SPTSSA serine palmitoyltransferase small subunit A [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPTSSAprovided by HGNC
Official Full Name: serine palmitoyltransferase small subunit Aprovided by HGNC
Primary source: HGNC:HGNC:20361
See related: Ensembl:ENSG00000165389 MIM:613540; AllianceGenome:HGNC:20361
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SPG90A; SPG90B; SSSPTA; C14orf147
Summary: Serine palmitoyltransferase (SPT; EC 2.3.1.50) catalyzes the first committed and rate-limiting step in sphingolipid biosynthesis. SSSPTA is a small SPT subunit that stimulates SPT activity and confers acyl-CoA preference to the SPT catalytic heterodimer of SPTLC1 (MIM 605712) and either SPTLC2 (MIM 605713) or SPTLC3 (MIM 611120) (Han et al., 2009 [PubMed 19416851]).[supplied by OMIM, Nov 2010]
Expression: Ubiquitous expression in adrenal (RPKM 46.3), colon (RPKM 28.8) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q13.1

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (34432788..34462240, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (28631319..28661012, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (34901994..34931446, 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?

SPTSSA variants alter sphingolipid synthesis and cause a complex hereditary spastic paraplegia.
Title: SPTSSA variants alter sphingolipid synthesis and cause a complex hereditary spastic paraplegia.
A genome-wide CRISPR/Cas9 screen reveals that the aryl hydrocarbon receptor stimulates sphingolipid levels.
Title: A genome-wide CRISPR/Cas9 screen reveals that the aryl hydrocarbon receptor stimulates sphingolipid levels.
ssSPTa is identified as an LPIAT1-interacting protein.
Title: Identification of small subunit of serine palmitoyltransferase a as a lysophosphatidylinositol acyltransferase 1-interacting protein.
discovery of 2 proteins, ssSPTa and ssSPTb, which each interacts with both hLCB1 and hLCB2, suggesting[ssSPTa] [ssSPTb]
Title: Identification of small subunits of mammalian serine palmitoyltransferase that confer distinct acyl-CoA substrate specificities.

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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
Spastic paraplegia 90A, autosomal dominant MedGen: C5830574 OMIM: 620416 GeneReviews: Not available	not available
Spastic paraplegia 90B, autosomal recessive MedGen: C5830578 OMIM: 620417 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-16004 (e-PCR)
- UniSTS:64771

G36287 (e-PCR)
- UniSTS:24098

RH102993 (e-PCR)
- UniSTS:97327

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
contributes_to 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
involved_in protein localization	IDA Inferred from Direct Assay more info	PubMed
involved_in sphingolipid biosynthetic process	TAS Traceable Author Statement more info	PubMed
involved_in sphingosine biosynthetic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
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	IBA Inferred from Biological aspect of Ancestor 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 small subunit A

Names: small subunit of serine palmitoyltransferase A

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.