SPTLC3

Protein identityUniProt · HPA

UniProt accession

Q9NUV7

Gene

SPTLC3

Ensembl

ENSG00000172296

Chromosome

20

Canonical length

552 aa

Protein class

Enzymes, Metabolic proteins, Predicted intracellular proteins, Predicted membrane proteins

Subcellular location

Microtubules

OverviewNCBI Gene

This gene encodes a subunit of the serine palmitoyltransferase complex which catalyzes the rate-limiting step in sphingolipid biosynthesis. This subunit metabolizes lauroyl- and myristoyl-CoA and generates C14 and C16-sphingoid bases. [provided by RefSeq, Mar 2017]

Canonical amino-acid sequenceUniProt

552 residues, UniProt reviewed canonical sequence.

>Q9NUV7|SPTLC3
     1  MANPGGGAVC NGKLHNHKKQ SNGSQSRNCT KNGIVKEAQQ NGKPHFYDKL IVESFEEAPL
    61  HVMVFTYMGY GIGTLFGYLR DFLRNWGIEK CNAAVERKEQ KDFVPLYQDF ENFYTRNLYM
   121  RIRDNWNRPI CSAPGPLFDL MERVSDDYNW TFRFTGRVIK DVINMGSYNF LGLAAKYDES
   181  MRTIKDVLEV YGTGVASTRH EMGTLDKHKE LEDLVAKFLN VEAAMVFGMG FATNSMNIPA
   241  LVGKGCLILS DELNHTSLVL GARLSGATIR IFKHNNTQSL EKLLRDAVIY GQPRTRRAWK
   301  KILILVEGVY SMEGSIVHLP QIIALKKKYK AYLYIDEAHS IGAVGPTGRG VTEFFGLDPH
   361  EVDVLMGTFT KSFGASGGYI AGRKDLVDYL RVHSHSAVYA SSMSPPIAEQ IIRSLKLIMG
   421  LDGTTQGLQR VQQLAKNTRY FRQRLQEMGF IIYGNENASV VPLLLYMPGK VAAFARHMLE
   481  KKIGVVVVGF PATPLAEARA RFCVSAAHTR EMLDTVLEAL DEMGDLLQLK YSRHKKSARP
   541  ELYDETSFEL ED

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SPTLC3 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

Other membrane

Secreted

No

Transmembrane segments

1

Mean surface accessibility (rSASA)

0.3

Highest tissue expression

24 nTPM

Expression across tissuesHPA

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SPTLC3.

Disease | GeneticClinVar

1 pathogenic / likely-pathogenic of 81 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

• Peripheral neuropathy
• Sensory neuropathy

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)

0.83

gnomAD pLI

0

gnomAD missense Z

1.17

DepMap mean gene effect

0.04

DepMap dependency class

none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• ceramide biosynthetic process
• sphingolipid biosynthetic process
• sphingosine biosynthetic process
• sphingoid biosynthetic process

Molecular functions

• pyridoxal phosphate binding
• serine C-palmitoyltransferase activity

Cellular components

• endoplasmic reticulum membrane
• serine palmitoyltransferase complex

Protein domainsUniProt · Pfam · InterPro

• Aminotransferase, class-II, pyridoxal-phosphate binding site
• Aminotransferase, class I/classII, large domain
• Pyridoxal phosphate-dependent transferase, major domain
• Pyridoxal phosphate-dependent transferase, small domain
• Pyridoxal phosphate-dependent transferase
• 8-amino-7-oxononanoate synthase class-II
• Aminotransferase class I and II

KeywordsUniProt

• Acyltransferase
• Endoplasmic reticulum
• Lipid metabolism
• Membrane
• Pyridoxal phosphate
• Sphingolipid metabolism
• Transferase
• Transmembrane
• Transmembrane helix