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FLASH GENE

Symbol

SPTLC1

contributors: mct - updated : 30-08-2023

HGNC name	serine palmitoyltransferase, long chain base subunit 1
HGNC id	11277

FLASH GENE DNA RNA EXPRESSION PROTEIN DISORDER ANIMAL & CELL MODELS

Corresponding disease	ALS27 amyotrophic lateral sclerosis 27, juvenile HSAN1 hereditary sensory and autonomic neuropathy, type 1
Location	9q22.31      Physical location : 94.793.426 - 94.877.690
Synonym name	serine-palmitoyl-CoA transferase 1
	long chain base biosynthesis protein 1
Synonym symbol(s)	LBC1, SPT1, HSN1, LCB1, MGC14645, SPTI, ALS27, HSAN1, SPTI
EC.number	2.3.1.50

DNA

TYPE	functioning gene
STRUCTURE	84.27 kb     15 Exon(s)

10 Kb 5' upstream gene genomic sequence study

MAPPING

cloned

Y

linked

N

status

provisional

Map	cen - D9S1841 - ROR2 - SPTLC1 - OGN - ECM2 - OMD OMD - FGD3 - NINJ1 - D9S197 - qter

RNA

TRANSCRIPTS	type	messenger

identification nb exons type bp product Protein kDa AA specific expression Year Pubmed NM_006415 15 - 2780 NP_006406 - 473 - 2005 16210380 NM_178324 6 - 998 NP_847894 - 143 - 2005 16210380 NM_001368272 16 - 2916 NP_001355201 - 351 - 2005 16210380 NM_001281303 15 - 2751 NP_001268232 - 513 - 2005 16210380 NM_001368273 16 - 2928 NP_001355202 - 318 - 2005 16210380

EXPRESSION

Type	ubiquitous

expressed in	(based on citations)
organ(s)	System Organ level 1 Organ level 2 Organ level 3 Organ level 4 Level Pubmed Species Stage Rna symbol Digestive intestine large intestine colon   highly Endocrine neuroendocrine pituitary     highly Lymphoid/Immune spleen       highly

tissue

System Tissue Tissue level 1 Tissue level 2 Level Pubmed Species Stage Rna symbol Nervous peripherous

cell lineage

cell lines

fluid/secretion

at STAGE

PROTEIN

PHYSICAL PROPERTIES

STRUCTURE

motifs/domains	extracellular N and C termini
	two transmembrane segments in the N terminal region,
	several myristoylation sites
	a putative glycosylation site

HOMOLOGY

Homologene

FAMILY

class-II pyridoxal-phosphate-dependent aminotransferase family

CATEGORY

enzyme

SUBCELLULAR LOCALIZATION	intracellular
	intracellular,cytoplasm,organelle,membrane
	intracellular,cytoplasm,organelle,endoplasmic reticulum
	intracellular,nucleus
text	in addition to its "traditional" localization in the ER for de novo sphingolipid biosynthesis, is present in other cellular compartments, including focal adhesions where it is associated with cell morphology

basic FUNCTION	initial step in sphingolipid biosynthesis, key enzyme for regulating cellular sphingolipid content
	binds PARD3 that modulates monocyte serine palmitoyltransferase activity and chemotaxis
	inhibits ABCA1 activity leading to the blockade of the exit of ABCA1 from the endoplasmic reticulum
	is the rate-limiting enzyme for sphingolipid biosynthesis
	inhibits cell growth via modulating AKT1/FOXO1 pathway in renal cell carcinoma cells
	is essential for myeloid differentiation and hematopoietic homeostasis

CELLULAR PROCESS

PHYSIOLOGICAL PROCESS

PATHWAY

metabolism

lipid/lipoprotein

signaling

a component

mitochondrial SPTLC2 interacts and forms a complex in trans with the ER-localized SPT subunit SPTLC1

INTERACTION

DNA

RNA

small molecule	cofactor,
	pyridoxal 5'-phosphate

protein	protein-protein interaction between SPTLC1 and the PDZ protein PARD3 (is able to associate with the SPTLC1/2 holoenzyme by binding the C-terminal SPTLC1 PDZ motif)
	interacting with ABCA1 (inhibition of ABCA1 activity led to the blockade of the exit of ABCA1 from the endoplasmic reticulum)
	physical interaction of ABCA1 and SPTLC1 results in reduction of ABCA1 activity and inhibition of this interaction produces enhanced cholesterol efflux
	SPTSSA, SPTSSB share a conserved hydrophobic central domain predicted to reside in the membrane, and each interacts with both SPTLC1 and SPTLC2
	SPTLC1 activity indirectly regulates ORMDL1, ORMDL2, ORMDL3 expression 2)
	ORMDL3 might influence de novo sphingolipid metabolism downstream of SPTLC1

cell & other

REGULATION

ASSOCIATED DISORDERS

corresponding disease(s)

HSAN1 , ALS27

related resource

Mutation Database of Inherited Peripheral Neuropathies

Other morbid association(s)

Type Gene Modification Chromosome rearrangement Protein expression Protein Function tumoral     --low   decreased in renal cell carcinoma (RCC) tissues compared to non-tumor tissues, and low SPTLC1 expression was associated with poor overall survival of RCC patients

Susceptibility

Variant & Polymorphism

Candidate gene
Marker
Therapy target
	System Type Disorder Pubmed neurology neurodegenerative alzheimer SPTLC1, SPTLC2, SPTLC3 and MIR137 may be potential therapeutic targets for sporadic Alzheimer disease

ANIMAL & CELL MODELS