Seroatlas · Human Serome Atlas

SMPD2

Sphingomyelin phosphodiesterase 2

Also known as: ISC1, NSMA_HUMAN, nSMase

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: O60906
Gene: SMPD2
Ensembl: ENSG00000135587
Chromosome: 6
Canonical length: 423 aa
Protein class: Enzymes, Metabolic proteins, Predicted intracellular proteins, Predicted membrane proteins
Subcellular location: Vesicles,Plasma membrane,Cell Junctions

OverviewNCBI Gene

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]

Canonical amino-acid sequenceUniProt

423 residues, UniProt reviewed canonical sequence.

>O60906|SMPD2
     1  MKPNFSLRLR IFNLNCWGIP YLSKHRADRM RRLGDFLNQE SFDLALLEEV WSEQDFQYLR
    61  QKLSPTYPAA HHFRSGIIGS GLCVFSKHPI QELTQHIYTL NGYPYMIHHG DWFSGKAVGL
   121  LVLHLSGMVL NAYVTHLHAE YNRQKDIYLA HRVAQAWELA QFIHHTSKKA DVVLLCGDLN
   181  MHPEDLGCCL LKEWTGLHDA YLETRDFKGS EEGNTMVPKN CYVSQQELKP FPFGVRIDYV
   241  LYKAVSGFYI SCKSFETTTG FDPHRGTPLS DHEALMATLF VRHSPPQQNP SSTHGPAERS
   301  PLMCVLKEAW TELGLGMAQA RWWATFASYV IGLGLLLLAL LCVLAAGGGA GEAAILLWTP
   361  SVGLVLWAGA FYLFHVQEVN GLYRAQAELQ HVLGRAREAQ DLGPEPQPAL LLGQQEGDRT
   421  KEQ

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SMPD2 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Cell surface
Secreted: No
Transmembrane segments: 2
Mean surface accessibility (rSASA): 0.28
Highest tissue expression: 50 nTPM

Expression across tissuesHPA

Tissue

testis: 50 nTPM
esophagus: 24 nTPM
choroid plexus: 23 nTPM
parathyroid gland: 21 nTPM
skin: 21 nTPM
fallopian tube: 20 nTPM

Single-cell type

late spermatids: 567 nCPM
late primary spermatocytes: 209 nCPM
early spermatids: 172 nCPM
fallopian tube ciliated cells: 101 nCPM
respiratory ciliated cells: 79 nCPM
esophageal apical cells: 74 nCPM

Immune cell

naive B-cell: 21 nTPM
memory B-cell: 14 nTPM
plasmacytoid DC: 14 nTPM
myeloid DC: 11 nTPM
eosinophil: 11 nTPM
classical monocyte: 9 nTPM

Brain region

choroid plexus: 24 nTPM
cerebellum: 12 nTPM
white matter: 11 nTPM
midbrain: 9 nTPM
cerebral cortex: 8.6 nTPM
medulla oblongata: 8.6 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 1.58
gnomAD pLI: 0
gnomAD missense Z: 0.14
DepMap mean gene effect: 0.01
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads SMPD2 as an antibody target. Whether an autoantibody or antibody against SMPD2 could matter depends on whether native SMPD2 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SMPD2 is annotated at the cell surface, where native SMPD2 is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label SMPD2 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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