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SMPD4 sphingomyelin phosphodiesterase 4 [ Homo sapiens (human) ]

Gene ID: 55627, updated on 27-Jun-2020

Summary

Official Symbol
SMPD4provided by HGNC
Official Full Name
sphingomyelin phosphodiesterase 4provided by HGNC
Primary source
HGNC:HGNC:32949
See related
Ensembl:ENSG00000136699 MIM:610457
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SKNY; NET13; NEDMABA; NEDMEBA; NSMASE3; NSMASE-3
Summary
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]
Expression
Ubiquitous expression in bone marrow (RPKM 16.4), testis (RPKM 14.6) and 25 other tissues See more
Orthologs

Genomic context

See SMPD4 in Genome Data Viewer
Location:
2q21.1
Exon count:
21
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (130151392..130181757, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (130908965..130940323, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene POTE ankyrin domain family member F Neighboring gene RNA, U6 small nuclear 1049, pseudogene Neighboring gene POTEF antisense RNA 1 Neighboring gene mediator complex subunit 15 pseudogene 9 Neighboring gene coiled-coil domain containing 74B Neighboring gene mitotic spindle organizing protein 2B Neighboring gene tubulin alpha 3e

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 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

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

Clone Names

  • FLJ20297, FLJ20756, KIAA1418

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
sphingomyelin phosphodiesterase D activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sphingomyelin phosphodiesterase D activity IDA
Inferred from Direct Assay
more info
PubMed 
sphingomyelin phosphodiesterase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cellular response to tumor necrosis factor IDA
Inferred from Direct Assay
more info
PubMed 
ceramide biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ceramide biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
glycerophospholipid catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glycerophospholipid catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
glycosphingolipid metabolic process TAS
Traceable Author Statement
more info
 
in utero embryonic development IEA
Inferred from Electronic Annotation
more info
 
sphingomyelin catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sphingomyelin catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
nuclear envelope ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear outer membrane IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
sphingomyelin phosphodiesterase 4
Names
neutral sphingomyelinase 3
neutral sphingomyelinase III
sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)
NP_001164554.1
NP_060221.2
NP_060421.2
XP_011509745.1
XP_011509746.1
XP_011509747.1
XP_016859937.1
XP_016859938.1
XP_024308746.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_053070.1 RefSeqGene

    Range
    5994..36359
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001171083.2NP_001164554.1  sphingomyelin phosphodiesterase 4 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two alternate exons resulting in the loss of an in-frame segment in the 5' coding region, and it also lacks an alternate in-frame exon in the central coding region, compared to variant 2. The resulting isoform (3) is shorter than isoform 2.
    Source sequence(s)
    AC018804, AI393912, AK299185, DA797873
    Consensus CDS
    CCDS54398.1
    UniProtKB/Swiss-Prot
    Q9NXE4
    Related
    ENSP00000405187.2, ENST00000431183.6
    Conserved Domains (1) summary
    pfam14724
    Location:47709
    mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase
  2. NM_017751.4NP_060221.2  sphingomyelin phosphodiesterase 4 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an alternate in-frame exon in the central coding region, compared to variant 2, resulting in an isoform (1) that is shorter than isoform 2.
    Source sequence(s)
    AI393912, AK000304, DA797873
    Consensus CDS
    CCDS2156.2
    UniProtKB/Swiss-Prot
    Q9NXE4
    UniProtKB/TrEMBL
    H7BXF4
    Related
    ENSP00000259217.8, ENST00000351288.10
    Conserved Domains (1) summary
    pfam14724
    Location:47782
    mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase
  3. NM_017951.4NP_060421.2  sphingomyelin phosphodiesterase 4 isoform 2

    See identical proteins and their annotated locations for NP_060421.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) encodes the longest isoform (2).
    Source sequence(s)
    AC018804, AI393912, DA797873, EU367941
    Consensus CDS
    CCDS42751.1
    UniProtKB/Swiss-Prot
    Q9NXE4
    UniProtKB/TrEMBL
    B1PBA3
    Related
    ENSP00000386531.1, ENST00000409031.5
    Conserved Domains (1) summary
    pfam14724
    Location:47811
    mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

RNA

  1. NR_033231.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate internal exon in the 5' region, compared to variant 2. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC018804, AI393912, BC064947, DA797873
    Related
    ENST00000454468.5
  2. NR_033232.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks an alternate internal exon in both the 5' and central regions, compared to variant 2. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC018804, AI393912, AK303519, DA797873
    Related
    ENST00000412570.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    130151392..130181757 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011511443.2XP_011509745.1  sphingomyelin phosphodiesterase 4 isoform X1

    Conserved Domains (1) summary
    pfam14724
    Location:125889
    mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase
  2. XM_011511445.2XP_011509747.1  sphingomyelin phosphodiesterase 4 isoform X3

    See identical proteins and their annotated locations for XP_011509747.1

    UniProtKB/Swiss-Prot
    Q9NXE4
    Related
    ENSP00000401648.1, ENST00000439886.5
    Conserved Domains (1) summary
    pfam14724
    Location:1680
    mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase
  3. XM_017004448.2XP_016859937.1  sphingomyelin phosphodiesterase 4 isoform X4

    UniProtKB/Swiss-Prot
    Q9NXE4
    Conserved Domains (1) summary
    pfam14724
    Location:97552
    mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase
  4. XM_017004449.2XP_016859938.1  sphingomyelin phosphodiesterase 4 isoform X5

    UniProtKB/Swiss-Prot
    Q9NXE4
    Conserved Domains (1) summary
    pfam14724
    Location:1373
    mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase
  5. XM_024452978.1XP_024308746.1  sphingomyelin phosphodiesterase 4 isoform X4

    Conserved Domains (1) summary
    pfam14724
    Location:97552
    mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase
  6. XM_011511444.3XP_011509746.1  sphingomyelin phosphodiesterase 4 isoform X2

    Conserved Domains (1) summary
    pfam14724
    Location:125860
    mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

RNA

  1. XR_002959315.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001171084.1: Suppressed sequence

    Description
    NM_001171084.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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