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

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	55512
Gene name	Sphingomyelin phosphodiesterase 3
Gene symbol	SMPD3
Synonyms (NCBI Gene)	NSMASE2
Chromosome	16
Chromosome location	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 (76)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000137	Component	Golgi cis cisterna	IEA
GO:0000139	Component	Golgi membrane	IEA
GO:0001501	Process	Skeletal system development	IEA
GO:0001503	Process	Ossification	IEA
GO:0001786	Function	Phosphatidylserine binding	IEA
GO:0001786	Function	Phosphatidylserine binding	ISS
GO:0001958	Process	Endochondral ossification	IEA
GO:0002063	Process	Chondrocyte development	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:0003824	Function	Catalytic activity	IEA
GO:0004767	Function	Sphingomyelin phosphodiesterase activity	IBA
GO:0004767	Function	Sphingomyelin phosphodiesterase activity	IDA	14741383
GO:0004767	Function	Sphingomyelin phosphodiesterase activity	IEA
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
GO:0005794	Component	Golgi apparatus	IEA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	ISS
GO:0005886	Component	Plasma membrane	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006665	Process	Sphingolipid metabolic process	IEA
GO:0006665	Process	Sphingolipid metabolic process	IEA
GO:0006672	Process	Ceramide metabolic process	IEA
GO:0006684	Process	Sphingomyelin metabolic process	IBA
GO:0006684	Process	Sphingomyelin metabolic process	IEA
GO:0006684	Process	Sphingomyelin metabolic process	ISS
GO:0006685	Process	Sphingomyelin catabolic process	IDA	14741383
GO:0006685	Process	Sphingomyelin catabolic process	IEA
GO:0006685	Process	Sphingomyelin catabolic process	TAS	10823942
GO:0007165	Process	Signal transduction	IEA
GO:0008081	Function	Phosphoric diester hydrolase activity	IDA	14741383
GO:0008081	Function	Phosphoric diester hydrolase activity	IEA
GO:0015774	Process	Polysaccharide transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0030072	Process	Peptide hormone secretion	IEA
GO:0030282	Process	Bone mineralization	IEA
GO:0030324	Process	Lung development	IEA
GO:0030509	Process	BMP signaling pathway	IEA
GO:0032963	Process	Collagen metabolic process	IEA
GO:0034614	Process	Cellular response to reactive oxygen species	IEA
GO:0035264	Process	Multicellular organism growth	IEA
GO:0042802	Function	Identical protein binding	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:0051216	Process	Cartilage development	IEA
GO:0051898	Process	Negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IEA
GO:0060348	Process	Bone development	IEA
GO:0060541	Process	Respiratory system development	IEA
GO:0061035	Process	Regulation of cartilage development	IEA
GO:0061751	Function	Neutral sphingomyelin phosphodiesterase activity	IEA
GO:0070300	Function	Phosphatidic acid binding	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:1900125	Process	Regulation of hyaluronan biosynthetic process	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

MIM	HGNC	e!Ensembl
605777	14240	ENSG00000103056

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

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (8)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEUKEMIA	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYELODYSPLASTIC SYNDROMES	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (46)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Aggressive Periodontitis	Aggressive Periodontitis	BEFREE	28221099		★★★★★ ★☆☆☆☆ Found in Text Mining only
Arteriosclerosis	Arteriosclerosis	BEFREE	29794115		★★★★★ ★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	Pubtator	25335167	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Atherosclerosis	Atherosclerosis	BEFREE	29794115		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	18836996, 19698806		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	15051724, 18403594, 25428807, 25833198	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Calcinosis	Calcinosis	Pubtator	25711438	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	24012984	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Chronic Kidney Diseases	Kidney Disease	BEFREE	31780737		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognitive disorder	BEFREE	27535912		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dermatitis Atopic	Atopic dermatitis	Pubtator	35462437	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	BEFREE	15764706, 31199918		★★★★★ ★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	37322935	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Giant Cell Tumor of Bone	Giant cell tumor of bone	Pubtator	34096319	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Guillain-Barre Syndrome	Guillain-Barre Syndrome	BEFREE	29601870		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	34758154	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperphosphatemia (disorder)	Hyperphosphatemia	BEFREE	31780737		★★★★★ ★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	BEFREE	27535912, 29725009		★★★★★ ★☆☆☆☆ Found in Text Mining only
leukemia	Leukemia	CTD_human_DG	18283525		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
leukemia	Leukemia	BEFREE	18299447		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Leukemia	Leukemia	Pubtator	20836852	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	18299447		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	LHGDN	18299447		★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	24012984, 29567647		★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver neoplasms	Liver neoplasms	BEFREE	29567647		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphoid leukemia	Lymphoid leukemia	LHGDN	18299447		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	18836996, 19698806		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	18299447, 19698806, 23439645, 23889969, 30890560, 30921693		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	18836996		★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	30866785		★★★★★ ★☆☆☆☆ Found in Text Mining only
MYELODYSPLASTIC SYNDROME	Myelodysplastic Syndrome	CTD_human_DG	18283525		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nasopharyngeal Carcinoma	Nasopharyngeal carcinoma	Pubtator	27350400	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	22415137, 23439645, 23487440, 24012984, 29567647		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nervous System Diseases	Nervous system disease	Pubtator	22258513	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
nervous system disorder	Nervous System Disorder	BEFREE	30921693, 31273753		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neurodegenerative Diseases	Neurodegenerative disorder	Pubtator	30890560	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	Pubtator	29518789	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	Pubtator	33033337	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteogenesis Imperfecta	Osteogenesis Imperfecta	BEFREE	31199918		★★★★★ ★☆☆☆☆ Found in Text Mining only
PACHYONYCHIA CONGENITA 3	Pachyonychia Congenita	BEFREE	19796718		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	38095640	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Panhypopituitarism	Panhypopituitarism	BEFREE	15764706		★★★★★ ★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	BEFREE	31555088		★★★★★ ★☆☆☆☆ Found in Text Mining only
Psoriasis	Psoriasis	Pubtator	27185339	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Pulmonary Disease Chronic Obstructive	Chronic obstructive pulmonary disease	Pubtator	33106845	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	GWASCAT_DG	31374203		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

SMPD3 (sphingomyelin phosphodiesterase 3)