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SMPD1 (sphingomyelin phosphodiesterase 1)

Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
6609
Gene nameGene Name - the full gene name approved by the HGNC.
Sphingomyelin phosphodiesterase 1
Gene symbolGene Symbol - the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name.
SMPD1
SynonymsGene synonyms aliases
ASM, ASMASE, NPD
ChromosomeChromosome number
11
Chromosome locationChromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
11p15.4
SummarySummary of gene provided in NCBI Entrez Gene.
The protein encoded by this gene is a lysosomal acid sphingomyelinase that converts sphingomyelin to ceramide. The encoded protein also has phospholipase C activity. Defects in this gene are a cause of Niemann-Pick disease type A (NPA) and Niemann-Pick di
SNPsSNP information provided by dbSNP.
SNP ID Visualize variation Clinical significance Consequence
rs1803161 G>A,C Pathogenic, uncertain-significance Intron variant, missense variant, 5 prime UTR variant, coding sequence variant, non coding transcript variant
rs120074117 G>A,C,T Likely-pathogenic, pathogenic Coding sequence variant, non coding transcript variant, missense variant
rs120074118 GCC>- Pathogenic Coding sequence variant, non coding transcript variant, inframe deletion, 3 prime UTR variant
rs120074119 G>A Likely-pathogenic Coding sequence variant, non coding transcript variant, missense variant, 3 prime UTR variant
rs120074120 T>A Pathogenic Coding sequence variant, intron variant, 5 prime UTR variant, stop gained, non coding transcript variant
miRNAmiRNA information provided by mirtarbase database.
miRTarBase ID miRNA Experiments Reference
MIRT648380 hsa-miR-3184-3p HITS-CLIP 23824327
MIRT648379 hsa-miR-3691-3p HITS-CLIP 23824327
MIRT648378 hsa-miR-1289 HITS-CLIP 23824327
MIRT648377 hsa-miR-4294 HITS-CLIP 23824327
MIRT648376 hsa-miR-516b-5p HITS-CLIP 23824327
Transcription factors
Transcription factor Regulation Reference
SP1 Activation 10224156
Gene ontology (GO)Gene ontology information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0001778 Process Plasma membrane repair IDA 20530211
GO:0004767 Function Sphingomyelin phosphodiesterase activity IDA 9660788, 21098024, 22573858
GO:0004767 Function Sphingomyelin phosphodiesterase activity TAS
GO:0005515 Function Protein binding IPI 16787399, 21157428
GO:0005615 Component Extracellular space IBA 21873635
Other IDsOther ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM
HGNC
e!Ensembl
Protein
UniProt ID P17405
Protein name Sphingomyelin phosphodiesterase (EC 3.1.4.12) (EC 3.1.4.3) (Acid sphingomyelinase) (aSMase) [Cleaved into: Sphingomyelin phosphodiesterase, processed form]
Protein function Converts sphingomyelin to ceramide (PubMed:12563314, PubMed:1840600, PubMed:18815062, PubMed:25339683, PubMed:25920558, PubMed:27659707, PubMed:33163980). Exists as two enzymatic forms that arise from alternative trafficking of a single protein
PDB 5I81 , 5I85 , 5I8R , 5JG8
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00149 Metallophos
201 463
Calcineurin-like phosphoesterase
Domain
Sequence
MPRYGASLRQSCPRSGREQGQDGTAGAPGLLWMGLVLALALALALALALSDSRVLWAPAE
AHPLSPQGHPARLHRIVPRLRDVFGWGNLTCPICKGLFTAINLGLKKEPNVARVGSVAIK
LCNLLKIAPPAVCQSIVHLFEDDMVEVWRRSVLSPSEACGLLLGSTCGHWDIFSSWNISL
PTVPKPPPKPPSPPAPGAPVSRILFLTDLHWDHDYLEGTDPDCADPLCCRRGSGLPPASR
PGAGYWGEYSKCDLPLRTLESLLSGLGPAGPFDMVYWTGDIPAHDVWHQTRQDQLRALTT
VTALVRKFLGPVPVYPAVGNHESTPVNSFPPPFIEGNHSSRWLYEAMAKAWEPWLPAEAL
RTLRIGGFYALSPYPGLRLISLNMNFCSRENFWLLINSTDPAGQLQWLVGELQAAEDRGD
KVHIIGHIPPGHCLKSWSWNYYRIVARYENTLAAQFFGHTHVD
EFEVFYDEETLSRPLAV
AFLAPSATTYIGLNPGYRVYQIDGNYSGSSHVVLDHETYILNLTQANIPGAIPHWQLLYR
ARETYGLPNTLPTAWHNLVYRMRGDMQLFQTFWFLYHKGHPPSEPCGTPCRLATLCAQLS
ARADSPALCRHLMPDGSLPEAQSLWPRPLFC
Sequence length 631
Interactions View interactions
PathwaysPathway information has different metabolic/signaling pathways associated with genes. Each record is hyperlinked to a complete information page which also includes links to the KEGG/Reactome pathway database.
 
KEGG
 
Reactome
  Sphingolipid metabolism
Metabolic pathways
Sphingolipid signaling pathway
Lysosome
Necroptosis
  Glycosphingolipid metabolism
Associated diseases
Causal
Disease name Disease term dbSNP ID References
Anemia Iron-Refractory Iron Deficiency Anemia rs118204044, rs118204045, rs118204046, rs121918330, rs869320719, rs869312029, rs121918332, rs869320724, rs767094129, rs786205058, rs786205059, rs137853119, rs137853120, rs137853121, rs1384933966, rs137853122, rs137853123, rs786205060, rs267607121, rs121908584, rs80338697, rs80338699, rs120074166, rs120074167, rs1050828, rs74575103, rs137852314, rs5030868, rs137852316, rs137852317, rs137852318, rs137852319, rs137852320, rs137852321, rs137852322, rs137852323, rs137852324, rs72554665, rs387906468, rs5030872, rs137852326, rs137852333, rs137852327, rs137852328, rs137852329, rs137852330, rs137852331, rs137852332, rs137852334, rs137852335, rs137852336, rs137852339, rs76645461, rs137852340, rs137852341, rs78478128, rs137852343, rs137852344, rs137852345, rs587776730, rs137852346, rs137852347, rs137852349, rs2070404412, rs2070350038, rs2070350009, rs137852303, rs137852304, rs33946267, rs34378160, rs33933298, rs11549407, rs35724775, rs34598529, rs41469945, rs267607201, rs80338694, rs80338696, rs387907018, rs398123546, rs78365220, rs587777100, rs587777101, rs483352840, rs869312752, rs765487627, rs1557229599, rs1557230040, rs1555524842, rs782090947, rs1358275550, rs1557229736, rs1557230573, rs1556323334, rs1233124208, rs1293528130, rs146864395, rs1595503440, rs1603411214, rs137852325, rs1575247302, rs1603411177, rs1336651679, rs782322505
Apraxia Apraxias rs121908377, rs121908378, rs1135401820, rs1178491246, rs1584969672
Attention deficit hyperactivity disorder Attention deficit hyperactivity disorder rs120074176, rs786205019
Cholelithiasis Cholelithiasis rs121918440, rs72552778, rs387906528, rs759202962, rs377160065, rs1051861187, rs757693457, rs752563752
Unknown
Disease name Disease term dbSNP ID References
Bipolar disorder Bipolar Disorder
Cirrhosis Cirrhosis rs119465999, rs144369314, rs8056684, rs112053857, rs75998507
Coronary arteriosclerosis Coronary Arteriosclerosis
Dwarfism Dwarfism

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