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 2... See more...

Aliases for SMPD1 Gene

Aliases for SMPD1 Gene

  • Sphingomyelin Phosphodiesterase 1 2 3 5
  • Acid Sphingomyelinase 2 3 4
  • Sphingomyelin Phosphodiesterase 1, Acid Lysosomal 2 3
  • Sphingomyelin Phosphodiesterase 3 4
  • ASM 3 4
  • EC 3.1.4.12 4
  • ASMASE 3
  • ASMase 4
  • NPD 3

External Ids for SMPD1 Gene

Previous GeneCards Identifiers for SMPD1 Gene

  • GC11P007154
  • GC11P006873
  • GC11P006370
  • GC11P006376
  • GC11P006368
  • GC11P006070
  • GC11P006411

Summaries for SMPD1 Gene

Entrez Gene Summary for SMPD1 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 disease type B (NPB). Multiple transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2010]

GeneCards Summary for SMPD1 Gene

SMPD1 (Sphingomyelin Phosphodiesterase 1) is a Protein Coding gene. Diseases associated with SMPD1 include Niemann-Pick Disease, Type A and Niemann-Pick Disease, Type B. Among its related pathways are NGF Pathway and IL2 signaling events mediated by PI3K. Gene Ontology (GO) annotations related to this gene include hydrolase activity and sphingomyelin phosphodiesterase activity. An important paralog of this gene is SMPDL3A.

UniProtKB/Swiss-Prot Summary for SMPD1 Gene

  • Converts sphingomyelin to ceramide (PubMed:1840600, PubMed:18815062, PubMed:27659707, PubMed:25920558). Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol.
  • Isoform 2 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.
  • Isoform 3 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.

Gene Wiki entry for SMPD1 Gene

Additional gene information for SMPD1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SMPD1 Gene

Genomics for SMPD1 Gene

GeneHancer (GH) Regulatory Elements for SMPD1 Gene

Promoters and enhancers for SMPD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J006387 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 514 -0.5 -545 4.9 FOXK2 HNRNPK ZBTB40 ZNF217 EP300 NRF1 POLR2G USF1 SP1 TEAD4 SMPD1 lnc-APBB1-2-001 lnc-APBB1-2-002 FJ601684-056
GH11J006479 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.4 +91.1 91131 3.6 FOXK2 ZBTB40 ZNF217 EP300 SIN3A NRF1 TCF12 POLR2G SP1 GTF2E2 TIMM10B ARFIP2 ENSG00000283977 lnc-TRIM3-1 APBB1 SMPD1
GH11J006473 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.4 +84.8 84814 5 CTCF NRF1 POLR2G USF1 PHF8 ZBTB5 POLR2A CLOCK ZBTB26 RFX1 TRIM3 lnc-ARFIP2-3-002 APBB1 SMPD1 TIMM10B ARFIP2 lnc-TRIM3-1
GH11J006742 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.3 +354.8 354831 6.7 SIN3A ZBTB5 RCOR1 MYC TRIM22 POLR2A RELA NR2F2 NCOR1 NFRKB GVINP1 MRPL17 lnc-OR2AG2-1 RRP8 OR2AG2 CAVIN3 ILK DCHS1 ENSG00000254641 TAF10
GH11J006400 Promoter/Enhancer 1.3 Ensembl ENCODE dbSUPER 13.4 +13.1 13069 5.5 ZBTB40 SP1 TEAD4 RFX1 TOE1 RAD51 CBFB USF1 MXI1 GABPA SMPD1 HPX ARFIP2 TIMM10B CAVIN3 APBB1 lnc-HPX-2 RF00017-849
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SMPD1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SMPD1

Top Transcription factor binding sites by QIAGEN in the SMPD1 gene promoter:
  • Meis-1
  • NF-1
  • NF-AT
  • NF-AT1
  • NF-AT2
  • NF-AT3
  • NF-AT4
  • Nkx2-5
  • RORalpha2
  • ZID

Genomic Locations for SMPD1 Gene

Genomic Locations for SMPD1 Gene
chr11:6,390,301-6,394,998
(GRCh38/hg38)
Size:
4,698 bases
Orientation:
Plus strand
chr11:6,411,644-6,416,228
(GRCh37/hg19)
Size:
4,585 bases
Orientation:
Plus strand

Genomic View for SMPD1 Gene

Genes around SMPD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMPD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMPD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMPD1 Gene

Proteins for SMPD1 Gene

  • Protein details for SMPD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P17405-ASM_HUMAN
    Recommended name:
    Sphingomyelin phosphodiesterase
    Protein Accession:
    P17405
    Secondary Accessions:
    • A8K8M3
    • E9PKS3
    • P17406
    • Q13811
    • Q16837
    • Q16841

    Protein attributes for SMPD1 Gene

    Size:
    631 amino acids
    Molecular mass:
    69936 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Monomer.
    Miscellaneous:
    • There are two types of sphingomyelinases: ASM (acid), and NSM (neutral).
    • [Isoform 1]: Most abundant (90%).
    • [Isoform 2]: Intermediate abundance (10%).
    • [Isoform 3]: Low abundance (<1%).

    Three dimensional structures from OCA and Proteopedia for SMPD1 Gene

    Alternative splice isoforms for SMPD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMPD1 Gene

Post-translational modifications for SMPD1 Gene

  • Glycosylation at Asn88, Asn177, Asn337, Asn397, Asn505, and Asn522
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

No data available for DME Specific Peptides for SMPD1 Gene

Domains & Families for SMPD1 Gene

Gene Families for SMPD1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for SMPD1 Gene

Suggested Antigen Peptide Sequences for SMPD1 Gene

GenScript: Design optimal peptide antigens:
  • Acid sphingomyelinase (ASM_HUMAN)
  • Sphingomyelin phosphodiesterase 1 isoform 1 (E9LUE6_HUMAN)
  • Sphingomyelin phosphodiesterase 1 isoform 5 (E9LUE7_HUMAN)
  • Sphingomyelin phosphodiesterase 1 isoform 6 (E9LUE8_HUMAN)
  • Sphingomyelin phosphodiesterase 1 isoform 7 (E9LUE9_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P17405

UniProtKB/Swiss-Prot:

ASM_HUMAN :
  • Belongs to the acid sphingomyelinase family.
Family:
  • Belongs to the acid sphingomyelinase family.
genes like me logo Genes that share domains with SMPD1: view

Function for SMPD1 Gene

Molecular function for SMPD1 Gene

UniProtKB/Swiss-Prot Function:
Converts sphingomyelin to ceramide (PubMed:1840600, PubMed:18815062, PubMed:27659707, PubMed:25920558). Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol.
UniProtKB/Swiss-Prot Function:
Isoform 2 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.
UniProtKB/Swiss-Prot Function:
Isoform 3 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + sphingomyelin = an N-acylsphing-4-enine + H(+) + phosphocholine; Xref=Rhea:RHEA:19253, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:17636, ChEBI:CHEBI:52639, ChEBI:CHEBI:295975; EC=3.1.4.12; Evidence={ECO:0000269 PubMed:15877209, ECO:0000269 PubMed:1718266, ECO:0000269 PubMed:1840600, ECO:0000269 PubMed:18815062, ECO:0000269 PubMed:26084044, ECO:0000269 PubMed:27349982, ECO:0000269 PubMed:8702487};.
GENATLAS Biochemistry:
sphingomyelin phosphodiesterase 1,lysosomal (acid sphingomyelinase),hydrolyzing sphingomyelin to ceramide and phosphocholine,activated by TNFRSF1A and initiating the apoptotic pathway

Enzyme Numbers (IUBMB) for SMPD1 Gene

Phenotypes From GWAS Catalog for SMPD1 Gene

Gene Ontology (GO) - Molecular Function for SMPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004767 sphingomyelin phosphodiesterase activity TAS --
GO:0005515 protein binding IPI 21157428
GO:0008081 phosphoric diester hydrolase activity IBA 21873635
GO:0008270 zinc ion binding IDA 8702487
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with SMPD1: view
genes like me logo Genes that share phenotypes with SMPD1: view

Human Phenotype Ontology for SMPD1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SMPD1 Gene

MGI Knock Outs for SMPD1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMPD1

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for SMPD1 Gene

Localization for SMPD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMPD1 Gene

Lysosome. Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SMPD1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endosome 5
lysosome 5
mitochondrion 3
cytoskeleton 2
nucleus 2
endoplasmic reticulum 2
cytosol 2
golgi apparatus 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for SMPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IBA,IDA 8702487
GO:0005764 lysosome IDA,IBA 18815062
GO:0005768 endosome IDA 20956541
GO:0005886 plasma membrane IDA 20956541
genes like me logo Genes that share ontologies with SMPD1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SMPD1 Gene

Pathways & Interactions for SMPD1 Gene

genes like me logo Genes that share pathways with SMPD1: view

Pathways by source for SMPD1 Gene

9 Qiagen pathways for SMPD1 Gene
  • Caspase Cascade
  • Ceramide Pathway
  • Fas Signaling
  • LDL Oxidation in Atherogenesis
  • NGF Pathway
1 Cell Signaling Technology pathway for SMPD1 Gene

SIGNOR curated interactions for SMPD1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for SMPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006672 ceramide metabolic process IEA --
GO:0006684 sphingomyelin metabolic process TAS 7670466
GO:0006685 sphingomyelin catabolic process IBA,IDA 18815062
GO:0006687 glycosphingolipid metabolic process TAS --
GO:0007165 signal transduction TAS 7670466
genes like me logo Genes that share ontologies with SMPD1: view

Drugs & Compounds for SMPD1 Gene

(30) Drugs for SMPD1 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Desipramine Approved, Investigational Pharma Target, inhibitor 41
Amlodipine Approved Pharma Target, inhibitor Calcium channel blocker 576
Chlorpromazine Approved, Investigational, Vet_approved Pharma Antagonist, Inverse agonist, Channel blocker, Target, inhibitor 21
Water Approved Pharma 0
Medical Cannabis Experimental, Investigational Pharma Target, inducer 0

(170) Additional Compounds for SMPD1 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
glucosylceramide
  • 1-O-b-D-Glucopyranosyl-ceramide
  • 1-O-beta-delta-Glucopyranosyl-ceramide
  • Ganglioside GL1a
  • Gaucher cerebroside
  • GLC-beta1->1'cer
phosphorylcholine
  • Choline phosphate
  • CHOP
  • N-Trimethyl-2-aminoethylphosphonate
  • O-Phosphocholine
  • Phosphoryl-choline
3616-04-4
3-O-Sulfogalactosylceramide (d18:1/12:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-SulfO-beta-D-galactosylceramide
  • 3-O-SulfO-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
852100-88-0
3-O-Sulfogalactosylceramide (d18:1/14:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-SulfO-beta-D-galactosylceramide
  • 3-O-SulfO-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
3-O-Sulfogalactosylceramide (d18:1/16:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-SulfO-beta-D-galactosylceramide
  • 3-O-SulfO-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
862509-48-6
genes like me logo Genes that share compounds with SMPD1: view

Transcripts for SMPD1 Gene

mRNA/cDNA for SMPD1 Gene

5 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMPD1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SMPD1 Gene

No ASD Table

Relevant External Links for SMPD1 Gene

GeneLoc Exon Structure for
SMPD1

Expression for SMPD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SMPD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SMPD1 Gene

This gene is overexpressed in Amniocyte (37.6), Islet of Langerhans (8.6), and Liver (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SMPD1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SMPD1

SOURCE GeneReport for Unigene cluster for SMPD1 Gene:

Hs.498173

Evidence on tissue expression from TISSUES for SMPD1 Gene

  • Nervous system(4.2)
  • Liver(2.7)
  • Blood(2.5)
  • Heart(2.5)
  • Kidney(2.5)
  • Lung(2.4)
  • Muscle(2.3)
  • Skin(2.3)
  • Intestine(2)
  • Urine(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SMPD1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • tongue
Thorax:
  • chest wall
  • clavicle
  • esophagus
  • heart
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • duodenum
  • intestine
  • large intestine
  • liver
  • pancreas
  • small intestine
  • spleen
  • stomach
Pelvis:
  • pelvis
  • rectum
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • lymph node
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • spinal cord
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with SMPD1: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for SMPD1 Gene

Orthologs for SMPD1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SMPD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMPD1 31 30
  • 98.99 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SMPD1 31 30
  • 86.08 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SMPD1 31 30
  • 85.88 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smpd1 30
  • 83.2 (n)
mouse
(Mus musculus)
Mammalia Smpd1 17 31 30
  • 82.93 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SMPD1 31
  • 78 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMPD1 31
  • 73 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMPD1 31 30
  • 68.22 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMPD1 31
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100487433 30
  • 64.43 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.2147 30
zebrafish
(Danio rerio)
Actinopterygii smpd1 31 30
  • 59.73 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3961 30
fruit fly
(Drosophila melanogaster)
Insecta CG3376 31 32 30
  • 52.78 (n)
OneToMany
CG15534 31 32
  • 7 (a)
OneToMany
CG15533 31 32
  • 5 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011940 30
  • 52.65 (n)
worm
(Caenorhabditis elegans)
Secernentea asm-2 31 30
  • 45.49 (n)
OneToOne
B0252.2 32
  • 34 (a)
ZK455.4 32
  • 33 (a)
W03G1.7 32
  • 30 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL091C 30
  • 44.39 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PPN1 31
  • 13 (a)
OneToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU06697 30
  • 43.77 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 10 (a)
OneToOne
Species where no ortholog for SMPD1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SMPD1 Gene

ENSEMBL:
Gene Tree for SMPD1 (if available)
TreeFam:
Gene Tree for SMPD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SMPD1: view image

Paralogs for SMPD1 Gene

Paralogs for SMPD1 Gene

(1) SIMAP similar genes for SMPD1 Gene using alignment to 17 proteins:

  • ASM_HUMAN
  • E7EWE2_HUMAN
  • E9LUE6_HUMAN
  • E9LUE7_HUMAN
  • E9LUE8_HUMAN
  • E9LUE9_HUMAN
  • E9PL59_HUMAN
  • E9PPK6_HUMAN
  • E9PQT3_HUMAN
  • G3V1E1_HUMAN
  • G3XAB5_HUMAN
  • H0YEP5_HUMAN
  • Q15494_HUMAN
  • Q15495_HUMAN
  • Q15496_HUMAN
  • Q8IUN0_HUMAN
  • Q8TEY3_HUMAN
genes like me logo Genes that share paralogs with SMPD1: view

Variants for SMPD1 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for SMPD1 Gene

ASM_HUMAN-P17405
A common polymorphism arises from a variable number of hexanucleotide repeat sequence within the signal peptide region.

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SMPD1 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
640937 Pathogenic: Niemann-Pick disease, type A; Niemann-Pick disease, type B 6,393,231(+) T/TG FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON_VARIANT
642425 Uncertain Significance: Niemann-Pick disease, type A; Niemann-Pick disease, type B 6,391,601(+) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,FIVE_PRIME_UTR_VARIANT
650777 Pathogenic: Niemann-Pick disease, type A; Niemann-Pick disease, type B 6,392,119(+) G/T NONSENSE,NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
661392 Uncertain Significance: Niemann-Pick disease, type A; Niemann-Pick disease, type B 6,390,705(+) T/TGGCGCTGGCGCTG NON_CODING_TRANSCRIPT_VARIANT,INFRAME_INSERTION,FIVE_PRIME_UTR_VARIANT
662004 Likely Pathogenic: Niemann-Pick disease, type A; Niemann-Pick disease, type B 6,394,013(+) T/G MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT

Additional dbSNP identifiers (rs#s) for SMPD1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SMPD1 Gene

Variant ID Type Subtype PubMed ID
nsv553371 CNV loss 21841781

Variation tolerance for SMPD1 Gene

Residual Variation Intolerance Score: 74% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.42; 81.88% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SMPD1 Gene

Human Gene Mutation Database (HGMD)
SMPD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMPD1

SNP Genotyping and Copy Number Assay Products

Disorders for SMPD1 Gene

MalaCards: The human disease database

(30) MalaCards diseases for SMPD1 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
niemann-pick disease, type a
  • sphingomyelin lipidosis
niemann-pick disease, type b
  • niemann-pick disease, type a
niemann-pick disease
  • niemann-pick disease, type a
ceroid lipofuscinosis, neuronal, 6
  • jansky-bielschowsky disease
acid sphingomyelinase deficiency
  • niemann-pick disease, type a
- elite association - COSMIC cancer census association via MalaCards
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UniProtKB/Swiss-Prot

ASM_HUMAN
  • Niemann-Pick disease A (NPDA) [MIM:257200]: 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. {ECO:0000269 PubMed:12556236, ECO:0000269 PubMed:1391960, ECO:0000269 PubMed:15221801, ECO:0000269 PubMed:15877209, ECO:0000269 PubMed:1618760, ECO:0000269 PubMed:1718266, ECO:0000269 PubMed:18815062, ECO:0000269 PubMed:19405096, ECO:0000269 PubMed:2023926, ECO:0000269 PubMed:20386867, ECO:0000269 PubMed:22818240, ECO:0000269 PubMed:23252888, ECO:0000269 PubMed:23430884, ECO:0000269 PubMed:26499107, ECO:0000269 PubMed:27338287, ECO:0000269 PubMed:8680412, ECO:0000269 PubMed:8693491, ECO:0000269 PubMed:9266408}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Niemann-Pick disease B (NPDB) [MIM:607616]: 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. {ECO:0000269 PubMed:12369017, ECO:0000269 PubMed:12556236, ECO:0000269 PubMed:1301192, ECO:0000269 PubMed:15241805, ECO:0000269 PubMed:16010684, ECO:0000269 PubMed:1618760, ECO:0000269 PubMed:16472269, ECO:0000269 PubMed:18815062, ECO:0000269 PubMed:1885770, ECO:0000269 PubMed:19050888, ECO:0000269 PubMed:19405096, ECO:0000269 PubMed:20386867, ECO:0000269 PubMed:21621718, ECO:0000269 PubMed:22613662, ECO:0000269 PubMed:22818240, ECO:0000269 PubMed:23252888, ECO:0000269 PubMed:23430512, ECO:0000269 PubMed:25920558, ECO:0000269 PubMed:26084044, ECO:0000269 PubMed:26499107, ECO:0000269 PubMed:27338287, ECO:0000269 PubMed:27659707, ECO:0000269 PubMed:8051942, ECO:0000269 PubMed:8664904}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for SMPD1 Gene

Niemann-Pick disease,types A & B

Additional Disease Information for SMPD1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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Publications for SMPD1 Gene

  1. Characterization of common SMPD1 mutations causing types A and B Niemann-Pick disease and generation of mutation-specific mouse models. (PMID: 18815062) Jones I … Schuchman EH (Molecular genetics and metabolism 2008) 3 4 23 54
  2. Sphingomyelin phosphodiesterase-1 (SMPD1) coding variants do not contribute to low levels of high-density lipoprotein cholesterol. (PMID: 18088425) Dastani Z … Marcil M (BMC medical genetics 2007) 3 4 23 54
  3. Functional in vitro characterization of 14 SMPD1 mutations identified in Italian patients affected by Niemann Pick Type B disease. (PMID: 16010684) Dardis A … Pittis MG (Human mutation 2005) 3 4 23 54
  4. Acid sphingomyelinase: identification of nine novel mutations among Italian Niemann Pick type B patients and characterization of in vivo functional in-frame start codon. (PMID: 15241805) Pittis MG … Bembi B (Human mutation 2004) 3 4 23 54
  5. Human acid sphingomyelinase. (PMID: 12631268) Lansmann S … Sandhoff K (European journal of biochemistry 2003) 3 4 23 54

Products for SMPD1 Gene

Sources for SMPD1 Gene