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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

SMPD1 Gene

protein-coding GIFtS: 69
GCID: GC11P006411

sphingomyelin phosphodiesterase 1, acid lysosomal

Explore 56 diseases affiliated with
SMPD1 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Sphingomyelin Phosphodiesterase 1, Acid Lysosomal¹ ²		ASMASE²
ASM¹ ² ³		Sphingomyelin Phosphodiesterase²
Acid Sphingomyelinase² ³		EC 3.1.4.12³
NPD² ⁵		ASMase¹

External Ids:	HGNC: 11120¹	Entrez Gene: 6609²	Ensembl: ENSG00000166311⁷	OMIM: 607608⁵	UniProtKB: P17405³

Export aliases for SMPD1 gene to outside databases

Previous GC identifers: GC11P007154 GC11P006873 GC11P006370 GC11P006376 GC11P006368 GC11P006070

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for SMPD1:

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 disease type B (NPB). Multiple transcript variants encoding different isoforms have been

identified. (provided by RefSeq, Jul 2010)

UniProtKB/Swiss-Prot: ASM_HUMAN, P17405

Function: Converts sphingomyelin to ceramide. Also has phospholipase C activities toward

1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol. Isoform 2 and isoform 3 have lost catalytic

activity

Gene Wiki entry for SMPD1 (Sphingomyelin phosphodiesterase 1)

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000011.9 NC_018922.1 NT_009237.18

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the SMPD1 gene promoter:
NF-1 Nkx2-5 RORalpha2 NF-AT NF-AT4 NF-AT2 NF-AT3 ZID Meis-1 NF-AT1
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: SMPD1 promoter sequence

Search SABiosciences Chromatin IP Primers for SMPD1

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SMPD1

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11p15.4-p15.1 Ensembl cytogenetic band: 11p15.4 HGNC cytogenetic band: 11p15.4-p15.1

SMPD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMPD1 gene location

GeneLoc information about chromosome 11 GeneLoc Exon Structure

GeneLoc location for GC11P006411: view genomic region (about GC identifiers)

Start:	6,411,644 bp from pter	End:	6,416,228 bp from pter
Size:	4,585 bases	Orientation:	plus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: ASM_HUMAN, P17405 (See protein sequence)

Recommended Name: Sphingomyelin phosphodiesterase precursor

Size: 629 amino acids; 69752 Da

Subunit: Monomer

Subcellular location: Lysosome

Miscellaneous: There are two types of sphingomyelinases: ASM (acid), and NSM (neutral)

Secondary accessions: P17406 Q13811 Q16837 Q16841

Alternative splicing: 3 isoforms: P17405-1 P17405-2 P17405-3 (Low abundance (<1%))

Explore the universe of human proteins at neXtProt for SMPD1: NX_P17405

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_P17405

SMPD1 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (2 alternative transcripts):

NP_000534.3 NP_001007594.2

ENSEMBL proteins:

ENSP00000340409 ENSP00000431479 ENSP00000434353 ENSP00000435350 ENSP00000435950

ENSP00000432625 ENSP00000436278 ENSP00000299397 ENSP00000349203

Reactome Protein details: P17405
Human Recombinant Protein Products:

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	Sino Biological Recombinant Protein for SMPD1
	Browse ProSpec Recombinant Proteins
	Uscn Proteins for SMPD1

Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005615	extracellular space	IEA	--
GO:0042599	lamellar body	IEA	--
GO:0043202	lysosomal lumen	TAS	--

SMPD1 for ontologies About GeneDecksing

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	Browse Enzo Life Sciences for kits & assays
	Uscn ELISAs and CLIAs for SMPD1

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

SMPD1 for domains About GeneDecksing

4 InterPro domains/families:

IPR004843 Metallo_PEstase_dom

IPR011160 Sphingomy_PDE

IPR011001 Saposin-like

IPR008139 SaposinB

Graphical View of Domain Structure for InterPro Entry P17405

ProtoNet protein and cluster: P17405

1 Blocks protein family: IPB008139 Saposin B

UniProtKB/Swiss-Prot: ASM_HUMAN, P17405

Similarity: Belongs to the acid sphingomyelinase family

Similarity: Contains 1 saposin B-type domain

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

UniProtKB/Swiss-Prot: ASM_HUMAN, P17405

Function: Converts sphingomyelin to ceramide. Also has phospholipase C activities toward

1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol. Isoform 2 and isoform 3 have lost catalytic

activity

Catalytic activity: Sphingomyelin + H(2)O = N-acylsphingosine + phosphocholine

Genatlas biochemistry entry for SMPD1:

sphingomyelin phosphodiesterase 1,lysosomal (acid sphingomyelinase),hydrolyzing sphingomyelin to ceramide and

phosphocholine,activated by TNFRSF1A and initiating the apoptotic pathway

Enzyme Number (IUBMB): EC 3.1.4.12¹

miRNA Products:		OriGene 3'-UTR Clone (see all 2): SMPD1 Browse MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SMPD1
		6 QIAGEN miScript miRNA Assays for microRNAs that regulate SMPD1:
		hsa-miR-424 hsa-miR-15a hsa-miR-16 hsa-miR-195 hsa-miR-497 hsa-miR-15b
		SwitchGear 3'UTR luciferase reporter plasmid: SMPD1 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for SMPD1 (see all 7) OriGene shRNA RFP: SMPD1 OriGene siRNA: SMPD1
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SMPD1

Gene Editing
Products:

DNA2.0 Custom Protein Engineering Service for SMPD1

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		GenScript: all cDNA clones in your preferred vector (see all 2): SMPD1 (NM_000543)
		Browse Sino Biological Human cDNA Clones
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		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SMPD1

Cell Line Products:		GenScript Custom overexpressing Cell Line Services for SMPD1
		LifeMap BioReagents: cell line associated with SMPD1: PureStem ES-210, Ecto-ntu Progenitor

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMPD1

Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0004767	sphingomyelin phosphodiesterase activity	IEA	--
GO:0016787	hydrolase activity	--	--
GO:0016798	hydrolase activity, acting on glycosyl bonds	IEA	--

SMPD1 for ontologies About GeneDecksing

4 GenomeRNAi human phenotypes for SMPD1:

Decreased POU5F1-GFP protein e

Downregulation of NF-kappaB pa

Increased cell number in S and

Animal Models:
Mouse knock-outs for SMPD1: Smpd1^tm1Wst Smpd1^tm1Esc
11 MGI mutant phenotypes (inferred from 2 alleles) (MGI details for Smpd1):

behavior/neurological	cellular	growth/size	hematopoietic system	homeostasis/metabolism
immune system	liver/biliary system	mortality/aging	nervous system	reproductive system
respiratory system

SMPD1 for phenotypes About GeneDecksing

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways - 5/18 super-pathways (see all 18) About this table

See pathways by source

Super-pathway

contained gene-specific pathways

Sphingolipid metabolism

	Sphingolipid metabolism	1.00			Sphingolipid metabolism	0.54
	Glycosphingolipid metabolism	0.54

Metabolism

	Metabolism	1.00			Metabolism of lipids and lipoproteins	0.34
	Metabolic pathways	0.38

TNF-Induced Apoptosis Implicating Sphingolipids

TNF-Induced Apoptosis Implicating Sphingolipids

1.00

Ceramide Pathway

0.32

TRAIL signaling pathway

TRAIL signaling pathway

1.00

FAS (CD95) signaling pathway

0.30

Ca, cAMP and Lipid Signaling

Ca, cAMP and Lipid Signaling

1.00

Pathway sources
See GeneCards unified pathways
Show all pathways

5/9 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for SMPD1 (see all 9)

	Caspase Cascade
	S-1P Stimulated Signaling
	TNF-Induced Apoptosis Implicating Sphingolipids
	LDL Oxidation in Atherogenesis
	Fas Signaling

1 Cell Signaling Technology (CST) Pathway for SMPD1

Ca, cAMP and Lipid Signaling

5/7 BioSystems Pathways for SMPD1 (see all 7)

	Ovarian Infertility Genes
	sphingomyelin metabolism
	IL2 signaling events mediated by PI3K
	FAS (CD95) signaling pathway
	TRAIL signaling pathway

4 Reactome Pathways for SMPD1

	Sphingolipid metabolism
	Glycosphingolipid metabolism
	Metabolism
	Metabolism of lipids and lipoproteins

3 Kegg Pathways (Kegg details for SMPD1):

	Sphingolipid metabolism
	Metabolic pathways
	Lysosome

SMPD1 for pathways About GeneDecksing

Interactions:

SABiosciences Gene Network Central^TM Interacting Genes and Proteins Network for SMPD1

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

5/56 Interacting proteins for SMPD1 (P17405^{2, 3} ENSP00000340409⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 56)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
CASP7	P55210²^,³	MINT-8095356 MINT-8095286 MINT-8095296 MINT-8095342 MINT-8095383 MINT-8095372 I2D: score=1
CASP8	Q14790²^,³, ENSP00000351273⁴	MINT-8095252 MINT-8095356 MINT-8095243 I2D: score=1 STRING: ENSP00000351273
ANXA7	P20073²^,³	MINT-8248724 I2D: score=2
DUSP23	Q9BVJ7²^,³	MINT-8254754 I2D: score=2
NR1H2	P55055²^,³	MINT-8263940 I2D: score=2

About this table

Gene Ontology (GO): 5/16 biological process terms (GO ID links to tree view) (see all 16): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006644	phospholipid metabolic process	TAS	--
GO:0006665	sphingolipid metabolic process	TAS	--
GO:0006684	sphingomyelin metabolic process	TAS	7670466
GO:0006685	sphingomyelin catabolic process	IEA	--
GO:0006687	glycosphingolipid metabolic process	TAS	--

SMPD1 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

SMPD1 for compounds About GeneDecksing

EMD Millipore small molecules for SMPD1:
Small Molecule - inhibitor

Enzo Life Sciences drugs & compounds for SMPD1

Browse Tocris compounds for SMPD1

10/152 HMDB Compounds for SMPD1 (see all 152) About this table

Compound	Synonyms	CAS #	PubMed Ids
3-O-Sulfogalactosylceramide (d18:1/12:0)	Sulfatide (d18:1/12:0) (see all 13)	852100-88-0	--
3-O-Sulfogalactosylceramide (d18:1/14:0)	Sulfatide (d18:1/14:0) (see all 13)	--	--
3-O-Sulfogalactosylceramide (d18:1/16:0)	Sulfatide (d18:1/16:0) (see all 13)	862509-48-6	--
3-O-Sulfogalactosylceramide (d18:1/18:0)	Sulfatide (d18:1/18:0) (see all 13)	244215-65-4	--
3-O-Sulfogalactosylceramide (d18:1/18:1(9Z))	Sulfatide (d18:1/18:1(9Z)) (see all 13)	--	--
3-O-Sulfogalactosylceramide (d18:1/20:0)	Sulfatide (d18:1/20:0) (see all 13)	265096-81-9	--
3-O-Sulfogalactosylceramide (d18:1/22:0)	Sulfatide (d18:1/22:0) (see all 13)	265096-83-1	--
3-O-Sulfogalactosylceramide (d18:1/24:0)	Sulfatide (d18:1/24:0) (see all 16)	151122-71-3	--
3-O-Sulfogalactosylceramide (d18:1/24:1(15Z))	Sulfatide (d18:1/24:1(15Z)) (see all 13)	151057-28-2	--
3-O-Sulfogalactosylceramide (d18:1/26:1(17Z))	Sulfatide (d18:1/26:1(17Z)) (see all 13)	928346-40-1	--

1 DrugBank Compound for SMPD1 About this table

Compound	Synonyms	CAS #	Type	Actions	PubMed Ids
Desipramine	Demethylimipramine (see all 12)	50-47-5	target	inhibitor	7945993 20502000 16803890 14689449 15705795 14960314

10/48 Novoseek chemical compound relationships for SMPD1 gene (see all 48) About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
ceramide	94.5	266	9516458 (6), 15888438 (5), 19635928 (5), 16636669 (4) (see all 99)
fantofarone	86.4	6	10930579 (1), 9716505 (1), 17329567 (1), 15201971 (1) (see all 5)
ceramides	72.1	8	16034716 (2), 9500792 (1), 17329567 (1), 19416641 (1) (see all 6)
phosphorylcholine	71.6	27	8053910 (1), 7727545 (1), 12631268 (1), 14515991 (1) (see all 16)
ceramide 1-phosphate	69.2	6	14523050 (2), 15978590 (1), 18510950 (1), 19416641 (1)
glucosylceramide	68.4	5	15271800 (2), 12586734 (1), 15679111 (1)
desipramine	63.4	20	16803890 (3), 15705795 (2), 7945993 (1), 14689449 (1) (see all 12)
sphingosine	63.1	4	16034716 (2), 18547682 (1), 12485859 (1)
mannose 6-phosphate	61.8	2	16787399 (2)
myriocin	61.5	1	16131844 (1)

Search CenterWatch for drugs/clinical trials and news about SMPD1 / ASM

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for SMPD1 gene (2 alternative transcripts):

NM_000543.4 NM_001007593.2

Unigene Cluster for SMPD1:

Sphingomyelin phosphodiesterase 1, acid lysosomal

Hs.498173 [show with all ESTs]

Unigene Representative Sequence: NM_000543

12 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000342245(uc021qcz.1 uc001mcv.2 uc009yew.3 uc001mcw.3 uc021qda.1)

ENST00000533196 ENST00000530395 ENST00000534405 ENST00000527275 ENST00000533123

ENST00000531303 ENST00000526280 ENST00000531336 ENST00000532367 ENST00000299397

ENST00000356761(uc009yex.3)

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		6 QIAGEN miScript miRNA Assays for microRNAs that regulate SMPD1:
		hsa-miR-424 hsa-miR-15a hsa-miR-16 hsa-miR-195 hsa-miR-497 hsa-miR-15b
		SwitchGear 3'UTR luciferase reporter plasmid: SMPD1 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for SMPD1 (see all 7) OriGene shRNA RFP: SMPD1 OriGene siRNA: SMPD1
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SMPD1

Clone Products:		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for SMPD1 (see all 4) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SMPD1 (see all 2) OriGene custom cloning services � gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector (see all 2): SMPD1 (NM_000543)
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for SMPD1
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SMPD1

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		SABiosciences RT² qPCR Primer Assay in human, mouse, rat SMPD1
		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SMPD1
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SMPD1

Additional cDNA sequence:

AB209775.1 AK292388.1 HQ132745.1 HQ132746.1 HQ132747.1 HQ132748.1 M59916.1 X52678.1

X52679.1 X59960.1

11 DOTS entries:

DT.97789320 DT.87017024 DT.95141668 DT.92431744 DT.95141654 DT.95141666 DT.95259806 DT.100788912

DT.100788914 DT.120699666 DT.95141656

24/259 AceView cDNA sequences (see all 259):

CR615854 BQ684187 BX280171 BM558202 BM694250 BG939305 AI708247 R93922

BI818723 CD365316 BM977655 CA313760 BQ187351 BU197048 CA417896 CN482223

CA449771 AI223155 BU845962 CB850692 CA391680 BG032323 CK904688 BQ021596

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

SMPD1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GAGTAGAGGC

About this image

SMPD1 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

2 LifeMap In Vivo Development Anatomical Compartments/Cells

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Brain

Neural Tube

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See SMPD1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for SMPD1

SOURCE GeneReport for Unigene cluster: Hs.498173

SABiosciences Expression via Pathway-Focused PCR Array including SMPD1:

Molecular Toxicology PathwayFinder 384HT in human mouse rat

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for SMPD1 Browse OriGene validated miRNA SYBR primer pairs
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		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SMPD1
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SMPD1

In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMPD1

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for SMPD1 gene from 6/24 species (see all 24) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	SMPD1¹	sphingomyelin phosphodiesterase 1, acid lysosomal	68.03(n) 66.29(a)		419077 XM_003640615.1 XP_003640663.1
lizard (Anolis carolinensis)	Reptilia	SMPD1⁶	--	65(a)	1 ↔ 1	GL344762.1(9508-14800)
African clawed frog (Xenopus laevis)	Amphibia	Xl.2147²	Xenopus laevis transcribed sequence with weak similarity more	79.79(n)		BQ399327.1
zebrafish (Danio rerio)	Actinopterygii	CD597777.1²	--	73.1(n)		CD597777.1
fruit fly (Drosophila melanogaster)	Insecta	CG3376^{1 , 3}	sphingomyelin phosphodiesterase³ CG3376¹	38(a) (best of 3)³ 53.77(n)¹ 44.2(a)¹		60C4³ 37884¹ NM_138060.2¹ NP_611904.1¹
worm (Caenorhabditis elegans)	Secernentea	B0252.2³ asm-2¹	Spingomyelin phosphodiesterase³ Protein ASM-2¹	34(a) (best of 3)³ 46.13(n)¹ 41.21(a)¹		II(6910015-6912507)³ 181323¹ NM_077493.3¹ NP_509894.2¹

ENSEMBL Gene Tree for SMPD1 (if available)
TreeFam Gene Tree for SMPD1 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for SMPD1 gene

SMPDL3A² SMPDL3B²

1 SIMAP similar gene for SMPD1 using alignment to 18 protein entries: ASM_HUMAN (see all proteins):

ASM

SMPD1 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

UniProtKB/Swiss-Prot: ASM_HUMAN, P17405

Polymorphism: A common polymorphism arises from a variable number of hexanucleotide repeat sequence within the signal

peptide region

SNP ID	Valid	Clinical significance	Chr 11 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs120074124^1,2	C	pathogenic	6072313(+)	`AGCACT/CTGTGA`	4	/P /L	mis¹		1		EU	1321
rs120074127^1,2	C	pathogenic	6414910(+)	`ATTACC/G/TGAATT`	6	R G *	mis¹ stg¹		0	--	--	--	--
rs267607075^1,2	C	pathogenic	6415236(+)	`CCTGGA/C/TACCCA`	6	E A V	mis¹		0	--	--	--	--
rs120074117^1,2	C	pathogenic	6415434(+)	`TTACCG/TTGTGT`	4	R L	mis¹		1		EU	1323
rs11040883^1,2	C,F,A,H,	--	6068885(+)	`ATACCG/AACTTC`	2	--	us2k¹ tfbs³		18		NS EA NA WA	1688
rs77303315^1,2	F,	--	6069024(+)	`CTCTGG/CACAAC`	2	--	us2k¹		1		WA	118
rs72896262^1,2	C,F,	--	6069518(+)	`NNNNTT/CAGGGT`	2	--	us2k¹		2		WA NA	238
rs116685366^1,2	C,F,	--	6069572(+)	`TCTGTA/GAAGGA`	2	--	us2k¹		1		WA	118
rs78106294^1,2	C,	--	6069792(+)	`TGAGGG/AGAAGA`	2	--	us2k¹		2		NA	122
rs7103750^1,2	C,F,A,H,	--	6070414(+)	`CTGCCC/GGCCCT`	2	--	us2k¹		7		NS EA WA NA	658

HapMap Linkage Disequilibrium report for SMPD1 (6411644 - 6416228 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for SMPD1: --
Human Gene Mutation Database (HGMD): SMPD1

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SMPD1

DNA2.0 Custom Variant and Variant Library Synthesis for SMPD1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

SMPD1 for disorders           About GeneDecksing

OMIM gene information: 607608
OMIM disorders: 257200  607616
UniProtKB/Swiss-Prot: ASM_HUMAN, P17405

Defects in SMPD1 are the cause of Niemann-Pick disease type A (NPDA) [MIM:257200]; also known as Niemann-Pick

disease classical infantile form. It is an early-onset lysosomal storage disorder caused by failure to hydrolyze

sphingomyelin to ceramide. It results in the accumulation of sphingomyelin and other metabolically related lipids in

reticuloendothelial and other cell types throughout the body, leading to cell death. Niemann-Pick disease type A is a

primarily neurodegenerative disorder characterized by onset within the first year of life, mental retardation,

digestive disorders, failure to thrive, major hepatosplenomegaly, and severe neurologic symptoms. The severe

neurological disorders and pulmonary infections lead to an early death, often around the age of four. Clinical

features are variable. A phenotypic continuum exists between type A (basic neurovisceral) and type B (purely visceral)

forms of Niemann-Pick disease, and the intermediate types encompass a cluster of variants combining clinical features

of both types A and B

Defects in SMPD1 are the cause of Niemann-Pick disease type B (NPDB) [MIM:607616]; also known as Niemann-Pick

disease visceral form. It is a late-onset lysosomal storage disorder caused by failure to hydrolyze sphingomyelin to

ceramide. It results in the accumulation of sphingomyelin and other metabolically related lipids in

reticuloendothelial and other cell types throughout the body, leading to cell death. Clinical signs involve only

visceral organs. The most constant sign is hepatosplenomegaly which can be associated with pulmonary symptoms.

Patients remain free of neurologic manifestations. However, a phenotypic continuum exists between type A (basic

neurovisceral) and type B (purely visceral) forms of Niemann-Pick disease, and the intermediate types encompass a

cluster of variants combining clinical features of both types A and B. In Niemann-Pick disease type B, onset of the

first symptoms occurs in early childhood and patients can survive into adulthood

20/56 diseases for SMPD1 (see all 56): About MalaCards

niemann-pick disease pick's disease sea-blue histiocytosis beckwith-wiedemann syndrome

acid sphingomyelinase deficiency lysosomal storage disease familial adenomatous polyposis graft versus host disease

hemophagocytic lymphohistiocytosis hemihypertrophy mucolipidosis ii major depressive disorder

mucolipidosis gaucher's disease metabolic disorders cystic fibrosis

acute promyelocytic leukemia histiocytosis alcohol dependence atopic dermatitis

2 diseases from the University of Copenhagen DISEASES database for SMPD1:

Niemann-Pick disease Narcissistic personality disorder

10/35 Novoseek disease relationships for SMPD1 gene (see all 35) About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
niemann-pick diseases	97.9	123	16099409 (3), 19944693 (2), 17011332 (2), 11023983 (2) (see all 71)
niemann-picks disease type b	94	7	10515006 (1), 12436303 (1), 8225311 (1), 12142792 (1) (see all 7)
i-cell disease	71.1	2	15997205 (1), 8106525 (1)
niemann-picks disease type c	59.2	3	16143556 (1), 8025130 (1), 16802107 (1)
lysosomal storage diseases	49.9	2	1618760 (1), 7600574 (1)
lipidosis	47.5	3	14736491 (2), 2153272 (1)
hemihypertrophy	41	1	11310411 (1)
necrosis	36.2	15	11255263 (2), 7981153 (2), 16803890 (1), 10601312 (1) (see all 10)
oligodendroglioma	34.9	1	15086520 (1)
beckwith-wiedemann syndrome	27.3	4	11173664 (2), 11310411 (1)

Genatlas disease: SMPD1

Niemann-Pick disease,types A & B

GeneTests: SMPD1

Acid Sphingomyelinase Deficiency

Human Genome Epidemiology (HuGE) Navigator: SMPD1 (8 documents)

Export disorders for SMPD1 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for SMPD1 gene, integrated from 9 sources (see all 340):
(articles sorted by number of sources associating them with SMPD1)

Utopia: connect your pdf to the dynamic
world of online information

Identification and expression of five mutations in the human acid sphingomyelinase gene causing types A and B Niemann-Pick disease. Molecular evidence for genetic heterogeneity in the neuronopathic and non-neuronopathic forms. (PubMed id 1618760)^{1, 2, 9} Takahashi T.... Schuchman E.H. (1992)
Structural organization and complete nucleotide sequence of the gene encoding human acid sphingomyelinase (SMPD1). (PubMed id 1740330)^{1, 2, 9} Schuchman E.H.... Desnick R.J. (1992)
Niemann-Pick disease: a frequent missense mutation in the acid sphingomyelinase gene of Ashkenazi Jewish type A and B patients. (PubMed id 2023926)^{1, 2, 9} Levran O.... Schuchman E.H. (1991)
Sphingomyelin phosphodiesterase-1 (SMPD1) coding variants do not contribute to low levels of high-density lipoprotein cholesterol. (PubMed id 18088425)^{1, 2, 9} Dastani Z.... Marcil M. (2007)
Functional characterization of the N-glycosylation sites of human acid sphingomyelinase by site-directed mutagenesis. (PubMed id 9030779)^{1, 2, 9} Ferlinz K....Sandhoff K. (1997)
Identification and expression of a common missense mutation (L302P) in the acid sphingomyelinase gene of Ashkenazi Jewish type A Niemann- Pick disease patients. (PubMed id 1391960)^{1, 2, 9} Levran O.... Schuchman E.H. (1992)
Functional in vitro characterization of 14 SMPD1 mutations identified in Italian patients affected by Niemann Pick type B disease. (PubMed id 16010684)^{1, 2, 9} Dardis A....Pittis M.G. (2005)
Acid sphingomyelinase: identification of nine novel mutations among Italian Niemann Pick type B patients and characterization of in vivo functional in-frame start codon. (PubMed id 15241805)^{1, 2, 9} Pittis M.G.... Bembi B. (2004)
Identification and expression of a missense mutation (Y446C) in the acid sphingomyelinase gene from a Japanese patient with type A Niemann-Pick disease. (PubMed id 8693491)^{1, 2, 9} Takahashi T.... Takada G. (1995)
Acid sphingomyelinase deficiency. Phenotype variability with prevalence of intermediate phenotype in a series of twenty-five Czech and Slovak patients. A multi-approach study. (PubMed id 15877209)^{1, 2, 9} Pavlu-Pereira H....Elleder M. (2005)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 6609	HGNC: 11120	AceView: SMPD1	Ensembl:ENSG00000166311	euGenes: HUgn6609
ECgene: SMPD1	Kegg: 6609	H-InvDB: SMPD1

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for SMPD1	Pharmacogenomics, SNPs, Pathways
GeneReviews	http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SMPD1

Intellectual Property for SMPD1 gene
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Patent Information for SMPD1 gene:
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GeneCards and IP:
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sphingomyelin phosphodiesterase 1, acid lysosomal

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SMPD1 Gene

sphingomyelin phosphodiesterase 1, acid lysosomal

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