SPTLC3 serine palmitoyltransferase long chain base subunit 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPTLC3provided by HGNC
Official Full Name: serine palmitoyltransferase long chain base subunit 3provided by HGNC
Primary source: HGNC:HGNC:16253
See related: Ensembl:ENSG00000172296 MIM:611120; AllianceGenome:HGNC:16253
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: LCB3; SPT3; LCB 3; LCB2B; SPT 3; hLCB2b; SPTLC2L; C20orf38; dJ718P11; dJ718P11.1
Summary: 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]
Expression: Broad expression in placenta (RPKM 7.5), thyroid (RPKM 7.0) and 22 other tissues See more
Orthologs: all
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Genomic context

Location:: 20p12.1

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2025_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (13008972..13169103)
RS_2025_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (13048743..13212449)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (12989620..13149750)

Chromosome 20 - NC_000020.11 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Serine Palmitoyltransferase Subunit 3 and Metabolic Diseases.
Title: Serine Palmitoyltransferase Subunit 3 and Metabolic Diseases.
The associations between individual plasma SFAs, serine palmitoyl-transferase long-chain base subunit 3 gene rs680379 polymorphism, and type 2 diabetes among Chinese adults.
Title: The associations between individual plasma SFAs, serine palmitoyl-transferase long-chain base subunit 3 gene rs680379 polymorphism, and type 2 diabetes among Chinese adults.
This study demonstrated that the association of SPTLC3insACAC (p = 0.055) with the treatment-resistant ophthalmoplegic subphenotype of myasthenia gravis.
Title: Exome sequencing identifies targets in the treatment-resistant ophthalmoplegic subphenotype of myasthenia gravis.
The association between the SPTLC3 rs364585 SNP and serum total cholesterol, high-density lipoprotein cholesterol and low-density lipoprotein cholesterol levels in the Han and Jing populations
Title: Association of the SPTLC3 rs364585 polymorphism and serum lipid profiles in two Chinese ethnic groups.
Data identified LC3B globular structures in esophageal adenocarcinoma patients strongly associated with patient outcome irrespective of treatment.
Title: LC3B globular structures correlate with survival in esophageal adenocarcinoma.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Observational study of gene-disease association. (HuGE Navigator)
Title: A genome-wide perspective of genetic variation in human metabolism.
Data show that the SPTLC3 subunit generates C(16)-sphingoid bases and that sphingolipids with a C(16) backbone constitute a significant proportion of plasma sphingolipids.
Title: The SPTLC3 subunit of serine palmitoyltransferase generates short chain sphingoid bases.
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?

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

EBI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites. EBI GWAS Catalog EBI GWAS CatalogPubMed
Discovery and refinement of loci associated with lipid levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
Gene-environment interactions and obesity traits among postmenopausal African-American and Hispanic women in the Women's Health Initiative SHARe Study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic determinants of circulating sphingolipid concentrations in European populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of personality traits in bipolar patients. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH48472 (e-PCR)
- UniSTS:50178

Z94384 (e-PCR)
- UniSTS:33303

SHGC-33870 (e-PCR)
- UniSTS:12570

A006P19 (e-PCR)
- UniSTS:3941

RH68830 (e-PCR)
- UniSTS:25189

Z94711 (e-PCR)
- UniSTS:24683

A009V27 (e-PCR)
- UniSTS:913

Z94369 (e-PCR)
- UniSTS:79782

D20S56 (e-PCR)
- UniSTS:146855

D20S58 (e-PCR)
- UniSTS:146857

G27414 (e-PCR)
- UniSTS:21678

WI-17312 (e-PCR)
- UniSTS:82608

SHGC-36445 (e-PCR)
- UniSTS:33968

G18103 (e-PCR)
- UniSTS:61618

D2S2887 (e-PCR)
- UniSTS:78538

G32882 (e-PCR)
- UniSTS:117461

D20S131E (e-PCR)
- UniSTS:48118

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
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
enables serine C-palmitoyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables serine C-palmitoyltransferase activity	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in ceramide biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within sphingoid biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in sphingolipid biosynthetic process	TAS Traceable Author Statement more info	PubMed
involved_in sphingolipid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in sphingosine biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in sphingosine biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in sphingosine biosynthetic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	NAS Non-traceable Author Statement more info	PubMed
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
part_of serine palmitoyltransferase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of serine palmitoyltransferase complex	IDA Inferred from Direct Assay more info	PubMed
part_of serine palmitoyltransferase complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: serine palmitoyltransferase 3

Names: long chain base biosynthesis protein 2b; long chain base biosynthesis protein 3; serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2); serine-palmitoyl-CoA transferase 3

NP_001336874.1

EC 2.3.1.50

NP_060797.2

EC 2.3.1.50

XP_011527581.1

EC 2.3.1.50

XP_011527582.1

EC 2.3.1.50

XP_047296211.1

EC 2.3.1.50

XP_047296212.1

EC 2.3.1.50

XP_054179588.1

EC 2.3.1.50

XP_054179589.1

EC 2.3.1.50

XP_054179590.1

EC 2.3.1.50

XP_054179591.1

EC 2.3.1.50

XP_054179592.1

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_053155.2 RefSeqGene

Range

5002..165133

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001349945.2 → NP_001336874.1 serine palmitoyltransferase 3

Status: REVIEWED

Source sequence(s)

AL050320, AL109983, AL133331, AL445589

Consensus CDS

CCDS13115.2

UniProtKB/Swiss-Prot

A2A2I4, B9EK64, Q05DQ8, Q5T1U4, Q9H1L1, Q9H1Z0, Q9NUV7

Conserved Domains (1) summary

PLN02483
Location:57 → 549

PLN02483; serine palmitoyltransferase
NM_018327.4 → NP_060797.2 serine palmitoyltransferase 3

See identical proteins and their annotated locations for NP_060797.2

Status: REVIEWED

Source sequence(s)

AL050320, AL109983, AL133331, AL445589

Consensus CDS

CCDS13115.2

UniProtKB/Swiss-Prot

A2A2I4, B9EK64, Q05DQ8, Q5T1U4, Q9H1L1, Q9H1Z0, Q9NUV7

Related

ENSP00000381968.2, ENST00000399002.7

Conserved Domains (1) summary

PLN02483
Location:57 → 549

PLN02483; serine palmitoyltransferase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

13008972..13169103

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011529279.2 → XP_011527581.1 serine palmitoyltransferase 3 isoform X1

Conserved Domains (2) summary

PLN02483
Location:57 → 514

PLN02483; serine palmitoyltransferase

COG0156
Location:109 → 517

BioF; 7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]
XM_047440255.1 → XP_047296211.1 serine palmitoyltransferase 3 isoform X1
XM_047440256.1 → XP_047296212.1 serine palmitoyltransferase 3 isoform X3

UniProtKB/TrEMBL

B4DTF0
XM_011529280.2 → XP_011527582.1 serine palmitoyltransferase 3 isoform X2

Conserved Domains (2) summary

PLN02483
Location:11 → 358

PLN02483; serine palmitoyltransferase

COG0156
Location:10 → 333

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

Alternate T2T-CHM13v2.0

Genomic

NC_060944.1 Alternate T2T-CHM13v2.0

Range

13048743..13212449

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054323613.1 → XP_054179588.1 serine palmitoyltransferase 3 isoform X4

UniProtKB/Swiss-Prot

A2A2I4, B9EK64, Q05DQ8, Q5T1U4, Q9H1L1, Q9H1Z0, Q9NUV7
XM_054323614.1 → XP_054179589.1 serine palmitoyltransferase 3 isoform X1
XM_054323615.1 → XP_054179590.1 serine palmitoyltransferase 3 isoform X1
XM_054323617.1 → XP_054179592.1 serine palmitoyltransferase 3 isoform X3

UniProtKB/TrEMBL

B4DTF0
XM_054323616.1 → XP_054179591.1 serine palmitoyltransferase 3 isoform X2