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

Gene Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	55512
Gene name Gene Name - the full gene name approved by the HGNC.	Sphingomyelin phosphodiesterase 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SMPD3
Synonyms (NCBI Gene) Gene synonyms aliases	NSMASE2
Chromosome Chromosome number	16
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	16q22.1

Show/Hide all(61)

miRTarBase ID	miRNA	Experiments	Reference
MIRT028920	hsa-miR-26b-5p	Microarray	19088304
MIRT1373834	hsa-miR-1245b-5p	CLIP-seq
MIRT1373835	hsa-miR-1283	CLIP-seq
MIRT1373836	hsa-miR-1299	CLIP-seq
MIRT1373837	hsa-miR-1911	CLIP-seq
MIRT1373838	hsa-miR-3121-3p	CLIP-seq
MIRT1373839	hsa-miR-3142	CLIP-seq
MIRT1373840	hsa-miR-345	CLIP-seq
MIRT1373841	hsa-miR-4318	CLIP-seq
MIRT1373842	hsa-miR-4469	CLIP-seq
MIRT1373843	hsa-miR-4474-3p	CLIP-seq
MIRT1373844	hsa-miR-4532	CLIP-seq
MIRT1373845	hsa-miR-4732-3p	CLIP-seq
MIRT1373846	hsa-miR-4782-5p	CLIP-seq
MIRT1373847	hsa-miR-494	CLIP-seq
MIRT1373848	hsa-miR-516b	CLIP-seq
MIRT1373849	hsa-miR-634	CLIP-seq
MIRT1373850	hsa-miR-765	CLIP-seq
MIRT1373851	hsa-miR-875-3p	CLIP-seq
MIRT1373852	hsa-miR-943	CLIP-seq
MIRT2111323	hsa-miR-1262	CLIP-seq
MIRT2111324	hsa-miR-1301	CLIP-seq
MIRT2111325	hsa-miR-1343	CLIP-seq
MIRT2111326	hsa-miR-2110	CLIP-seq
MIRT2111327	hsa-miR-2392	CLIP-seq
MIRT2111328	hsa-miR-2467-5p	CLIP-seq
MIRT2111329	hsa-miR-2682	CLIP-seq
MIRT2111330	hsa-miR-2861	CLIP-seq
MIRT2111331	hsa-miR-3135b	CLIP-seq
MIRT2111332	hsa-miR-3180	CLIP-seq
MIRT2111333	hsa-miR-3180-3p	CLIP-seq
MIRT2111334	hsa-miR-3192	CLIP-seq
MIRT2111335	hsa-miR-3196	CLIP-seq
MIRT2111336	hsa-miR-3612	CLIP-seq
MIRT2111337	hsa-miR-3689a-3p	CLIP-seq
MIRT2111338	hsa-miR-3689c	CLIP-seq
MIRT2111339	hsa-miR-4271	CLIP-seq
MIRT2111340	hsa-miR-4443	CLIP-seq
MIRT2111341	hsa-miR-449c	CLIP-seq
MIRT2111342	hsa-miR-4504	CLIP-seq
MIRT2111343	hsa-miR-4506	CLIP-seq
MIRT2111344	hsa-miR-4660	CLIP-seq
MIRT2111345	hsa-miR-4701-3p	CLIP-seq
MIRT2111346	hsa-miR-4725-3p	CLIP-seq
MIRT2111347	hsa-miR-4728-5p	CLIP-seq
MIRT2111348	hsa-miR-4731-5p	CLIP-seq
MIRT2111349	hsa-miR-5047	CLIP-seq
MIRT2111350	hsa-miR-550a	CLIP-seq
MIRT2111351	hsa-miR-650	CLIP-seq
MIRT2111352	hsa-miR-661	CLIP-seq
MIRT2111353	hsa-miR-940	CLIP-seq
MIRT2111324	hsa-miR-1301	CLIP-seq
MIRT2111329	hsa-miR-2682	CLIP-seq
MIRT2334448	hsa-miR-3127-3p	CLIP-seq
MIRT2111341	hsa-miR-449c	CLIP-seq
MIRT2334449	hsa-miR-4522	CLIP-seq
MIRT2111344	hsa-miR-4660	CLIP-seq
MIRT2111349	hsa-miR-5047	CLIP-seq
MIRT2334450	hsa-miR-760	CLIP-seq
MIRT2111353	hsa-miR-940	CLIP-seq
MIRT2394894	hsa-miR-149	CLIP-seq

Show/Hide all(53)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000137	Component	Golgi cis cisterna	IEA
GO:0000139	Component	Golgi membrane	IEA
GO:0001786	Function	Phosphatidylserine binding	ISS
GO:0001932	Process	Regulation of protein phosphorylation	IEA
GO:0001958	Process	Endochondral ossification	IEA
GO:0002244	Process	Hematopoietic progenitor cell differentiation	IEA
GO:0002685	Process	Regulation of leukocyte migration	IEA
GO:0003433	Process	Chondrocyte development involved in endochondral bone morphogenesis	IEA
GO:0004620	Function	Phospholipase activity	IBA	21873635
GO:0004767	Function	Sphingomyelin phosphodiesterase activity	IBA	21873635
GO:0004767	Function	Sphingomyelin phosphodiesterase activity	ISS
GO:0005515	Function	Protein binding	IPI	20080539
GO:0005576	Component	Extracellular region	IEA
GO:0005737	Component	Cytoplasm	IBA	21873635
GO:0005886	Component	Plasma membrane	ISS
GO:0005886	Component	Plasma membrane	TAS
GO:0006672	Process	Ceramide metabolic process	IEA
GO:0006684	Process	Sphingomyelin metabolic process	IBA	21873635
GO:0006684	Process	Sphingomyelin metabolic process	ISS
GO:0006685	Process	Sphingomyelin catabolic process	IEA
GO:0006687	Process	Glycosphingolipid metabolic process	TAS
GO:0015774	Process	Polysaccharide transport	IEA
GO:0030072	Process	Peptide hormone secretion	IEA
GO:0030282	Process	Bone mineralization	IEA
GO:0030509	Process	BMP signaling pathway	IEA
GO:0032963	Process	Collagen metabolic process	IEA
GO:0035264	Process	Multicellular organism growth	IEA
GO:0042802	Function	Identical protein binding	IEA
GO:0043491	Process	Protein kinase B signaling	IEA
GO:0045840	Process	Positive regulation of mitotic nuclear division	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0048008	Process	Platelet-derived growth factor receptor signaling pathway	IEA
GO:0048286	Process	Lung alveolus development	IEA
GO:0048661	Process	Positive regulation of smooth muscle cell proliferation	IEA
GO:0061035	Process	Regulation of cartilage development	IEA
GO:0061751	Function	Neutral sphingomyelin phosphodiesterase activity	IEA
GO:0070300	Function	Phosphatidic acid binding	ISS
GO:0070301	Process	Cellular response to hydrogen peroxide	IEA
GO:0070314	Process	G1 to G0 transition	IEA
GO:0071286	Process	Cellular response to magnesium ion	IEA
GO:0071356	Process	Cellular response to tumor necrosis factor	IEA
GO:0071461	Process	Cellular response to redox state	IEA
GO:0071897	Process	DNA biosynthetic process	IEA
GO:0085029	Process	Extracellular matrix assembly	IEA
GO:0090520	Process	Sphingolipid mediated signaling pathway	IEA
GO:0097187	Process	Dentinogenesis	IEA
GO:0098868	Process	Bone growth	IEA
GO:0140014	Process	Mitotic nuclear division	IEA
GO:0140052	Process	Cellular response to oxidised low-density lipoprotein particle stimulus	IEA
GO:1900126	Process	Negative regulation of hyaluronan biosynthetic process	IEA
GO:1901653	Process	Cellular response to peptide	IEA
GO:1903543	Process	Positive regulation of exosomal secretion	ISS
GO:2000304	Process	Positive regulation of ceramide biosynthetic process	TAS

MIM	HGNC	e!Ensembl
605777	14240	ENSG00000103056

Protein

UniProt ID

Q9NY59

Protein name

Sphingomyelin phosphodiesterase 3 (EC 3.1.4.12) (Neutral sphingomyelinase 2) (nSMase-2) (nSMase2) (Neutral sphingomyelinase II)

Protein function

Catalyzes the hydrolysis of sphingomyelin to form ceramide and phosphocholine. Ceramide mediates numerous cellular functions, such as apoptosis and growth arrest, and is capable of regulating these 2 cellular events independently. Also hydrolyze

PDB

5UVG

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF03372	Exo_endo_phos	319 → 627	Endonuclease/Exonuclease/phosphatase family	Domain

Tissue specificity

TISSUE SPECIFICITY: Predominantly expressed in brain. {ECO:0000269|PubMed:10823942}.

Sequence

MVLYTTPFPNSCLSALHCVSWALIFPCYWLVDRLAASFIPTTYEKRQRADDPCCLQLLCT
ALFTPIYLALLVASLPFAFLGFLFWSPLQSARRPYIYSRLEDKGLAGGAALLSEWKGTGP
GKSFCFATANVCLLPDSLARVNNLFNTQARAKEIGQRIRNGAARPQIKIYIDSPTNTSIS
AASFSSLVSPQGGDGVARAVPGSIKRTASVEYKGDGGRHPGDEAANGPASGDPVDSSSPE
DACIVRIGGEEGGRPPEADDPVPGGQARNGAGGGPRGQTPNHNQQDGDSGSLGSPSASRE
SLVKGRAGPDTSASGEPGANSKLLYKASVVKKAAARRRRHPDEAFDHEVSAFFPANLDFL
CLQEVFDKRAATKLKEQLHGYFEYILYDVGVYGCQGCCSFKCLNSGLLFASRYPIMDVAY
HCYPNKCNDDALASKGALFLKVQVGSTPQDQRIVGYIACTHLHAPQEDSAIRCGQLDLLQ
DWLADFRKSTSSSSAANPEELVAFDVVCGDFNFDNCSSDDKLEQQHSLFTHYRDPCRLGP
GEEKPWAIGTLLDTNGLYDEDVCTPDNLQKVLESEEGRREYLAFPTSKSSGQKGRKELLK
GNGRRIDYMLHAEEGLCPDWKAEVEEFSFITQLSGLTDHLPVAMRLMVSSGEEEA

Sequence length

655

Interactions

View interactions

	KEGG		Reactome
	Sphingolipid metabolism Metabolic pathways		Glycosphingolipid metabolism TNFR1-mediated ceramide production

Show/Hide Causal Diseases (3)

Disease term	Disease name	dbSNP ID	References
Causal
Leukemia	leukemia	rs121909646, rs121913488, rs587776834, rs752746786, rs869312821, rs767454740, rs1554564297	18283525
Myelodysplastic syndrome	MYELODYSPLASTIC SYNDROME	rs193303018, rs387906631, rs1576745225, rs373145711, rs752746786, rs377023736, rs373221034, rs1576749014, rs1600586587	18283525
Schizophrenia	Schizophrenia	rs13447324, rs387906932, rs387906933, rs863223354, rs863223355, rs776061422, rs863223349, rs748809996, rs759748655, rs863223353, rs863223350, rs863223356, rs781821239, rs863223348, rs863223346 View all (12 more)	31374203

Show/Hide Unknown Diseases (1)

Disease term	Disease name	Evidence	References	Source
Unknown
Metabolic Syndrome	Metabolic Syndrome			GWAS

Show/Hide Text Mining Associations (23)

Disease Name	Relationship Type	References
Associations from Text Mining
Asthma	Associate	25335167
Breast Neoplasms	Associate	15051724, 18403594, 25428807, 25833198
Calcinosis	Associate	25711438
Carcinoma Hepatocellular	Associate	24012984
Dermatitis Atopic	Inhibit	35462437
Endometrial Neoplasms	Associate	37322935
Giant Cell Tumor of Bone	Associate	34096319
Hearing Loss	Associate	34758154
Ige Responsiveness Atopic	Associate	30923181
Inflammation	Associate	17085432, 33033337
Leukemia	Associate	20836852
Nasopharyngeal Carcinoma	Associate	27350400
Neoplasms	Inhibit	22415137, 24012984
Neoplasms	Associate	30890560, 37322935, 38095640
Nervous System Diseases	Stimulate	22258513
Neurodegenerative Diseases	Associate	30890560
Niemann Pick Disease Type C	Associate	40294966
Obesity	Associate	29518789
Obesity	Stimulate	33033337
Pancreatic Neoplasms	Associate	38095640
Psoriasis	Associate	27185339
Pulmonary Disease Chronic Obstructive	Associate	33106845
Tachycardia Sinoatrial Nodal Reentry	Stimulate	34737220

SMPD3 (sphingomyelin phosphodiesterase 3)