SPTLC1 serine palmitoyltransferase long chain base subunit 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPTLC1provided by HGNC
Official Full Name: serine palmitoyltransferase long chain base subunit 1provided by HGNC
Primary source: HGNC:HGNC:11277
See related: Ensembl:ENSG00000090054 MIM:605712; AllianceGenome:HGNC:11277
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: HSN1; LBC1; LCB1; SPT1; SPTI; ALS27; HSAN1
Summary: This gene encodes a member of the class-II pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is the long chain base subunit 1 of serine palmitoyltransferase. Serine palmitoyltransferase converts L-serine and palmitoyl-CoA to 3-oxosphinganine with pyridoxal 5'-phosphate and is the key enzyme in sphingolipid biosynthesis. Mutations in this gene were identified in patients with hereditary sensory neuropathy type 1. Alternatively spliced variants encoding different isoforms have been identified. Pseudogenes of this gene have been defined on chromosomes 1, 6, 10, and 13. [provided by RefSeq, Jul 2013]
Expression: Ubiquitous expression in thyroid (RPKM 21.8), esophagus (RPKM 19.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q22.31

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (92031147..92115413, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (104197620..104281900, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (94793429..94877695, complement)

Chromosome 9 - NC_000009.12 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?

Mutation screening of SPTLC1 and SPTLC2 in amyotrophic lateral sclerosis.
Title: Mutation screening of SPTLC1 and SPTLC2 in amyotrophic lateral sclerosis.
Clinical feature difference between juvenile amyotrophic lateral sclerosis with SPTLC1 and FUS mutations.
Title: Clinical feature difference between juvenile amyotrophic lateral sclerosis with SPTLC1 and FUS mutations.
Pathogenic variants in the SPTLC1 gene cause hyperkeratosis lenticularis perstans.
Title: Pathogenic variants in the SPTLC1 gene cause hyperkeratosis lenticularis perstans.
The SPTLC1 p.S331 mutation bridges sensory neuropathy and motor neuron disease and has implications for treatment.
Title: The SPTLC1 p.S331 mutation bridges sensory neuropathy and motor neuron disease and has implications for treatment.
New Insights into the Neuromyogenic Spectrum of a Gain of Function Mutation in SPTLC1.
Title: New Insights into the Neuromyogenic Spectrum of a Gain of Function Mutation in SPTLC1.
Association of Variants in the SPTLC1 Gene With Juvenile Amyotrophic Lateral Sclerosis.
Title: Association of Variants in the SPTLC1 Gene With Juvenile Amyotrophic Lateral Sclerosis.
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.
Decreased SPTLC1 expression predicts worse outcomes in ccRCC patients.
Title: Decreased SPTLC1 expression predicts worse outcomes in ccRCC patients.
Yhe results revealed that forced expression of SPTLC1 could significantly inhibit cell growth in vitro and in vivo via, at least in part, modulating Akt/FOXO1 signaling pathway, thus representing a novel role of SPTLC1 in the regulation of tumor growth in renal cell carcinoma (RCC).
Title: SPTLC1 inhibits cell growth via modulating Akt/FOXO1 pathway in renal cell carcinoma cells.
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.

Submit: New GeneRIF Correction See all GeneRIFs (35)

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
Amyotrophic lateral sclerosis 27, juvenile MedGen: C5830359 OMIM: 620285 GeneReviews: Not available	not available
Hereditary sensory and autonomic neuropathy type 1 MedGen: C0020071 GeneReviews: SPTLC1-Related Hereditary Sensory Neuropathy	Compare labs
Neuropathy, hereditary sensory and autonomic, type 1A MedGen: C5235211 OMIM: 162400 GeneReviews: SPTLC1-Related Hereditary Sensory Neuropathy	Compare labs

EBI GWAS Catalog

Description
Genetic variation modifies risk for neurodegeneration based on biomarker status. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder. 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)

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 1 (SPTLC1, SPT1) 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

D11S2921 (e-PCR)
- UniSTS:152074

RH26813 (e-PCR)
- UniSTS:86287

D10S275 (e-PCR)
- UniSTS:147992

D11S2560 (e-PCR)
- UniSTS:37928

D8S2279 (e-PCR)
- UniSTS:473907

G19655 (e-PCR)
- UniSTS:8255

A001U11 (e-PCR)
- UniSTS:8256

D1S1425 (e-PCR)
- UniSTS:149621

G17347 (e-PCR)
- UniSTS:12680

G44365 (e-PCR)
- UniSTS:95151

D9S1996 (e-PCR)
- UniSTS:45041

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
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 ceramide biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
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 regulation of fat cell apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
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	TAS Traceable Author Statement more info	PubMed
involved_in sphingolipid metabolic 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
involved_in sphingosine biosynthetic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of SPOTS complex	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay 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 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

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Preferred Names: serine palmitoyltransferase 1

Names: long chain base biosynthesis protein 1; serine C-palmitoyltransferase; serine-palmitoyl-CoA transferase 1

NP_001268232.1

EC 2.3.1.50

NP_001355201.1

EC 2.3.1.50

NP_001355202.1

EC 2.3.1.50

NP_006406.1

EC 2.3.1.50

NP_847894.1

EC 2.3.1.50

XP_024303146.1

EC 2.3.1.50

XP_024303147.1

EC 2.3.1.50

XP_047278594.1

EC 2.3.1.50

XP_047278595.1

EC 2.3.1.50

XP_054217730.1

EC 2.3.1.50

XP_054217731.1

EC 2.3.1.50

XP_054217732.1

EC 2.3.1.50

XP_054217733.1

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_007950.1 RefSeqGene

Range

4935..89275

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_272

mRNA and Protein(s)

NM_001281303.2 → NP_001268232.1 serine palmitoyltransferase 1 isoform c

See identical proteins and their annotated locations for NP_001268232.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 3'-terminal exon, which results in a translational frameshift, compared to variant 1. The encoded isoform (c) has a longer and distinct C-terminus, compared to isoform a.

Source sequence(s)

AK291546, BC068537, DA305642

UniProtKB/TrEMBL

Q6NUL7

Conserved Domains (1) summary

cl18945
Location:11 → 442

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 ...
NM_001368272.1 → NP_001355201.1 serine palmitoyltransferase 1 isoform d

Status: REVIEWED

Source sequence(s)

AL354751, AL391219
NM_001368273.1 → NP_001355202.1 serine palmitoyltransferase 1 isoform e

Status: REVIEWED

Source sequence(s)

AL354751, AL391219

Related

ENST00000686799.1

Conserved Domains (1) summary

cl18945
Location:1 → 317

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 ...
NM_006415.4 → NP_006406.1 serine palmitoyltransferase 1 isoform a

See identical proteins and their annotated locations for NP_006406.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript, and encodes isoform a.

Source sequence(s)

AK291546, BC068537, DA305642

Consensus CDS

CCDS6692.1

UniProtKB/Swiss-Prot

A8K681, O15269, Q5VWB4, Q96IX6

UniProtKB/TrEMBL

A0A8I5QKQ8

Related

ENSP00000262554.2, ENST00000262554.7

Conserved Domains (1) summary

cl18945
Location:11 → 472

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 ...
NM_178324.3 → NP_847894.1 serine palmitoyltransferase 1 isoform b

See identical proteins and their annotated locations for NP_847894.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks several exons and its 3'-terminal exon extends past a splice site that is used in variant 1. The encoded isoform (b) has a shorter and distinct C-terminus, compared to isoform a.

Source sequence(s)

AF147304, BC007085, DA305642

Consensus CDS

CCDS6693.1

UniProtKB/TrEMBL

A0A2R8Y6A2

Related

ENSP00000337635.4, ENST00000337841.4

Conserved Domains (1) summary

cl18945
Location:11 → 141

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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

92031147..92115413 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047422638.1 → XP_047278594.1 serine palmitoyltransferase 1 isoform X1

Related

ENST00000689261.1
XM_024447379.2 → XP_024303147.1 serine palmitoyltransferase 1 isoform X3

Conserved Domains (1) summary

cl18945
Location:1 → 317

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 ...
XM_047422639.1 → XP_047278595.1 serine palmitoyltransferase 1 isoform X2
XM_024447378.2 → XP_024303146.1 serine palmitoyltransferase 1 isoform X3

Conserved Domains (1) summary

cl18945
Location:1 → 317

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 ...