Gene Gene information from NCBI Gene database.
Entrez ID 6609
Gene name Sphingomyelin phosphodiesterase 1
Gene symbol SMPD1
Synonyms (NCBI Gene)
ASMASMASENPD
Chromosome 11
Chromosome location 11p15.4
Summary The protein encoded by this gene is a lysosomal acid sphingomyelinase that converts sphingomyelin to ceramide. The encoded protein also has phospholipase C activity. Defects in this gene are a cause of Niemann-Pick disease type A (NPA) and Niemann-Pick di
SNPs SNP information provided by dbSNP.
146
SNP ID Visualize variation Clinical significance Consequence
rs1803161 G>A,C Pathogenic, uncertain-significance Intron variant, missense variant, 5 prime UTR variant, coding sequence variant, non coding transcript variant
rs120074117 G>A,C,T Likely-pathogenic, pathogenic Coding sequence variant, non coding transcript variant, missense variant
rs120074118 GCC>- Pathogenic Coding sequence variant, non coding transcript variant, inframe deletion, 3 prime UTR variant
rs120074119 G>A Likely-pathogenic Coding sequence variant, non coding transcript variant, missense variant, 3 prime UTR variant
rs120074120 T>A Pathogenic Coding sequence variant, intron variant, 5 prime UTR variant, stop gained, non coding transcript variant
miRNA miRNA information provided by mirtarbase database.
180
miRTarBase ID miRNA Experiments Reference
MIRT648380 hsa-miR-3184-3p HITS-CLIP 23824327
MIRT648379 hsa-miR-3691-3p HITS-CLIP 23824327
MIRT648378 hsa-miR-1289 HITS-CLIP 23824327
MIRT648377 hsa-miR-4294 HITS-CLIP 23824327
MIRT648376 hsa-miR-516b-5p HITS-CLIP 23824327
Transcription factors Transcription factors information provided by TRRUST V2 database.
1
Transcription factor Regulation Reference
SP1 Activation 10224156
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
69
GO ID Ontology Definition Evidence Reference
GO:0001778 Process Plasma membrane repair IDA 20530211
GO:0001778 Process Plasma membrane repair IEA
GO:0004767 Function Sphingomyelin phosphodiesterase activity IDA 9660788, 21098024, 22573858, 33163980
GO:0004767 Function Sphingomyelin phosphodiesterase activity IEA
GO:0004767 Function Sphingomyelin phosphodiesterase activity TAS 1718266
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
607608 11120 ENSG00000166311
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P17405
Protein name Sphingomyelin phosphodiesterase (EC 3.1.4.12) (EC 3.1.4.3) (Acid sphingomyelinase) (aSMase) [Cleaved into: Sphingomyelin phosphodiesterase, processed form]
Protein function Converts sphingomyelin to ceramide (PubMed:12563314, PubMed:1840600, PubMed:18815062, PubMed:25339683, PubMed:25920558, PubMed:27659707, PubMed:33163980). Exists as two enzymatic forms that arise from alternative trafficking of a single protein
PDB 5I81 , 5I85 , 5I8R , 5JG8
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00149 Metallophos 201 463 Calcineurin-like phosphoesterase Domain
Sequence
MPRYGASLRQSCPRSGREQGQDGTAGAPGLLWMGLVLALALALALALALSDSRVLWAPAE
AHPLSPQGHPARLHRIVPRLRDVFGWGNLTCPICKGLFTAINLGLKKEPNVARVGSVAIK
LCNLLKIAPPAVCQSIVHLFEDDMVEVWRRSVLSPSEACGLLLGSTCGHWDIFSSWNISL
PTVPKPPPKPPSPPAPGAPVSRILFLTDLHWDHDYLEGTDPDCADPLCCRRGSGLPPASR
PGAGYWGEYSKCDLPLRTLESLLSGLGPAGPFDMVYWTGDIPAHDVWHQTRQDQLRALTT
VTALVRKFLGPVPVYPAVGNHESTPVNSFPPPFIEGNHSSRWLYEAMAKAWEPWLPAEAL
RTLRIGGFYALSPYPGLRLISLNMNFCSRENFWLLINSTDPAGQLQWLVGELQAAEDRGD
KVHIIGHIPPGHCLKSWSWNYYRIVARYENTLAAQFFGHTHVD
EFEVFYDEETLSRPLAV
AFLAPSATTYIGLNPGYRVYQIDGNYSGSSHVVLDHETYILNLTQANIPGAIPHWQLLYR
ARETYGLPNTLPTAWHNLVYRMRGDMQLFQTFWFLYHKGHPPSEPCGTPCRLATLCAQLS
ARADSPALCRHLMPDGSLPEAQSLWPRPLFC
Sequence length 631
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Sphingolipid metabolism
Metabolic pathways
Sphingolipid signaling pathway
Lysosome
Necroptosis
  Glycosphingolipid metabolism
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
38
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Abnormality of metabolism/homeostasis Likely pathogenic; Pathogenic rs120074117 RCV001814072
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Acid sphingomyelinase deficiency Pathogenic; Likely pathogenic rs200763423, rs2134010914, rs387906289, rs2493820064, rs756366019, rs759389193 RCV005635328
RCV002275717
RCV005357060
RCV005636854
RCV005359522
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Ceroid lipofuscinosis, neuronal, 6A Pathogenic rs587779408 RCV000087097
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability Likely pathogenic; Pathogenic rs752000778 RCV001293359
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
ASTHMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CHRONIC VISCERAL ACID SPHINGOMYELINASE DEFICIENCY Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute Promyelocytic Leukemia Promyelocytic Leukemia HPO_DG
★☆☆☆☆
Found in Text Mining only
Adenomatous Polyposis Coli Multiple polyposis syndrome BEFREE 12774245
★☆☆☆☆
Found in Text Mining only
Adrenal Gland Pheochromocytoma Adrenal Gland Pheochromocytoma BEFREE 30238430
★☆☆☆☆
Found in Text Mining only
Aggressive Systemic Mastocytosis Systemic Mastocytosis BEFREE 25898364, 27868341
★☆☆☆☆
Found in Text Mining only
Alzheimer Disease Alzheimer disease Pubtator 25938590, 33925997 Associate
★☆☆☆☆
Found in Text Mining only
Amenorrhea Amenorrhea Pubtator 23356216 Associate
★☆☆☆☆
Found in Text Mining only
Anemia, Sickle Cell Anemia BEFREE 25075126
★☆☆☆☆
Found in Text Mining only
Anxiety Anxiety Disorder BEFREE 31333574
★☆☆☆☆
Found in Text Mining only
Anxiety Disorders Anxiety Disorder BEFREE 31333574
★☆☆☆☆
Found in Text Mining only
Apraxias Apraxia HPO_DG
★☆☆☆☆
Found in Text Mining only