SPTLC2 serine palmitoyltransferase long chain base subunit 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPTLC2provided by HGNC
Official Full Name: serine palmitoyltransferase long chain base subunit 2provided by HGNC
Primary source: HGNC:HGNC:11278
See related: Ensembl:ENSG00000100596 MIM:605713; Vega:OTTHUMG00000171540
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: LCB2; SPT2; HSN1C; LCB2A; NSAN1C; hLCB2a
Summary: 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]
Expression: Ubiquitous expression in esophagus (RPKM 11.7), colon (RPKM 11.4) and 25 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 14q24.3

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
109	current	GRCh38.p12 (GCF_000001405.38)	14	NC_000014.9 (77505997..77616767, complement)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (77972340..78083110, complement)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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 Jun 15 11:32:44 2016

Bibliography

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GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

2 families had late-onset autosomal dominant HSAN1C caused by a new variant in SPTLC2, c.547C>T, p.(Arg183Trp). The variant changed a conserved amino acid.
Title: The Variant p.(Arg183Trp) in SPTLC2 Causes Late-Onset Hereditary Sensory Neuropathy.
The activities of the hLCB2a mutants were measured in the presence of ssSPTa and ssSPTb and was found that all decrease enzyme activity.
Title: The pyridoxal 5'-phosphate (PLP)-dependent enzyme serine palmitoyltransferase (SPT): effects of the small subunits and insights from bacterial mimics of human hLCB2a HSAN1 mutations.
Mutations in SPTLC2 are associated with increased deoxySL formation causing hereditary sensory and autonomic neuropathy type 1 (HSANI) in a familial study.
Title: Hereditary sensory and autonomic neuropathy type 1 (HSANI) caused by a novel mutation in SPTLC2.
Observational study of gene-disease association. (HuGE Navigator)
Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Mutations in the SPTLC2 subunit of serine palmitoyltransferase cause hereditary sensory and autonomic neuropathy type I.
Title: Mutations in the SPTLC2 subunit of serine palmitoyltransferase cause hereditary sensory and autonomic neuropathy type I.
discovery of 2 proteins, ssSPTa and ssSPTb, which each interacts with both hLCB1 and hLCB2, suggesting that there are 4 distinct human SPT isozymes.
Title: Identification of small subunits of mammalian serine palmitoyltransferase that confer distinct acyl-CoA substrate specificities.
Results suggest that functional serine palmitoyltransferase is not a dimer, but a higher organized complex, composed of three distinct subunits (SPTLC1, SPTLC2 and SPTLC3) with a molecular mass of 480 kDa.
Title: Is the mammalian serine palmitoyltransferase a high-molecular-mass complex?
results suggest that SPTLC2 mutations are not a common cause for genetic sensory neuropathies.
Title: Exclusion of serine palmitoyltransferase long chain base subunit 2 (SPTLC2) as a common cause for hereditary sensory neuropathy.
an increase in transepidermal water loss is an obligatory trigger for the upregulation of serine palmitoyltransferase mRNA expression in human epidermis
Title: Permeability barrier disruption increases the level of serine palmitoyltransferase in human epidermis.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Hereditary sensory and autonomic neuropathy type IC MedGen: C3150896 OMIM: 613640 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat upregulates serine palmitoyltransferase, long chain base subunit 2 (SPTLC2, SPT2) expression in Jurkat T-cells	PubMed

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Pathways from BioSystems

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Ceramide biosynthesis, organism-specific biosystem (from KEGG)
Ceramide biosynthesis, organism-specific biosystemPathway module; Carbohydrate and lipid metabolism; Lipid metabolism
Ceramide biosynthesis, conserved biosystem (from KEGG)
Ceramide biosynthesis, conserved biosystemPathway module; Carbohydrate and lipid metabolism; Lipid metabolism
Metabolic pathways, organism-specific biosystem (from KEGG)
Metabolic pathways, organism-specific biosystem
Metabolic pathways
Metabolism, organism-specific biosystem (from REACTOME)
Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
Sphingolipid Metabolism, organism-specific biosystem (from WikiPathways)
Sphingolipid Metabolism, organism-specific biosystemThe sphingolipid metabolites and genes (with the gene abbreviations shown in boxes, or enzyme names where gene names are ambiguous) are given for the condensation of serine and palmitoyl-CoA to form ...
Sphingolipid de novo biosynthesis, organism-specific biosystem (from REACTOME)
Sphingolipid de novo biosynthesis, organism-specific biosystemThe main steps involved in de novo sphingolipid synthesis are annotated here (Merrill 2002, Gault et al. 2010).
Sphingolipid metabolism, organism-specific biosystem (from KEGG)
Sphingolipid metabolism, organism-specific biosystem
Sphingolipid metabolism
Sphingolipid metabolism, organism-specific biosystem (from REACTOME)
Sphingolipid metabolism, organism-specific biosystemSphingolipids are derivatives of long chain sphingoid bases such as sphingosine (trans-1,3-dihydroxy 2-amino-4-octadecene), an 18-carbon unsaturated amino alcohol which is the most abundant sphingoid...
Sphingolipid metabolism, conserved biosystem (from KEGG)
Sphingolipid metabolism, conserved biosystem
Sphingolipid metabolism
Sphingolipid signaling pathway, organism-specific biosystem (from KEGG)
Sphingolipid signaling pathway, organism-specific biosystemSphingomyelin (SM) and its metabolic products are now known to have second messenger functions in a variety of cellular signaling pathways. Particularly, the sphingolipid metabolites, ceramide (Cer) ...
Sphingolipid signaling pathway, conserved biosystem (from KEGG)
Sphingolipid signaling pathway, conserved biosystemSphingomyelin (SM) and its metabolic products are now known to have second messenger functions in a variety of cellular signaling pathways. Particularly, the sphingolipid metabolites, ceramide (Cer) ...
Sphingosine biosynthesis, organism-specific biosystem (from KEGG)
Sphingosine biosynthesis, organism-specific biosystemPathway module; Carbohydrate and lipid metabolism; Lipid metabolism
Sphingosine biosynthesis, conserved biosystem (from KEGG)
Sphingosine biosynthesis, conserved biosystemPathway module; Carbohydrate and lipid metabolism; Lipid metabolism
ceramide de novo biosynthesis, organism-specific biosystem (from BIOCYC)
ceramide de novo biosynthesis, organism-specific biosystemGeneral Background Ceramides belong to a diverse class of lipids called sphingolipids that have important biological properties and control many aspects of cellular metabolism . They are composed of...
ceramide de novo biosynthesis, conserved biosystem (from BIOCYC)
ceramide de novo biosynthesis, conserved biosystemGeneral Background |FRAME: Ceramides Ceramides| belong to a diverse class of lipids called sphingolipids that have important biological properties and control many aspects of cellular metabolism |CI...
sphingolipid biosynthesis (mammals), conserved biosystem (from BIOCYC)
sphingolipid biosynthesis (mammals), conserved biosystemGeneral Background Sphingolipids are ubiquitous components of eukaryotic cells. They are composed of a long-chain base (amino alcohol), an amide linked fatty acyl chain, and a polar head. The predom...

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH70479 (e-PCR)
- UniSTS:63240

G35447 (e-PCR)
- UniSTS:37899

D14S929 (e-PCR)
- UniSTS:24865

GDB:312794 (e-PCR)
- UniSTS:30247

D8S2279 (e-PCR)
- UniSTS:473907

RH17530 (e-PCR)
- UniSTS:28986

SHGC-35537 (e-PCR)
- UniSTS:82005

RH11203 (e-PCR)
- UniSTS:29316

D14S59 (e-PCR), detects polymorphism
- UniSTS:41094

G35451 (e-PCR)
- UniSTS:51339

A002Y12 (e-PCR)
- UniSTS:68757

L17877 (e-PCR)
- UniSTS:61334

G35529 (e-PCR)
- UniSTS:58781

L17809 (e-PCR)
- UniSTS:39087

G35466 (e-PCR)
- UniSTS:3016

G35534 (e-PCR)
- UniSTS:38601

G36021 (e-PCR)
- UniSTS:51433

D14S843 (e-PCR)
- UniSTS:37870

SHGC-30760 (e-PCR)
- UniSTS:78586

SHGC-132736 (e-PCR)
- UniSTS:182779

Homology

Homologs of the SPTLC2 gene: The SPTLC2 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, S.cerevisiae, K.lactis, E.gossypii, S.pombe, M.oryzae, N.crassa, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 214 organisms have orthologs with human gene SPTLC2
The Hierarchical Catalog of Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
pyridoxal phosphate binding	IEA Inferred from Electronic Annotation more info
serine C-palmitoyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
contributes_to serine C-palmitoyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
serine C-palmitoyltransferase activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
ceramide biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
positive regulation of lipophagy	IDA Inferred from Direct Assay more info	PubMed
sphinganine biosynthetic process	IEA Inferred from Electronic Annotation more info
sphingolipid biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
sphingolipid biosynthetic process	TAS Traceable Author Statement more info	PubMed
sphingomyelin biosynthetic process	IEA Inferred from Electronic Annotation more info
sphingosine biosynthetic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
endoplasmic reticulum membrane	TAS Traceable Author Statement more info
integral component of membrane	IEA Inferred from Electronic Annotation more info
serine C-palmitoyltransferase complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: serine palmitoyltransferase 2

Names: LCB 2; SPT 2; long chain base biosynthesis protein 2a; serine palmitoyltransferase, subunit II; serine-palmitoyl-CoA transferase 2

NP_004854.1

EC 2.3.1.50

XP_011535686.1

EC 2.3.1.50

NCBI Reference Sequences (RefSeq)

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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.