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Aliases for SMPDL3A Gene

Aliases for SMPDL3A Gene

  • Sphingomyelin Phosphodiesterase Acid Like 3A 2 3 5
  • Acid Sphingomyelinase-Like Phosphodiesterase 3a 2 3
  • ASM-Like Phosphodiesterase 3a 3 4
  • ASML3a 3 4
  • Sphingomyelin Phosphodiesterase Acid-Like 3A 2
  • 0610010C24Rik 3
  • EC 3.1.4.- 4
  • YR36GH4.1 3
  • EC 3.1.4 58
  • ASM3A 3

External Ids for SMPDL3A Gene

Previous GeneCards Identifiers for SMPDL3A Gene

  • GC06P123090
  • GC06P123091
  • GC06P123152
  • GC06P120686
  • GC06P123112

Summaries for SMPDL3A Gene

GeneCards Summary for SMPDL3A Gene

SMPDL3A (Sphingomyelin Phosphodiesterase Acid Like 3A) is a Protein Coding gene. GO annotations related to this gene include hydrolase activity and sphingomyelin phosphodiesterase activity. An important paralog of this gene is SMPDL3B.

UniProtKB/Swiss-Prot for SMPDL3A Gene

  • Has in vitro nucleotide phosphodiesterase activity with nucleoside triphosphates, such as ATP (PubMed:25288789, PubMed:26783088). Has in vitro activity with p-nitrophenyl-TMP (PubMed:25288789). Has lower activity with nucleoside diphosphates, and no activity with nucleoside monophosphates (PubMed:25288789, PubMed:26783088). Has in vitro activity with CDP-choline, giving rise to CMP and phosphocholine. Has in vitro activity with CDP-ethanolamine (PubMed:26783088). Does not have sphingomyelin phosphodiesterase activity (PubMed:25288789, PubMed:26783088).

Additional gene information for SMPDL3A Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMPDL3A Gene

Genomics for SMPDL3A Gene

Regulatory Elements for SMPDL3A Gene

Enhancers for SMPDL3A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06H122787 1.7 FANTOM5 ENCODE dbSUPER 9.7 +2.2 2247 6 PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF143 SMPDL3A PKIB GC06M122860
GH06H122735 0.8 ENCODE 16.3 -52.4 -52386 1 PKNOX1 ZNF146 ZSCAN4 INSM2 FEZF1 ZNF2 ZEB1 FOSL1 HIC1 ZNF366 SMPDL3A FABP7 PKIB RN7SL564P ENSG00000272472
GH06H122712 1.1 Ensembl ENCODE 10.3 -78.2 -78156 0 PKNOX1 ATF1 BMI1 ZNF766 ETV6 ATF7 RUNX3 CREM IKZF2 CBFB SMPDL3A PKIB TRDN RN7SL564P ENSG00000272472
GH06H122711 1.1 Ensembl ENCODE 10.3 -75.7 -75721 1 HDAC1 PKNOX1 TBL1XR1 ARNT NFRKB CHAMP1 TCF12 ZNF766 GATA2 IKZF2 SMPDL3A PKIB RN7SL564P ENSG00000272472
GH06H122753 0.7 FANTOM5 16 -34.6 -34609 0 JUND TAF1 MAX HNF4A REST ZBTB33 YY1 SMPDL3A FABP7 RN7SL564P
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SMPDL3A on UCSC Golden Path with GeneCards custom track

Promoters for SMPDL3A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000202089 1444 1801 PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF143

Genomic Location for SMPDL3A Gene

Chromosome:
6
Start:
122,788,456 bp from pter
End:
122,809,720 bp from pter
Size:
21,265 bases
Orientation:
Plus strand

Genomic View for SMPDL3A Gene

Genes around SMPDL3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMPDL3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMPDL3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMPDL3A Gene

Proteins for SMPDL3A Gene

  • Protein details for SMPDL3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92484-ASM3A_HUMAN
    Recommended name:
    Acid sphingomyelinase-like phosphodiesterase 3a
    Protein Accession:
    Q92484
    Secondary Accessions:
    • B7Z729
    • Q8WV13

    Protein attributes for SMPDL3A Gene

    Size:
    453 amino acids
    Molecular mass:
    51260 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Monomer.

    Three dimensional structures from OCA and Proteopedia for SMPDL3A Gene

    Alternative splice isoforms for SMPDL3A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMPDL3A Gene

Selected DME Specific Peptides for SMPDL3A Gene

Q92484:
  • DFIKNSGQ
  • HLDPTYHIT
  • SFMIWTGDSPPHVPV
  • LNTNLYY

Post-translational modifications for SMPDL3A Gene

  • N-glycosylated.
  • Glycosylation at isoforms=69, isoforms=131, isoforms=2222, Asn238, Asn263, isoforms=2356, and Asn437
  • Modification sites at PhosphoSitePlus

Domains & Families for SMPDL3A Gene

Gene Families for SMPDL3A Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for SMPDL3A Gene

Graphical View of Domain Structure for InterPro Entry

Q92484

UniProtKB/Swiss-Prot:

ASM3A_HUMAN :
  • Belongs to the acid sphingomyelinase family.
Family:
  • Belongs to the acid sphingomyelinase family.
genes like me logo Genes that share domains with SMPDL3A: view

Function for SMPDL3A Gene

Molecular function for SMPDL3A Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=326 uM for ATP {ECO:0000269 PubMed:26783088}; KM=306 uM for ADP {ECO:0000269 PubMed:26783088}; KM=348 uM for ADP-ribose {ECO:0000269 PubMed:26783088}; KM=390 uM for CDP-ethanolamine {ECO:0000269 PubMed:26783088}; KM=262 uM for CDP-choline {ECO:0000269 PubMed:26783088}; pH dependence: Optimum pH is 4-6. {ECO:0000269 PubMed:25288789};
UniProtKB/Swiss-Prot EnzymeRegulation:
Requires micromolar levels of Zn(2+) for activity (PubMed:26783088). Inhibited by millimolar levels of Zn(2+) (PubMed:25288789, PubMed:26783088).
UniProtKB/Swiss-Prot Function:
Has in vitro nucleotide phosphodiesterase activity with nucleoside triphosphates, such as ATP (PubMed:25288789, PubMed:26783088). Has in vitro activity with p-nitrophenyl-TMP (PubMed:25288789). Has lower activity with nucleoside diphosphates, and no activity with nucleoside monophosphates (PubMed:25288789, PubMed:26783088). Has in vitro activity with CDP-choline, giving rise to CMP and phosphocholine. Has in vitro activity with CDP-ethanolamine (PubMed:26783088). Does not have sphingomyelin phosphodiesterase activity (PubMed:25288789, PubMed:26783088).
UniProtKB/Swiss-Prot Induction:
Up-regulated in macrophages in response to cholesterol accumulation. Up-regulated by cAMP.

Enzyme Numbers (IUBMB) for SMPDL3A Gene

Phenotypes From GWAS Catalog for SMPDL3A Gene

Gene Ontology (GO) - Molecular Function for SMPDL3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004767 NOT sphingomyelin phosphodiesterase activity IDA 26783088
GO:0005515 protein binding IPI 12442002
GO:0008081 phosphoric diester hydrolase activity IDA 26783088
GO:0008270 zinc ion binding IDA 26783088
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with SMPDL3A: view
genes like me logo Genes that share phenotypes with SMPDL3A: view

Animal Model Products

  • Taconic Biosciences Mouse Models for SMPDL3A

CRISPR Products

miRNA for SMPDL3A Gene

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SMPDL3A
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SMPDL3A Gene

Localization for SMPDL3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMPDL3A Gene

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 SMPDL3A gene
Compartment Confidence
extracellular 5
lysosome 3
mitochondrion 2
nucleus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SMPDL3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IMP 26783088
GO:0070062 extracellular exosome IDA 23533145
genes like me logo Genes that share ontologies with SMPDL3A: view

Pathways & Interactions for SMPDL3A Gene

SuperPathways for SMPDL3A Gene

No Data Available

Interacting Proteins for SMPDL3A Gene

Gene Ontology (GO) - Biological Process for SMPDL3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006685 NOT sphingomyelin catabolic process IDA 26783088
GO:0008150 biological_process ND --
GO:0009143 nucleoside triphosphate catabolic process IDA 26783088
genes like me logo Genes that share ontologies with SMPDL3A: view

No data available for Pathways by source and SIGNOR curated interactions for SMPDL3A Gene

Drugs & Compounds for SMPDL3A Gene

No Compound Related Data Available

Transcripts for SMPDL3A Gene

Unigene Clusters for SMPDL3A Gene

Sphingomyelin phosphodiesterase, acid-like 3A:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SMPDL3A
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for SMPDL3A Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b
SP1: -
SP2: - - - -
SP3: - - - - - -
SP4: - - - - -
SP5: - -
SP6:
SP7: -

Relevant External Links for SMPDL3A Gene

GeneLoc Exon Structure for
SMPDL3A
ECgene alternative splicing isoforms for
SMPDL3A

Expression for SMPDL3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SMPDL3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SMPDL3A Gene

This gene is overexpressed in Cervix - Ectocervix (x4.1).

Protein differential expression in normal tissues from HIPED for SMPDL3A Gene

This gene is overexpressed in Serum (20.3) and Vitreous humor (10.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SMPDL3A Gene



NURSA nuclear receptor signaling pathways regulating expression of SMPDL3A Gene:

SMPDL3A

SOURCE GeneReport for Unigene cluster for SMPDL3A Gene:

Hs.486357

mRNA Expression by UniProt/SwissProt for SMPDL3A Gene:

Q92484-ASM3A_HUMAN
Tissue specificity: Detected in blood serum. Detected in macrophages (at protein level).

Evidence on tissue expression from TISSUES for SMPDL3A Gene

  • Liver(4.8)
  • Nervous system(4.2)
  • Kidney(3.5)
  • Eye(3.1)
  • Intestine(3.1)
  • Lung(2.9)
  • Skin(2.7)
  • Heart(2.5)
  • Stomach(2.3)
  • Muscle(2)
genes like me logo Genes that share expression patterns with SMPDL3A: view

Primer Products

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMPDL3A Gene

Orthologs for SMPDL3A Gene

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

Orthologs for SMPDL3A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMPDL3A 33 34
  • 99.48 (n)
dog
(Canis familiaris)
Mammalia SMPDL3A 33 34
  • 87.54 (n)
cow
(Bos Taurus)
Mammalia SMPDL3A 33 34
  • 86.86 (n)
mouse
(Mus musculus)
Mammalia Smpdl3a 33 16 34
  • 82.54 (n)
rat
(Rattus norvegicus)
Mammalia Smpdl3a 33
  • 82.24 (n)
oppossum
(Monodelphis domestica)
Mammalia SMPDL3A 34
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SMPDL3A 34
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMPDL3A 33 34
  • 71.19 (n)
lizard
(Anolis carolinensis)
Reptilia SMPDL3A 34
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smpdl3a 33
  • 67.61 (n)
zebrafish
(Danio rerio)
Actinopterygii smpdl3a 33 34
  • 64.21 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG32052 34
  • 28 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ZK856.5 34
  • 7 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PPN1 34
  • 12 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 4 (a)
ManyToMany
Species where no ortholog for SMPDL3A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 SMPDL3A Gene

ENSEMBL:
Gene Tree for SMPDL3A (if available)
TreeFam:
Gene Tree for SMPDL3A (if available)

Paralogs for SMPDL3A Gene

Paralogs for SMPDL3A Gene

(2) SIMAP similar genes for SMPDL3A Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with SMPDL3A: view

Variants for SMPDL3A Gene

Sequence variations from dbSNP and Humsavar for SMPDL3A Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000251994 -- 122,785,371(+) TAATT(C/T)AAAGT upstream-variant-2KB
rs1000275135 -- 122,791,584(+) AGTTA(C/T)AAAAT intron-variant
rs1000437841 -- 122,798,313(+) CTTGG(C/G)AACAA intron-variant
rs1000551467 -- 122,800,376(+) AGCTT(A/G)TAATA intron-variant
rs1000618323 -- 122,798,556(+) TTGTA(C/T)ATAGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SMPDL3A Gene

Variant ID Type Subtype PubMed ID
nsv1035007 CNV gain 25217958
nsv819111 CNV loss 19587683
nsv823834 CNV gain 20364138
nsv830791 CNV gain 17160897

Variation tolerance for SMPDL3A Gene

Residual Variation Intolerance Score: 71.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.95; 74.60% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SMPDL3A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMPDL3A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMPDL3A Gene

Disorders for SMPDL3A Gene

Relevant External Links for SMPDL3A

Human Genome Epidemiology (HuGE) Navigator
SMPDL3A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMPDL3A

No disorders were found for SMPDL3A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SMPDL3A Gene

Publications for SMPDL3A Gene

  1. Sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) is a novel nucleotide phosphodiesterase regulated by cholesterol in human macrophages. (PMID: 25288789) Traini M … Kritharides L (The Journal of biological chemistry 2014) 2 3 4 60
  2. Increased expression of the acid sphingomyelinase-like protein ASML3a in bladder tumors. (PMID: 12442002) Wright KO … Reeder JE (The Journal of urology 2002) 2 3 22 60
  3. The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a--an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity. (PMID: 26783088) Lim SM … Nordlund P (The FEBS journal 2016) 3 4 60
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60
  5. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall AJ … Beck S (Nature 2003) 3 4 60

Products for SMPDL3A Gene

Sources for SMPDL3A Gene

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