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; AllianceGenome:HGNC:11278
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
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 14q24.3

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (77505997..77616637, complement)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (71715382..71825999, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (77972340..78082980, complement)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Rare mutations in ATL3, SPTLC2 and SCN9A explaining hereditary sensory neuropathy and congenital insensitivity to pain in a Brazilian cohort.
Title: Rare mutations in ATL3, SPTLC2 and SCN9A explaining hereditary sensory neuropathy and congenital insensitivity to pain in a Brazilian cohort.
Structural insights into the assembly and substrate selectivity of human SPT-ORMDL3 complex.
Title: Structural insights into the assembly and substrate selectivity of human SPT-ORMDL3 complex.
A Novel Variant (Asn177Asp) in SPTLC2 Causing Hereditary Sensory Autonomic Neuropathy Type 1C.
Title: A Novel Variant (Asn177Asp) in SPTLC2 Causing Hereditary Sensory Autonomic Neuropathy Type 1C.
Increased expression of serine palmitoyl transferase and ORMDL3 polymorphism are associated with eosinophilic inflammation and airflow limitation in aspirin-exacerbated respiratory disease.
Title: Increased expression of serine palmitoyl transferase and ORMDL3 polymorphism are associated with eosinophilic inflammation and airflow limitation in aspirin-exacerbated respiratory disease.
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.

Submit: New GeneRIF Correction See all GeneRIFs (15)

Phenotypes

Go to the top of the page Help

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
Neuropathy, hereditary sensory and autonomic, type 1C MedGen: C3150896 OMIM: 613640 GeneReviews: Not available	Compare labs

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

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

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

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: 366 organisms have orthologs with human gene SPTLC2
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables pyridoxal phosphate binding	IEA Inferred from Electronic Annotation more info
enables serine C-palmitoyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
contributes_to serine C-palmitoyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables serine C-palmitoyltransferase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in adipose tissue development	ISS Inferred from Sequence or Structural Similarity more info
involved_in ceramide biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of_or_within ceramide biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of lipophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in sphinganine biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within sphingolipid biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in sphingolipid biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in sphingolipid biosynthetic process	TAS Traceable Author Statement more info	PubMed
involved_in sphingomyelin biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in sphingosine biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in sphingosine biosynthetic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
part_of serine C-palmitoyltransferase complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of serine C-palmitoyltransferase complex	IDA Inferred from Direct Assay more info	PubMed
part_of serine C-palmitoyltransferase complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

Go to the top of the page Help

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)

Go to the top of the page Help

NEW Try the new Transcript table

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_004863.4 → 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, Q16685

UniProtKB/TrEMBL

A0A024R6H1

Related

ENSP00000216484.2, ENST00000216484.7

Conserved Domains (1) summary

cl18945
Location:67 → 542

AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

77505997..77616637 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011537384.3 → 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]