SPTLC2

Protein identityUniProt · HPA

UniProt accession

O15270

Gene

SPTLC2

Ensembl

ENSG00000100596

Chromosome

14

Canonical length

562 aa

Protein class

Disease related genes, Enzymes, Human disease related genes, Metabolic proteins, Plasma proteins, Potential drug targets, Predicted membrane proteins

Subcellular location

Plasma membrane,Cell Junctions

OverviewNCBI Gene

This gene encodes a long chain base subunit of serine palmitoyltransferase. Serine palmitoyltransferase, which consists of two different subunits, is the key enzyme in sphingolipid biosynthesis. It catalyzes the pyridoxal-5-prime-phosphate-dependent condensation of L-serine and palmitoyl-CoA to 3-oxosphinganine. Mutations in this gene were identified in patients with hereditary sensory neuropathy type I. [provided by RefSeq, Mar 2011]

Canonical amino-acid sequenceUniProt

562 residues, UniProt reviewed canonical sequence.

>O15270|SPTLC2
     1  MRPEPGGCCC RRTVRANGCV ANGEVRNGYV RSSAAAAAAA AAGQIHHVTQ NGGLYKRPFN
    61  EAFEETPMLV AVLTYVGYGV LTLFGYLRDF LRYWRIEKCH HATEREEQKD FVSLYQDFEN
   121  FYTRNLYMRI RDNWNRPICS VPGARVDIME RQSHDYNWSF KYTGNIIKGV INMGSYNYLG
   181  FARNTGSCQE AAAKVLEEYG AGVCSTRQEI GNLDKHEELE ELVARFLGVE AAMAYGMGFA
   241  TNSMNIPALV GKGCLILSDE LNHASLVLGA RLSGATIRIF KHNNMQSLEK LLKDAIVYGQ
   301  PRTRRPWKKI LILVEGIYSM EGSIVRLPEV IALKKKYKAY LYLDEAHSIG ALGPTGRGVV
   361  EYFGLDPEDV DVMMGTFTKS FGASGGYIGG KKELIDYLRT HSHSAVYATS LSPPVVEQII
   421  TSMKCIMGQD GTSLGKECVQ QLAENTRYFR RRLKEMGFII YGNEDSPVVP LMLYMPAKIG
   481  AFGREMLKRN IGVVVVGFPA TPIIESRARF CLSAAHTKEI LDTALKEIDE VGDLLQLKYS
   541  RHRLVPLLDR PFDETTYEET ED

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SPTLC2 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)

0.29

Highest tissue expression

30 nTPM

Expression across tissuesHPA

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SPTLC2.

Disease | AllUniProt

Conditions SPTLC2 is implicated in, by any mechanism.

• Neuropathy, hereditary sensory and autonomic, 1C (HSAN1C) MIM:613640

Disease | GeneticClinVar

10 pathogenic / likely-pathogenic of 700 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

• Neuropathy, hereditary sensory and autonomic, type 1C
• NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE IC, SEVERE
• Inborn genetic diseases
• Hereditary neuropathy or pain disorder
• Charcot-Marie-Tooth disease

Disease | ImmuneIEDB

Conditions an epitope on SPTLC2 was assayed in.

• melanoma T cell

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)

0.39

gnomAD pLI

0.78

gnomAD missense Z

2.04

DepMap mean gene effect

-0.28

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

• adipose tissue development
• ceramide biosynthetic process
• positive regulation of lipophagy
• sphinganine biosynthetic process
• sphingolipid biosynthetic process
• sphingomyelin biosynthetic process
• sphingosine 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
• Neurodegeneration
• Neuropathy
• Pyridoxal phosphate
• Sphingolipid metabolism
• Transferase
• Transmembrane
• Transmembrane helix

InteractionsUniProt · HPA

Protein binding partners of SPTLC2 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

• PTPRN
• SPTLC1