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
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
109.20191205	current	GRCh38.p13 (GCF_000001405.39)	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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Go to reference sequence details

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 Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Elevated levels of atypical deoxysphingolipids, caused by variant SPTLC1 or SPTLC2 or by low serine levels, were risk factors for macular telangiectasia type 2, as well as for peripheral neuropathy.
Title: Serine and Lipid Metabolism in Macular Disease and Peripheral Neuropathy.
HSAN-I-associated mutations in serine palmitoyltransferase subunit SPTLC2 dampened human T cell responses. SPTLC2 underpins protective immunity by translating extracellular stimuli into intracellular anabolic signals and antagonizes endoplasmic reticulum stress to promote T cell metabolic fitness.
Title: Loss of Neurological Disease HSAN-I-Associated Gene SPTLC2 Impairs CD8<sup>+</sup> T Cell Responses to Infection by Inhibiting T Cell Metabolic Fitness.
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.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

Go to the HIV-1, Human Interaction Database

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: 252 organisms have orthologs with human gene SPTLC2
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

Process	Evidence Code	Pubs
adipose tissue development	ISS Inferred from Sequence or Structural Similarity more info
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.

Genomic

NG_028282.1 RefSeqGene

Range

5001..115771

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_371

mRNA and Protein(s)

NM_004863.3 → NP_004854.1 serine palmitoyltransferase 2

See identical proteins and their annotated locations for NP_004854.1

Status: REVIEWED

Source sequence(s)

AB011098, AF111168, BQ338973

Consensus CDS

CCDS9865.1

UniProtKB/Swiss-Prot

O15270

UniProtKB/TrEMBL

A0A024R6H1

Related

ENSP00000216484.2, ENST00000216484.6

Conserved Domains (1) summary

PLN02483
Location:67 → 542

PLN02483; serine palmitoyltransferase

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000014.9 Reference GRCh38.p13 Primary Assembly

Range

77505997..77616767 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011537384.2 → XP_011535686.1 serine palmitoyltransferase 2 isoform X1

See identical proteins and their annotated locations for XP_011535686.1

Related

ENSP00000452189.1, ENST00000554901.1

Conserved Domains (2) summary

PLN02483
Location:67 → 435

PLN02483; serine palmitoyltransferase

COG0156
Location:117 → 426

BioF; 7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]