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The protein encoded by this gene is a sphingomyelinase that catalyzes the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide. This gene is activated by DNA damage, cellular stress, and tumor necrosis factor, but it is downregulated by wild-type p53. The encoded protein localizes to the endoplasmic reticulum and Golgi network. [provided by RefSeq, Mar 20... See more...
Aliases for SMPD4 Gene
Aliases for SMPD4 Gene
External Ids for SMPD4 Gene
- HGNC: 32949
- NCBI Entrez Gene: 55627
- Ensembl: ENSG00000136699
- OMIM®: 610457
- UniProtKB/Swiss-Prot: Q9NXE4
Previous GeneCards Identifiers for SMPD4 Gene
- GC02M130626
- GC02M130908
- GC02M123204
Summaries for SMPD4 Gene
-
The protein encoded by this gene is a sphingomyelinase that catalyzes the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide. This gene is activated by DNA damage, cellular stress, and tumor necrosis factor, but it is downregulated by wild-type p53. The encoded protein localizes to the endoplasmic reticulum and Golgi network. [provided by RefSeq, Mar 2017]
GeneCards Summary for SMPD4 Gene
SMPD4 (Sphingomyelin Phosphodiesterase 4) is a Protein Coding gene. Diseases associated with SMPD4 include Neurodevelopmental Disorder With Microcephaly, Arthrogryposis, And Structural Brain Anomalies and Microcephaly With Simplified Gyral Pattern. Among its related pathways are Sphingolipid metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include sphingomyelin phosphodiesterase activity and sphingomyelin phosphodiesterase D activity.
UniProtKB/Swiss-Prot Summary for SMPD4 Gene
-
Catalyzes the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide (PubMed:16517606, PubMed:25180167). It has a relevant role in the homeostasis of membrane sphingolipids, thereby influencing membrane integrity, and endoplasmic reticulum organization and function (PubMed:31495489). May sensitize cells to DNA damage-induced apoptosis (PubMed:18505924). In skeletal muscle, mediates TNF-stimulated oxidant production (By similarity).
Additional gene information for SMPD4 Gene
- HGNC (32949)
- NCBI Entrez Gene (55627)
- Ensembl (ENSG00000136699)
- OMIM® (610457)
- UniProtKB/Swiss-Prot (Q9NXE4)
- Open Targets Platform(ENSG00000136699)
- Alliance of Genome Resources
- Search for SMPD4 at DataMed
- Search for SMPD4 at HumanCyc
No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SMPD4 Gene
Genomics for SMPD4 Gene
GeneHancer (GH) Regulatory Elements Pubs
Promoters and enhancers for SMPD4 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association
Download GeneHancer data from 2017 publication |
Request up-to-date GeneHancer data (full dataset)
GeneHancers around SMPD4 on the GeneHancer Hub at the UCSC Golden Path
Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SMPD4
- Top Transcription factor binding sites by QIAGEN in the SMPD4 gene promoter:
-
- AREB6
- Arnt
- CUTL1
- E47
- FOXI1
- HFH-3
- RORalpha1
- Sox5
- Sp1
- XBP-1
Genomic Locations for SMPD4 Gene
Latest Assembly
- chr2:130,151,392-130,182,750
- (GRCh38/hg38)
- Size:
- 31,359 bases
- Orientation:
- Minus strand
Previous Assembly
- chr2:130,908,965-130,939,330
- (GRCh37/hg19 by Entrez Gene)
- Size:
- 30,366 bases
- Orientation:
- Minus strand
Genomic View for SMPD4 Gene
Genes around SMPD4 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 2q21.1 by HGNC
- 2q21.1 by Entrez Gene
- 2q21.1 by Ensembl
SMPD4 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene Density
RefSeq DNA sequence for SMPD4 Gene
Proteins for SMPD4 Gene
-
Protein details for SMPD4 Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- Q9NXE4-NSMA3_HUMAN
- Recommended name:
- Sphingomyelin phosphodiesterase 4
- Protein Accession:
- Q9NXE4
- B1PBA3
- B4DM23
- B4DQ31
- B4DRB8
- B4DWK7
- B4E0L6
- E7ESA2
- E9PCE6
- Q6FI76
- Q6P1P7
- Q6ZT43
- Q9H0M2
- Q9NW20
- Q9NWL2
- Q9P2C9
Protein attributes for SMPD4 Gene
- Size:
- 866 amino acids
- Molecular mass:
- 97810 Da
- Cofactor:
- Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
- Quaternary structure:
- No Data Available
- SequenceCaution:
-
- Sequence=AAY14883.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAA91070.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAA91368.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAA91567.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAA92656.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
Protein Expression for SMPD4 Gene
Post-translational modifications for SMPD4 Gene
Other Protein References for SMPD4 Gene
- ENSEMBL proteins:
-
- ENSP00000405187
- ENSP00000407591
- ENSP00000403002
- ENSP00000397278
- ENSP00000259217
- ENSP00000506463
- ENSP00000401648
- ENSP00000386531
- ENSP00000506367
- ENSP00000505716
- ENSP00000505271
- ENSP00000506346
- ENSP00000397078
- ENSP00000403915
- ENSP00000406325
- ENSP00000405363
- ENSP00000393791
- ENSP00000505151
- ENSP00000416208
- ENSP00000406458
- Q9NXE4.137
- REFSEQ proteins:
Antibodies for research
-
Custom Antibody ServicesOriGene Antibodies for SMPD4
- Novus Biologicals Antibodies for SMPD4
- Invitrogen Antibodies for SMPD4 (AFLGC-SMPD4)
-
Boster Bio Antibodies for SMPD4
-
Custom Antibody ServicesProSci Antibodies for SMPD4
Protein products for research
-
OriGene Purified Proteins for SMPD4
- Search Origene for MassSpec and Protein Over-expression Lysates for SMPD4
- Origene Custom Protein Services for SMPD4
- Novus Biologicals proteins for SMPD4
Assay products for research
No data available for DME Specific Peptides for SMPD4 Gene
Domains & Families for SMPD4 Gene
Gene Families for SMPD4 Gene
- Human Protein Atlas (HPA):
-
- Enzymes
- Predicted intracellular proteins
- Predicted membrane proteins
Protein Domains for SMPD4 Gene
- InterPro:
Suggested Antigen Peptide Sequences for SMPD4 Gene
- GenScript: Design optimal peptide antigens:
-
- cDNA FLJ59341, highly similar to Homo sapiens sphingomyelin phosphodiesterase 4, neutral membrane, transcript variant 1, mRNA (B4DM23_HUMAN)
- cDNA FLJ53156, highly similar to Homo sapiens sphingomyelin phosphodiesterase 4, neutral membrane, transcript variant 2, mRNA (B4DQ31_HUMAN)
- cDNA FLJ58546, highly similar to Homo sapiens sphingomyelin phosphodiesterase 4, neutral membrane, transcript variant 1, mRNA (B4DWK7_HUMAN)
- cDNA FLJ53260, highly similar to Homo sapiens sphingomyelin phosphodiesterase 4, neutral membrane, transcript variant 2, mRNA (B4E0L6_HUMAN)
- Neutral sphingomyelinase III (NSMA3_HUMAN)
No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SMPD4 Gene
Function for SMPD4 Gene
Molecular function for SMPD4 Gene
- UniProtKB/Swiss-Prot Function:
- Catalyzes the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide (PubMed:16517606, PubMed:25180167). It has a relevant role in the homeostasis of membrane sphingolipids, thereby influencing membrane integrity, and endoplasmic reticulum organization and function (PubMed:31495489). May sensitize cells to DNA damage-induced apoptosis (PubMed:18505924). In skeletal muscle, mediates TNF-stimulated oxidant production (By similarity).
- UniProtKB/Swiss-Prot CatalyticActivity:
- Reaction=a sphingomyelin + H2O = 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:16517606, ECO:0000269|PubMed:25180167};.
- UniProtKB/Swiss-Prot Induction:
- Expression is induced by DNA-damage and TNF.
- UniProtKB/Swiss-Prot BiophysicochemicalProperties:
- pH dependence: Optimum pH is 7.0. {ECO:0000269|PubMed:16517606};
- UniProtKB/Swiss-Prot EnzymeRegulation:
- Activated by phosphatidylserine and tumor necrosis factor (TNF). Inhibited by scyphostatin.
Enzyme Numbers (IUBMB) for SMPD4 Gene
Phenotypes From GWAS Catalog for SMPD4 Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0004767 | sphingomyelin phosphodiesterase activity | IEA | -- |
| GO:0016787 | hydrolase activity | IEA | -- |
| GO:0046872 | metal ion binding | IEA | -- |
| GO:0050290 | sphingomyelin phosphodiesterase D activity | IEA,IDA | 16517606 |
Phenotypes for SMPD4 Gene
- MGI mutant phenotypes for SMPD4:
- inferred from 1 alleles
- GenomeRNAi human phenotypes for SMPD4:
Animal Models for SMPD4 Gene
- MGI Knock Outs for SMPD4:
-
- Smpd4 Smpd4<tm2b(KOMP)Wtsi>
Animal Models for research
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
CRISPR products for research
- Applied Biological Materials (abm): CRISPR Clones for SMPD4 - Starting at $85 >
- * SMPD4 CRISPR as ready-to-use vector or virus: Non-viral | Lenti- | Adeno- | AAV- | siRNA - Browse All
- * Cas9 Nucleases, Nickases, Null Mutants, and GFP tag also available.
-
OriGene CRISPR knockouts for SMPD4
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for SMPD4
-
Santa Cruz Biotechnology (SCBT) CRISPR for SMPD4
miRNA for SMPD4 Gene
- miRTarBase miRNAs that target SMPD4
-
- hsa-miR-124-3p (MIRT022153)
- hsa-miR-16-5p (MIRT031423)
- hsa-miR-331-3p (MIRT043289)
- mmu-miR-466i-5p (MIRT585791)
- mmu-miR-466l-5p (MIRT585792)
- mmu-miR-466d-5p (MIRT585793)
- mmu-miR-466k (MIRT585794)
- mmu-miR-1199-5p (MIRT597213)
- mmu-miR-1195 (MIRT597214)
- mmu-miR-3089-5p (MIRT597215)
- mmu-miR-1896 (MIRT601593)
miRNA products for research
Inhibitory RNAs for research
- Origene shrna, sirna, and RNAi products in human, mouse, rat for SMPD4
- Browse OriGene Inhibitory RNA Products For SMPD4
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMPD4
Clone products for research
- Applied Biological Materials (abm): Clones for SMPD4 - Starting at $45 >
- * SMPD4 as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Retro- | Protein Vector - Browse All
- * Viral Packaging Services and High Titer Production Services also available.
-
- MG210696
- MG216855
- MG218291
- MG219037
- MR210696
- MR210696L3
- MR210696L4
- MR216855
- MR216855L3
- MR216855L4
- MR218291
- MR218291L3
- MR218291L4
- MR219037
- MR219037L3
- MR219037L4
- RC214161
- RC214161L3
- RC214161L4
- RC219824
- RC219824L3
- RC219824L4
- RC230482
- RC230482L3
- RC230482L4
- RG214161
- RG219824
- RG230482
- RR217236
- MR210696L3V
- MR210696L4V
- MR216855L3V
- MR216855L4V
- MR218291L3V
- MR218291L4V
- MR219037L3V
- MR219037L4V
- RC214161L3V
- RC214161L4V
- RC219824L3V
- RC219824L4V
- RC230482L3V
- RC230482L4V
- Custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
- Sino Biological Human cDNA Clone for SMPD4
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for SMPD4
Cell Lines for research
-
Horizon Cell Lines for SMPD4
No data available for Transcription Factor Targets and HOMER Transcription for SMPD4 Gene
Localization for SMPD4 Gene
Subcellular locations from UniProtKB/Swiss-Prot for SMPD4 Gene
- Endoplasmic reticulum membrane. Single-pass membrane protein. Golgi apparatus membrane. Single-pass membrane protein. Nucleus envelope. Cell membrane, sarcolemma.
| Compartment | Confidence |
|---|---|
| plasma membrane | 5 |
| nucleus | 5 |
| endoplasmic reticulum | 5 |
| golgi apparatus | 4 |
| mitochondrion | 2 |
| lysosome | 2 |
| extracellular | 1 |
| endosome | 1 |
| cytosol | 1 |
| peroxisome | 0 |
- Nuclear membrane (2)
- Cytosol (1)
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000139 | Golgi membrane | IEA | -- |
| GO:0005634 | nucleus | IEA | -- |
| GO:0005635 | nuclear envelope | ISS | -- |
| GO:0005640 | nuclear outer membrane | IDA | 31495489 |
| GO:0005783 | endoplasmic reticulum | IEA,IDA | 16517606 |
Pathways & Interactions for SMPD4 Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | Metabolism |
.40
|
|
| 2 | Sphingolipid metabolism | ||
Pathways by source for SMPD4 Gene
4 Reactome pathways for SMPD4 Gene
2 KEGG pathways for SMPD4 Gene
Interacting Proteins for SMPD4 Gene
Selected Interacting proteins:
Q9NXE4-NSMA3_HUMAN
ENSP00000386531
for SMPD4 Gene via
MINT
STRING
IID
GPS-Prot Interaction Network for SMPD4
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0006685 | sphingomyelin catabolic process | IBA,IDA | 16517606 |
| GO:0006687 | glycosphingolipid metabolic process | TAS | -- |
| GO:0007029 | endoplasmic reticulum organization | IMP | 31495489 |
| GO:0046475 | glycerophospholipid catabolic process | IDA | 16517606 |
| GO:0046513 | ceramide biosynthetic process | IDA | 16517606 |
No data available for SIGNOR curated interactions for SMPD4 Gene
Drugs & Compounds for SMPD4 Gene
| Name | Synonyms | Role | CAS Number | PubChem IDs | PubMed IDs | |
|---|---|---|---|---|---|---|
| 3-O-Sulfogalactosylceramide (d18:1/12:0) |
|
852100-88-0 |
|
|||
| 3-O-Sulfogalactosylceramide (d18:1/14:0) |
|
|
||||
| 3-O-Sulfogalactosylceramide (d18:1/16:0) |
|
862509-48-6 |
|
|||
| 3-O-Sulfogalactosylceramide (d18:1/18:0) |
|
244215-65-4 |
|
|||
| 3-O-Sulfogalactosylceramide (d18:1/18:1(9Z)) |
|
|
Transcripts for SMPD4 Gene
mRNA/cDNA for SMPD4 Gene
- 4 REFSEQ mRNAs :
- 22 NCBI additional mRNA sequence :
- 27 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
-
- ENST00000351288 3661 nts (view in UCSC)
- ENST00000409031 4896 nts (view in UCSC)
- ENST00000412570 3601 nts (view in UCSC)
- ENST00000430682 820 nts (view in UCSC)
- ENST00000431183 3614 nts (view in UCSC)
CRISPR products for research
- Applied Biological Materials (abm): CRISPR Clones for SMPD4 - Starting at $85 >
- * SMPD4 CRISPR as ready-to-use vector or virus: Non-viral | Lenti- | Adeno- | AAV- | siRNA - Browse All
- * Cas9 Nucleases, Nickases, Null Mutants, and GFP tag also available.
-
OriGene CRISPR knockouts for SMPD4
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for SMPD4
-
Santa Cruz Biotechnology (SCBT) CRISPR for SMPD4
miRNA products for research
Inhibitory RNAs for research
- Origene shrna, sirna, and RNAi products in human, mouse, rat for SMPD4
- Browse OriGene Inhibitory RNA Products For SMPD4
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMPD4
Clone products for research
- Applied Biological Materials (abm): Clones for SMPD4 - Starting at $45 >
- * SMPD4 as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Retro- | Protein Vector - Browse All
- * Viral Packaging Services and High Titer Production Services also available.
-
- MG210696
- MG216855
- MG218291
- MG219037
- MR210696
- MR210696L3
- MR210696L4
- MR216855
- MR216855L3
- MR216855L4
- MR218291
- MR218291L3
- MR218291L4
- MR219037
- MR219037L3
- MR219037L4
- RC214161
- RC214161L3
- RC214161L4
- RC219824
- RC219824L3
- RC219824L4
- RC230482
- RC230482L3
- RC230482L4
- RG214161
- RG219824
- RG230482
- RR217236
- MR210696L3V
- MR210696L4V
- MR216855L3V
- MR216855L4V
- MR218291L3V
- MR218291L4V
- MR219037L3V
- MR219037L4V
- RC214161L3V
- RC214161L4V
- RC219824L3V
- RC219824L4V
- RC230482L3V
- RC230482L4V
- Custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
- Sino Biological Human cDNA Clone for SMPD4
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for SMPD4
Relevant External Links for SMPD4 Gene
- GeneLoc Exon Structure for
- SMPD4
Expression for SMPD4 Gene
This gene is overexpressed in Bone (8.8) and Peripheral blood mononuclear cells (6.8).
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SMPD4 Gene
- Elite partner
Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SMPD4
SOURCE GeneReport for Unigene cluster for SMPD4 Gene:
Hs.516450mRNA Expression by UniProt/SwissProt for SMPD4 Gene:
Q9NXE4-NSMA3_HUMAN
Tissue specificity:
Widely expressed, with highest levels in heart and skeletal muscle.
Evidence on tissue expression from TISSUES for SMPD4 Gene
- Nervous system(4.9)
- Lung(4.5)
- Liver(2.3)
- Blood(2.3)
- Muscle(2.3)
- Skin(2.2)
- Kidney(2.2)
- Intestine(2.1)
Primer products for research
-
OriGene qPCR primer pairs for SMPD4
-
OriGene qPCR primer pairs and template standards for SMPD4
Gene Expression Assays for research
No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMPD4 Gene
Orthologs for SMPD4 Gene
This gene was present in the common ancestor of animals.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| Chimpanzee (Pan troglodytes) |
Mammalia | SMPD4 29 |
|
||
| Dog (Canis familiaris) |
Mammalia | SMPD4 29 30 |
|
OneToOne | |
| Rat (Rattus norvegicus) |
Mammalia | Smpd4 29 |
|
||
| Mouse (Mus musculus) |
Mammalia | Smpd4 29 16 30 |
|
OneToOne | |
| Cow (Bos Taurus) |
Mammalia | SMPD4 29 30 |
|
OneToOne | |
| Oppossum (Monodelphis domestica) |
Mammalia | SMPD4 30 |
|
OneToOne | |
| Platypus (Ornithorhynchus anatinus) |
Mammalia | -- 30 |
|
OneToMany | |
| -- 30 |
|
OneToMany | |||
| Chicken (Gallus gallus) |
Aves | SMPD4 29 30 |
|
OneToOne | |
| Lizard (Anolis carolinensis) |
Reptilia | SMPD4 30 |
|
OneToOne | |
| Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | smpd4 29 |
|
||
| Str.6070 29 |
|
||||
| African clawed frog (Xenopus laevis) |
Amphibia | Xl.4713 29 |
|
||
| Zebrafish (Danio rerio) |
Actinopterygii | smpd4 29 30 |
|
OneToOne | |
| wufb22d05 29 |
|
||||
| Rainbow Trout (Oncorhynchus mykiss) |
Actinopterygii | Omy.4009 29 |
|
||
| African malaria mosquito (Anopheles gambiae) |
Insecta | AgaP_AGAP000405 29 |
|
||
| Fruit Fly (Drosophila melanogaster) |
Insecta | CG6962 29 30 |
|
OneToOne | |
| Sea Squirt (Ciona savignyi) |
Ascidiacea | -- 30 |
|
OneToOne |
- Species where no ortholog for SMPD4 was found in the sources mined by GeneCards:
-
- A. gosspyii yeast (Eremothecium gossypii)
- Actinobacteria (Mycobacterium tuberculosis)
- Alicante grape (Vitis vinifera)
- Alpha proteobacteria (Wolbachia pipientis)
- Amoeba (Dictyostelium discoideum)
- Archea (Pyrococcus horikoshii)
- Baker's yeast (Saccharomyces cerevisiae)
- 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)
- Rice (Oryza sativa)
- Rice Blast Fungus (Magnaporthe grisea)
- Schistosome Parasite (Schistosoma mansoni)
- Sea Anemone (Nematostella vectensis)
- Sea Vase (Ciona intestinalis)
- 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)
- Worm (Caenorhabditis elegans)
Evolution for SMPD4 Gene
- ENSEMBL:
- Gene Tree for SMPD4 (if available)
- TreeFam:
- Gene Tree for SMPD4 (if available)
- Aminode:
- Evolutionary constrained regions (ECRs) for SMPD4: view image
- Alliance of Genome Resources:
- Additional Orthologs for SMPD4
Paralogs for SMPD4 Gene
Pseudogenes.org Pseudogenes for SMPD4 Gene
No data available for Paralogs for SMPD4 Gene
Variants for SMPD4 Gene
Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SMPD4 Gene
| SNP ID | Clinical significance and condition | Chr 02 pos | Variation | AA Info | Type |
|---|---|---|---|---|---|
| 1030617 | Likely Pathogenic: Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies | 130,153,700(-) |
A/G NM_017951.5(SMPD4):c.1893+2T>C |
SPLICE_DONOR | |
| 870336 | Uncertain Significance: Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies | 130,153,730(-) |
G/A NM_017951.4(SMPD4):c.1982C>T (p.Ala661Val) |
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT | |
| 870337 | Likely Pathogenic: Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies | 130,173,530(-) |
C/A NM_017951.4(SMPD4):c.370G>T (p.Glu124Ter) |
NONSENSE,NON_CODING_TRANSCRIPT_VARIANT,INTRON | |
| 870338 | Likely Pathogenic: Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies | 130,172,433(-) |
A/G NM_017951.4(SMPD4):c.692T>C (p.Leu231Pro) |
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT | |
| 870339 | Uncertain Significance: Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies | 130,152,875(-) |
G/A NM_017951.4(SMPD4):c.2281C>T (p.Gln761Ter) |
NONSENSE,NON_CODING_TRANSCRIPT |
All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).
| Variant ID | Type | Subtype | PubMed ID |
|---|---|---|---|
| dgv2032n106 | OTHER | inversion | 24896259 |
| dgv4072n100 | CNV | loss | 25217958 |
| dgv4073n100 | CNV | gain | 25217958 |
| dgv7079n54 | CNV | loss | 21841781 |
| esv2751826 | CNV | gain | 17911159 |
| esv2759092 | CNV | gain+loss | 17122850 |
| esv2760631 | CNV | gain+loss | 21179565 |
| esv2763387 | CNV | loss | 21179565 |
| esv3584065 | CNV | loss | 25503493 |
| esv3592440 | CNV | loss | 21293372 |
| esv3592441 | CNV | gain | 21293372 |
| esv3893326 | CNV | gain | 25118596 |
| nsv1001337 | CNV | loss | 25217958 |
| nsv1004301 | CNV | loss | 25217958 |
| nsv1005664 | CNV | loss | 25217958 |
| nsv1008911 | CNV | gain | 25217958 |
| nsv1008970 | CNV | loss | 25217958 |
| nsv1011360 | CNV | loss | 25217958 |
| nsv428403 | CNV | loss | 18775914 |
| nsv459274 | CNV | loss | 19166990 |
| nsv482053 | CNV | gain | 20164927 |
| nsv520559 | CNV | gain+loss | 19592680 |
| nsv583046 | CNV | loss | 21841781 |
| nsv583113 | CNV | gain | 21841781 |
| nsv7327 | OTHER | inversion | 18451855 |
| nsv821629 | CNV | loss | 15273396 |
| nsv834375 | CNV | loss | 17160897 |
| nsv961882 | CNV | duplication | 23825009 |
| nsv998333 | CNV | gain+loss | 25217958 |
Residual Variation Intolerance Score:
40.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
3.24;
52.56% of all genes are more intolerant (likely to be disease-causing)
Additional Variant Information for SMPD4 Gene
SNP Genotyping and Copy Number Assays for research
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMPD4 Gene
Disorders for SMPD4 Gene
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies |
|
|
| microcephaly with simplified gyral pattern |
|
|
| coffin-siris syndrome 1 |
|
|
| microcephaly |
|
|
| nanophthalmos |
|
|
Search SMPD4 in MalaCards
View complete list of genes associated with diseases
UniProtKB/Swiss-Prot
NSMA3_HUMAN- Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies (NEDMABA) [MIM:618622]: An autosomal recessive disorder characterized by severe global developmental delay, severely impaired intellectual development with poor or absent speech, severe encephalopathy, microcephaly with simplified gyral pattern, hypomyelination, thin corpus callosum, mild cerebellar hypoplasia, brainstem hypoplasia, congenital arthrogryposis, dysmorphic features, and respiratory problems often leading to early demise. {ECO:0000269 PubMed:31495489}. Note=The disease is caused by variants affecting the gene represented in this entry.
Additional Disease Information for SMPD4
- Human Genome Epidemiology Navigator
- (HuGE)
- Atlas
- ATLAS of Genetics and Cytogenetics in Oncology and Haematology
- Open Targets Platform
- Open Targets Platform
No data available for Genatlas for SMPD4 Gene
Publications for SMPD4 Gene
- Novel tumor necrosis factor-responsive mammalian neutral sphingomyelinase-3 is a C-tail-anchored protein. (PMID: 16517606) Krut O … Krönke M (The Journal of biological chemistry 2006) 2 3 4 25
- Loss of SMPD4 Causes a Developmental Disorder Characterized by Microcephaly and Congenital Arthrogryposis. (PMID: 31495489) Magini P … Mancini GMS (American journal of human genetics 2019) 3 4 72
- Neutral sphingomyelinase-3 mediates TNF-stimulated oxidant activity in skeletal muscle. (PMID: 25180167) Moylan JS … Reid MB (Redox biology 2014) 3 4
- Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 40
- Neutral sphingomyelinase-3 is a DNA damage and nongenotoxic stress-regulated gene that is deregulated in human malignancies. (PMID: 18505924) Corcoran CA … Sheikh MS (Molecular cancer research : MCR 2008) 3 4
ExternalLinks
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Sources for SMPD4 Gene
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