SMPD4

Sphingomyelin phosphodiesterase
4 is an enzyme that in humans is
encoded by the SMPD4 gene.[5][6]
Aliases
Model organisms
Model organisms have been used in
the study of SMPD4 function. A
External
conditional knockout mouse line
IDs
called Smpd4tm2b(KOMP)Wtsi was
generated at the Wellcome Trust
Sanger Institute.[7] Male and female
animals underwent a standardized
phenotypic screen[8] to determine the
effects of deletion.[9][10][11][12]
Additional screens performed: - In-
depth immunological
phenotyping [13]
SMPD4
Identifiers
SMPD4 (https://www.genenames.org/data/gene-symbol-r
eport/#!/hgnc_id/32949), NET13, NSMASE-3, NSMASE3,
sphingomyelin phosphodiesterase 4, SKNY, NEDMABA,
NEDMEBA
OMIM: 610457 (https://omim.org/entry/610457) MGI:
1924876 (http://www.informatics.jax.org/marker/MGI:192
4876) HomoloGene: 9813 (https://www.ncbi.nlm.nih.gov/
entrez/query.fcgi?cmd=Retrieve&db=homologene&dopt=
HomoloGene&list_uids=9813) GeneCards: SMPD4 (http
s://www.genecards.org/cgi-bin/carddisp.pl?gene=SMPD
4)
Gene location (Human)

Chr. Chromosome 2 (human)[1]

Band 2q21.1 Start 130,151,392 bp[1]

End 130,182,750 bp[1]

Gene location (Mouse)

Chr. Chromosome 16 (mouse)[2]

Band 16|16 A3 Start 17,619,354 bp[2]

End 17,644,828 bp[2]
 RNA expression pattern

More reference expression data (http://biogps.org/gene/55627/)

Gene ontology
Molecular • sphingomyelin phosphodiesterase activity (http://ami
function go.geneontology.org/amigo/term/GO:0004767)
• hydrolase activity (http://amigo.geneontology.org/ami
go/term/GO:0016787)
• metal ion binding (http://amigo.geneontology.org/ami
go/term/GO:0046872)
• sphingomyelin phosphodiesterase D activity (http://a
migo.geneontology.org/amigo/term/GO:0050290)
Cellular • integral component of membrane (http://amigo.gene
component ontology.org/amigo/term/GO:0016021)
• Golgi membrane (http://amigo.geneontology.org/ami
go/term/GO:0000139)
• trans-Golgi network (http://amigo.geneontology.org/a
migo/term/GO:0005802)
• Golgi apparatus (http://amigo.geneontology.org/amig
o/term/GO:0005794)
• endoplasmic reticulum membrane (http://amigo.gen
eontology.org/amigo/term/GO:0005789)
• endoplasmic reticulum (http://amigo.geneontology.or
g/amigo/term/GO:0005783)
• membrane (http://amigo.geneontology.org/amigo/ter
m/GO:0016020)
Biological • ceramide biosynthetic process (http://amigo.geneont
process ology.org/amigo/term/GO:0046513)
• cellular response to tumor necrosis factor (http://ami
go.geneontology.org/amigo/term/GO:0071356)
• sphingomyelin catabolic process (http://amigo.geneo
ntology.org/amigo/term/GO:0006685)
• glycosphingolipid metabolic process (http://amigo.ge
neontology.org/amigo/term/GO:0006687)
• glycerophospholipid catabolic process (http://amigo.
geneontology.org/amigo/term/GO:0046475)
 • metabolism (http://amigo.geneontology.org/amigo/te
rm/GO:0008152)
Sources:Amigo (http://amigo.geneontology.org/) / QuickGO (https://
www.ebi.ac.uk/QuickGO/)

Orthologs
Species Human Mouse
Entrez
55627 (https://www.nc 77626 (https://www.ncbi.
bi.nlm.nih.gov/entrez/q nlm.nih.gov/entrez/query.f
uery.fcgi?db=gene&c cgi?db=gene&cmd=retrie
md=retrieve&dopt=def ve&dopt=default&list_uid
ault&list_uids=55627 s=77626&rn=1)
&rn=1)

Ensembl
ENSG00000136699 ENSMUSG00000005899
(http://www.ensembl.o (http://www.ensembl.org/
rg/Homo_sapiens/gen Mus_musculus/genevie
eview?gene=ENSG00 w?gene=ENSMUSG000
000136699;db=core) 00005899;db=core)

UniProt
Q9NXE4 (https://www. Q6ZPR5 (https://www.uni
uniprot.org/uniprot/Q9 prot.org/uniprot/Q6ZPR5)
NXE4)

RefSeq
(mRNA) NM_001171083 (http NM_001164609 (https://
s://www.ncbi.nlm.nih.g www.ncbi.nlm.nih.gov/ent
ov/entrez/viewer.fcgi? rez/viewer.fcgi?val=NM_
val=NM_001171083) 001164609)
NM_001171084 (http NM_001164610 (https://
s://www.ncbi.nlm.nih.g www.ncbi.nlm.nih.gov/ent
ov/entrez/viewer.fcgi? rez/viewer.fcgi?val=NM_
val=NM_001171084) 001164610)
NM_017751 (https://w NM_001164611 (https://
ww.ncbi.nlm.nih.gov/e www.ncbi.nlm.nih.gov/ent
ntrez/viewer.fcgi?val= rez/viewer.fcgi?val=NM_
NM_017751) 001164611)
NM_017951 (https://w NM_029945 (https://ww
ww.ncbi.nlm.nih.gov/e w.ncbi.nlm.nih.gov/entre
ntrez/viewer.fcgi?val= z/viewer.fcgi?val=NM_02
NM_017951) 9945)

RefSeq
(protein) NP_001164554 (http NP_001158081 (https://w
s://www.ncbi.nlm.nih.g ww.ncbi.nlm.nih.gov/entr
ov/entrez/viewer.fcgi? ez/viewer.fcgi?val=NP_0
 val=NP_001164554) 01158081)
NP_060221 (https://w NP_001158082 (https://w
ww.ncbi.nlm.nih.gov/e ww.ncbi.nlm.nih.gov/entr
ntrez/viewer.fcgi?val= ez/viewer.fcgi?val=NP_0
NP_060221) 01158082)
NP_060421 (https://w NP_001158083 (https://w
ww.ncbi.nlm.nih.gov/e ww.ncbi.nlm.nih.gov/entr
ntrez/viewer.fcgi?val= ez/viewer.fcgi?val=NP_0
NP_060421) 01158083)
NP_060421.2 (https:// NP_084221 (https://www.
www.ncbi.nlm.nih.gov/ ncbi.nlm.nih.gov/entrez/vi
entrez/viewer.fcgi?val ewer.fcgi?val=NP_08422
=NP_060421.2) 1)

Location Chr 2: 130.15 – 130.18 Chr 16: 17.62 – 17.64 Mb (ht

(UCSC) Mb (https://genome.ucsc. tps://genome.ucsc.edu/cgi-bi
edu/cgi-bin/hgTracks?org n/hgTracks?org=Mouse&db=
=Human&db=hg38&positi mm0&position=chr16:176193
on=chr2:130151392-1301 54-17644828)
82750)
PubMed [3] [4]

search
Wikidata

View/Edit Human View/Edit Mouse

 Smpd4 knockout mouse phenotype
Characteristic Phenotype

All data available at.[8][13]

Insulin Normal
Homozygous viability at P14 Abnormal
Recessive lethal study Normal
Homozygous Fertility Abnormal
Body weight Normal
Neurological assessment Normal
Grip strength Normal
Dysmorphology Normal
Indirect calorimetry Normal
Glucose tolerance test Normal
Auditory brainstem response Normal
DEXA Normal
Radiography Normal
Eye morphology Normal
Clinical chemistry Normal
Haematology 16 Weeks Normal
Peripheral blood leukocytes 16 Weeks Normal
Heart weight Normal
Salmonella infection Normal
Spleen Immunophenotyping Normal
Mesenteric Lymph Node Immunophenotyping Normal
Epidermal Immune Composition Normal
Influenza Challenge Normal

References
1. GRCh38: Ensembl release 89: ENSG00000136699 (http://May2017.archive.ensembl.org/Hom
o_sapiens/Gene/Summary?db=core;g=ENSG00000136699) - Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000005899 (http://May2017.archive.ensembl.org/
Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000005899) - Ensembl, May 2017
3. "Human PubMed Reference:" (https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&
LinkName=gene_pubmed&from_uid=55627). National Center for Biotechnology Information,
U.S. National Library of Medicine.
4. "Mouse PubMed Reference:" (https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&
LinkName=gene_pubmed&from_uid=77626). National Center for Biotechnology Information,
U.S. National Library of Medicine.
 5. Krut O, Wiegmann K, Kashkar H, Yazdanpanah B, Krönke M (May 2006). "Novel tumor
necrosis factor-responsive mammalian neutral sphingomyelinase-3 is a C-tail-anchored
protein" (https://doi.org/10.1074%2Fjbc.M511306200). The Journal of Biological Chemistry.
281 (19): 13784–93. doi:10.1074/jbc.M511306200 (https://doi.org/10.1074%2Fjbc.M51130620
0). PMID 16517606 (https://pubmed.ncbi.nlm.nih.gov/16517606).
6. "Entrez Gene: SMPD4 sphingomyelin phosphodiesterase 4, neutral membrane (neutral
sphingomyelinase-3)" (https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetail
View&TermToSearch=55627).
7. Gerdin AK (2010). "The Sanger Mouse Genetics Programme: high throughput characterisation
of knockout mice". Acta Ophthalmologica. 88: 925–7. doi:10.1111/j.1755-3768.2010.4142.x (htt
ps://doi.org/10.1111%2Fj.1755-3768.2010.4142.x). S2CID 85911512 (https://api.semanticschol
ar.org/CorpusID:85911512).
8. "International Mouse Phenotyping Consortium" (http://www.mousephenotype.org/data/search?
q=Smpd4#fq=*:*&facet=gene).
9. Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W, Iyer V, Mujica AO, Thomas M,
Harrow J, Cox T, Jackson D, Severin J, Biggs P, Fu J, Nefedov M, de Jong PJ, Stewart AF,
Bradley A (Jun 2011). "A conditional knockout resource for the genome-wide study of mouse
gene function" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3572410). Nature. 474 (7351):
337–42. doi:10.1038/nature10163 (https://doi.org/10.1038%2Fnature10163). PMC 3572410 (htt
ps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3572410). PMID 21677750 (https://pubmed.ncbi.nl
m.nih.gov/21677750).
10. Dolgin E (Jun 2011). "Mouse library set to be knockout" (https://doi.org/10.1038%2F474262a).
Nature. 474 (7351): 262–3. doi:10.1038/474262a (https://doi.org/10.1038%2F474262a).
PMID 21677718 (https://pubmed.ncbi.nlm.nih.gov/21677718).
11. Collins FS, Rossant J, Wurst W (Jan 2007). "A mouse for all reasons". Cell. 128 (1): 9–13.
doi:10.1016/j.cell.2006.12.018 (https://doi.org/10.1016%2Fj.cell.2006.12.018). PMID 17218247
(https://pubmed.ncbi.nlm.nih.gov/17218247). S2CID 18872015 (https://api.semanticscholar.org/
CorpusID:18872015).
12. White JK, Gerdin AK, Karp NA, Ryder E, Buljan M, Bussell JN, Salisbury J, Clare S, Ingham
NJ, Podrini C, Houghton R, Estabel J, Bottomley JR, Melvin DG, Sunter D, Adams NC,
Tannahill D, Logan DW, Macarthur DG, Flint J, Mahajan VB, Tsang SH, Smyth I, Watt FM,
Skarnes WC, Dougan G, Adams DJ, Ramirez-Solis R, Bradley A, Steel KP (Jul 2013).
"Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for
many genes" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717207). Cell. 154 (2): 452–64.
doi:10.1016/j.cell.2013.06.022 (https://doi.org/10.1016%2Fj.cell.2013.06.022). PMC 3717207
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717207). PMID 23870131 (https://pubmed.ncb
i.nlm.nih.gov/23870131).
13. "Infection and Immunity Immunophenotyping (3i) Consortium" (http://www.immunophenotyping.
org/data/search?keys=Smpd4&field_gene_construct_tid=All).

Further reading
Andersson B, Wentland MA, Ricafrente JY,
Liu W, Gibbs RA (Apr 1996). "A "double
adaptor" method for improved shotgun
library construction". Analytical
Biochemistry. 236 (1): 107–13.
doi:10.1006/abio.1996.0138 (https://doi.org/
10.1006%2Fabio.1996.0138).
PMID 8619474 (https://pubmed.ncbi.nlm.nih.
gov/8619474).
Hillier LD, Lennon G, Becker M, Bonaldo
MF, Chiapelli B, Chissoe S, Dietrich N,
DuBuque T, Favello A, Gish W, Hawkins M,
Hultman M, Kucaba T, Lacy M, Le M, Le N,
Mardis E, Moore B, Morris M, Parsons J,
Prange C, Rifkin L, Rohlfing T, Schellenberg
K, Bento Soares M, Tan F, Thierry-Meg J,
Trevaskis E, Underwood K, Wohldman P,
Waterston R, Wilson R, Marra M (Sep 1996).
"Generation and analysis of 280,000 human
expressed sequence tags" (https://doi.org/1
0.1101%2Fgr.6.9.807). Genome Research.
6 (9): 807–28. doi:10.1101/gr.6.9.807 (http
s://doi.org/10.1101%2Fgr.6.9.807).
PMID 8889549 (https://pubmed.ncbi.nlm.nih.
gov/8889549).
Yu W, Andersson B, Worley KC, Muzny DM,
Ding Y, Liu W, Ricafrente JY, Wentland MA,
Lennon G, Gibbs RA (Apr 1997). "Large-
scale concatenation cDNA sequencing" (htt
ps://www.ncbi.nlm.nih.gov/pmc/articles/PMC
139146). Genome Research. 7 (4): 353–8.
doi:10.1101/gr.7.4.353 (https://doi.org/10.11
01%2Fgr.7.4.353). PMC 139146 (https://ww
w.ncbi.nlm.nih.gov/pmc/articles/PMC13914
6). PMID 9110174 (https://pubmed.ncbi.nlm.
nih.gov/9110174).
Nagase T, Kikuno R, Ishikawa KI, Hirosawa
M, Ohara O (Feb 2000). "Prediction of the
coding sequences of unidentified human
genes. XVI. The complete sequences of 150
new cDNA clones from brain which code for
large proteins in vitro" (https://doi.org/10.109
3%2Fdnares%2F7.1.65). DNA Research. 7
(1): 65–73. doi:10.1093/dnares/7.1.65 (http
s://doi.org/10.1093%2Fdnares%2F7.1.65).
PMID 10718198 (https://pubmed.ncbi.nlm.ni
h.gov/10718198).
Wiemann S, Weil B, Wellenreuther R,
Gassenhuber J, Glassl S, Ansorge W,
Böcher M, Blöcker H, Bauersachs S, Blum
H, Lauber J, Düsterhöft A, Beyer A, Köhrer
K, Strack N, Mewes HW, Ottenwälder B,
Obermaier B, Tampe J, Heubner D, Wambutt
R, Korn B, Klein M, Poustka A (Mar 2001).
"Toward a catalog of human genes and
proteins: sequencing and analysis of 500
novel complete protein coding human
cDNAs" (https://www.ncbi.nlm.nih.gov/pmc/a
rticles/PMC311072). Genome Research. 11
(3): 422–35. doi:10.1101/gr.GR1547R (http
s://doi.org/10.1101%2Fgr.GR1547R).
PMC 311072 (https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC311072). PMID 11230166
(https://pubmed.ncbi.nlm.nih.gov/11230166).
Lehner B, Sanderson CM (Jul 2004). "A
protein interaction framework for human
mRNA degradation" (https://www.ncbi.nlm.ni
h.gov/pmc/articles/PMC442147). Genome
Research. 14 (7): 1315–23.
doi:10.1101/gr.2122004 (https://doi.org/10.1
101%2Fgr.2122004). PMC 442147 (https://w
ww.ncbi.nlm.nih.gov/pmc/articles/PMC4421
47). PMID 15231747 (https://pubmed.ncbi.nl
m.nih.gov/15231747).
Jana A, Pahan K (Oct 2004). "Human
immunodeficiency virus type 1 gp120
induces apoptosis in human primary
neurons through redox-regulated activation
of neutral sphingomyelinase" (https://www.n
cbi.nlm.nih.gov/pmc/articles/PMC1955476).
The Journal of Neuroscience. 24 (43):
9531–40. doi:10.1523/JNEUROSCI.3085-
04.2004 (https://doi.org/10.1523%2FJNEUR
OSCI.3085-04.2004). PMC 1955476 (https://
www.ncbi.nlm.nih.gov/pmc/articles/PMC195
5476). PMID 15509740 (https://pubmed.ncb
i.nlm.nih.gov/15509740).
 Kimura K, Wakamatsu A, Suzuki Y, Ota T,
Nishikawa T, Yamashita R, Yamamoto J,
Sekine M, Tsuritani K, Wakaguri H, Ishii S,
Sugiyama T, Saito K, Isono Y, Irie R,
Kushida N, Yoneyama T, Otsuka R, Kanda
K, Yokoi T, Kondo H, Wagatsuma M,
Murakawa K, Ishida S, Ishibashi T,
Takahashi-Fujii A, Tanase T, Nagai K,
Kikuchi H, Nakai K, Isogai T, Sugano S (Jan
2006). "Diversification of transcriptional
modulation: large-scale identification and
characterization of putative alternative
promoters of human genes" (https://www.nc
bi.nlm.nih.gov/pmc/articles/PMC1356129).
Genome Research. 16 (1): 55–65.
doi:10.1101/gr.4039406 (https://doi.org/10.1
101%2Fgr.4039406). PMC 1356129 (https://
www.ncbi.nlm.nih.gov/pmc/articles/PMC135
6129). PMID 16344560 (https://pubmed.ncb
i.nlm.nih.gov/16344560).
Ewing RM, Chu P, Elisma F, Li H, Taylor P,
Climie S, McBroom-Cerajewski L, Robinson
MD, O'Connor L, Li M, Taylor R, Dharsee M,
Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky
O, Bukhman YV, Ethier M, Sheng Y,
Vasilescu J, Abu-Farha M, Lambert JP,
Duewel HS, Stewart II, Kuehl B, Hogue K,
Colwill K, Gladwish K, Muskat B, Kinach R,
Adams SL, Moran MF, Morin GB, Topaloglou
T, Figeys D (2007). "Large-scale mapping of
human protein-protein interactions by mass
spectrometry" (https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC1847948). Molecular
Systems Biology. 3 (1): 89.
doi:10.1038/msb4100134 (https://doi.org/10.
1038%2Fmsb4100134). PMC 1847948 (http
s://www.ncbi.nlm.nih.gov/pmc/articles/PMC1
847948). PMID 17353931 (https://pubmed.n
cbi.nlm.nih.gov/17353931).

Retrieved from "https://en.wikipedia.org/w/index.php?title=SMPD4&oldid=994665560"

This page was last edited on 16 December 2020, at 22:10 (UTC).

Text is available under the Creative Commons Attribution-ShareAlike License; additional terms may apply. By using this
site, you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia
Foundation, Inc., a non-profit organization.