seq
MIRT2504927	hsa-miR-3926	CLIP-seq
MIRT2504928	hsa-miR-4261	CLIP-seq
MIRT2504929	hsa-miR-4265	CLIP-seq
MIRT2504930	hsa-miR-4288	CLIP-seq
MIRT2504931	hsa-miR-4296	CLIP-seq
MIRT2504932	hsa-miR-4322	CLIP-seq
MIRT2504933	hsa-miR-4324	CLIP-seq
MIRT2504934	hsa-miR-4326	CLIP-seq
MIRT2504935	hsa-miR-4419a	CLIP-seq
MIRT2504936	hsa-miR-4435	CLIP-seq
MIRT2504937	hsa-miR-4496	CLIP-seq
MIRT2504938	hsa-miR-4510	CLIP-seq
MIRT2504939	hsa-miR-4517	CLIP-seq
MIRT2504940	hsa-miR-4648	CLIP-seq
MIRT2504941	hsa-miR-4654	CLIP-seq
MIRT2504942	hsa-miR-4700-3p	CLIP-seq
MIRT2504943	hsa-miR-4701-5p	CLIP-seq
MIRT2201877	hsa-miR-4705	CLIP-seq
MIRT2504944	hsa-miR-4708-5p	CLIP-seq
MIRT2504945	hsa-miR-4716-5p	CLIP-seq
MIRT2504946	hsa-miR-4723-3p	CLIP-seq
MIRT2504947	hsa-miR-4735-3p	CLIP-seq
MIRT2504948	hsa-miR-4747-5p	CLIP-seq
MIRT2504949	hsa-miR-4769-5p	CLIP-seq
MIRT2504950	hsa-miR-4770	CLIP-seq
MIRT2201880	hsa-miR-483-3p	CLIP-seq
MIRT2504951	hsa-miR-491-3p	CLIP-seq
MIRT2504952	hsa-miR-501-3p	CLIP-seq
MIRT2504953	hsa-miR-502-3p	CLIP-seq
MIRT2201881	hsa-miR-508-5p	CLIP-seq
MIRT2678317	hsa-miR-515-5p	CLIP-seq
MIRT2504954	hsa-miR-544b	CLIP-seq
MIRT2678318	hsa-miR-548b-3p	CLIP-seq
MIRT2504955	hsa-miR-548s	CLIP-seq
MIRT2504956	hsa-miR-550a	CLIP-seq
MIRT2504957	hsa-miR-569	CLIP-seq
MIRT2504958	hsa-miR-584	CLIP-seq
MIRT2504959	hsa-miR-588	CLIP-seq
MIRT2504960	hsa-miR-605	CLIP-seq
MIRT2504961	hsa-miR-632	CLIP-seq
MIRT2504962	hsa-miR-649	CLIP-seq
MIRT2504963	hsa-miR-767-5p	CLIP-seq
MIRT2504964	hsa-miR-889	CLIP-seq
MIRT2678319	hsa-miR-921	CLIP-seq

Show/Hide all(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
GO:0005765	Component	Lysosomal membrane	IDA	12134079
GO:0005775	Component	Vacuolar lumen	IEA
GO:0005783	Component	Endoplasmic reticulum	IDA	12134079
GO:0005794	Component	Golgi apparatus	IDA	12134079
GO:0005829	Component	Cytosol	IEA
GO:0006465	Process	Signal peptide processing	IDA	20052765
GO:0007040	Process	Lysosome organization	IBA
GO:0007040	Process	Lysosome organization	IEA
GO:0007042	Process	Lysosomal lumen acidification	IMP	11722572
GO:0007420	Process	Brain development	IEP	10992246
GO:0007601	Process	Visual perception	IEA
GO:0016020	Component	Membrane	IDA	12134079, 28442266
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	NAS	9662406
GO:0016740	Function	Transferase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016798	Function	Hydrolase activity, acting on glycosyl bonds	IBA
GO:0022008	Process	Neurogenesis	IEP	10992246
GO:0030163	Process	Protein catabolic process	NAS	10740217
GO:0042147	Process	Retrograde transport, endosome to Golgi	IMP	22431521
GO:0042551	Process	Neuron maturation	NAS	10992246
GO:0048471	Component	Perinuclear region of cytoplasm	IDA	10992246
GO:0052816	Function	Long-chain fatty acyl-CoA hydrolase activity	IDA	35427157
GO:0052816	Function	Long-chain fatty acyl-CoA hydrolase activity	IEA
GO:0070062	Component	Extracellular exosome	HDA	23533145
GO:0070085	Process	Glycosylation	IDA	16399764
GO:0160121	Function	Bis(monoacylglycero)phosphate synthase activity	IDA	37708259
GO:1904426	Process	Positive regulation of GTP binding	IMP	22431521

MIM	HGNC	e!Ensembl
608102	2076	ENSG00000102805

Protein

UniProt ID

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

MAQEVDTAQGAEMRRGAGAARGRASWCWALALLWLAVVPGWSRVSGIPSRRHWPVPYKRF
DFRPKPDPYCQAKYTFCPTGSPIPVMEGDDDIEVFRLQAPVWEFKYGDLLGHLKIMHDAI
GFRSTLTGKNYTMEWYELFQLGNCTFPHLRPEMDAPFWCNQGAACFFEGIDDVHWKENGT
LVQVATISGNMFNQMAKWVKQDNETGIYYETWNVKASPEKGAETWFDSYDCSKFVLRTFN
KLAEFGAEFKNIETNYTRIFLYSGEPTYLGNETSVFGPTGNKTLGLAIKRFYYPFKPHLP
TKEFLLSLLQIFDAVIVHKQFYLFYNFEYWFLPMKFPFIKITYEEIPLPIRNKTLSGL

Sequence length

358

Interactions

View interactions

	KEGG
	Lysosome

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
neuronal ceroid lipofuscinosis	Neuronal ceroid lipofuscinosis 5, Neuronal ceroid lipofuscinosis	rs546989392, rs386833965, rs1555274373, rs2034349431, rs750935331, rs386833973, rs386833982, rs104894386, rs1555274343, rs869312751, rs386833966, rs1555274387, rs386833974, rs1555273882, rs1739482158 View all (42 more)	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Pontoneocerebellar hypoplasia	Pontocerebellar hypoplasia type 2D	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (27)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
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
Dystonia	Associate	39525553
Dystonic Disorders	Associate	39525553
Epilepsy	Associate	34680045
Fetal Growth Retardation	Stimulate	36430274
Heredodegenerative Disorders Nervous System	Associate	24058541
Laryngeal Neoplasms	Associate	36347825
Li Fraumeni Syndrome	Associate	31982899
Macular Degeneration	Associate	33507209
Neoplasms	Associate	32487141
Neuroaxonal Dystrophies	Associate	31982899
Neurodegenerative Diseases	Associate	35427157
Neurologic Manifestations	Associate	33507209, 34680045
Neuronal Ceroid Lipofuscinoses	Associate	19383612, 23464991, 24058541, 28468312, 28542837, 31982899, 33507209, 34680045, 35921411, 36368077, 38141358, 39525553, 7942847, 8661106
Retinal Dystrophies	Associate	33507209, 40384762
Seizures	Associate	28542837, 33507209
Vision Disorders	Associate	34680045
von Hippel Lindau Disease	Associate	32487141

CLN5 (CLN5 lysosomal BMP synthase)