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SMPD2 sphingomyelin phosphodiesterase 2 [ Homo sapiens (human) ]

Gene ID: 6610, updated on 22-Sep-2022

Summary

Official Symbol
SMPD2provided by HGNC
Official Full Name
sphingomyelin phosphodiesterase 2provided by HGNC
Primary source
HGNC:HGNC:11121
See related
Ensembl:ENSG00000135587 MIM:603498; AllianceGenome:HGNC:11121
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ISC1; NSMASE; NSMASE1
Summary
This gene encodes a protein which was initially identified as a sphingomyelinase based on sequence similarity between bacterial sphingomyelinases and a yeast protein. Subsequent studies showed that its biological function is less likely to be as a sphingomyelinase and instead as a lysophospholipase. [provided by RefSeq, Oct 2009]
Expression
Broad expression in testis (RPKM 17.9), skin (RPKM 6.8) and 24 other tissues See more
Orthologs
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Genomic context

See SMPD2 in Genome Data Viewer
Location:
6q21
Exon count:
10
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (109440724..109443919)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (110618762..110621957)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (109761927..109765122)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 15445 Neighboring gene CD164 molecule Neighboring gene peptidylprolyl isomerase like 6 Neighboring gene microtubule associated monooxygenase, calponin and LIM domain containing 1 Neighboring gene zinc finger and BTB domain containing 24 Neighboring gene ZBTB24 divergent transcript Neighboring gene adenylate kinase 9

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Treatment of cells with sphingomyelinase inhibits viral fusion after the engagement of HIV-1 gp120 with CD4 and sphingomyelinase restricts CD4 mobility. This inhibition is dependent on CD4 expression levels PubMed
env HIV-1 gp120 binding to CXCR4 induces NADPH oxidase-mediated production of superoxide radicals in neurons, which is involved in the activation of neutral sphingomyelinase PubMed
env In human primary neurons, HIV-1 gp120 induces the activation of sphingomyelinases (primarily neutral sphingomyelinase); antisense knockdown of neutral sphingomyelinase markedly inhibits gp120-mediated apoptosis and cell death of primary neurons PubMed
Nef nef HIV-1 Nef inhibits sphingomyelinase activity in human podocyte PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables phospholipase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables phosphoric diester hydrolase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sphingomyelin phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables sphingomyelin phosphodiesterase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in ceramide biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in sphingolipid catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in sphingomyelin catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in sphingomyelin metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
is_active_in caveola IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in cell periphery IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
sphingomyelin phosphodiesterase 2
Names
N-SMase
lyso-PAF-PLC
lyso-platelet-activating factor-phospholipase C
neutral sphingomyelinase
NP_003071.2
XP_011534381.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_003080.3NP_003071.2  sphingomyelin phosphodiesterase 2

    See identical proteins and their annotated locations for NP_003071.2

    Status: VALIDATED

    Source sequence(s)
    AJ222801, AL109947, CA314251, DA672570
    Consensus CDS
    CCDS5075.1
    UniProtKB/Swiss-Prot
    O60906, Q9BWR3
    Related
    ENSP00000258052.3, ENST00000258052.8
    Conserved Domains (1) summary
    cl00490
    Location:14279
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    109440724..109443919
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011536079.2XP_011534381.1  sphingomyelin phosphodiesterase 2 isoform X1

    Conserved Domains (1) summary
    cl00490
    Location:6174
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

RNA

  1. XR_942566.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    110618762..110621957
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)