SPTLC1 Gene (Protein Coding)

Serine Palmitoyltransferase Long Chain Base Subunit 1

GC09M092002
GIFtS:
47
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 ident... See more...

Aliases for SPTLC1 Gene

Aliases for SPTLC1 Gene

  • Serine Palmitoyltransferase Long Chain Base Subunit 1 2 3 5
  • LCB1 2 3 4
  • Long Chain Base Biosynthesis Protein 1 3 4
  • Serine-Palmitoyl-CoA Transferase 1 3 4
  • Serine Palmitoyltransferase 1 3 4
  • EC 2.3.1.50 4 50
  • HSAN1 2 3
  • SPT1 3 4
  • SPTI 2 3
  • Hereditary Sensory Neuropathy, Type 1 2
  • Serine C-Palmitoyltransferase 3
  • SPTLC1 5
  • HLCB1 2
  • LCB 1 4
  • SPT 1 4
  • HSN1 3
  • LBC1 3

External Ids for SPTLC1 Gene

Previous HGNC Symbols for SPTLC1 Gene

  • HSN1

Previous GeneCards Identifiers for SPTLC1 Gene

  • GC09M085621
  • GC09M086522
  • GC09M088092
  • GC09M090134
  • GC09M091873
  • GC09M093833
  • GC09M094793
  • GC09M064471
  • GC09M092031

Summaries for SPTLC1 Gene

Entrez Gene Summary for SPTLC1 Gene

  • 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]

GeneCards Summary for SPTLC1 Gene

SPTLC1 (Serine Palmitoyltransferase Long Chain Base Subunit 1) is a Protein Coding gene. Diseases associated with SPTLC1 include Neuropathy, Hereditary Sensory And Autonomic, Type Ia and Hereditary Sensory And Autonomic Neuropathy Type 1. Among its related pathways are Sphingolipid metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include pyridoxal phosphate binding and serine C-palmitoyltransferase activity. An important paralog of this gene is SPTLC2.

UniProtKB/Swiss-Prot Summary for SPTLC1 Gene

  • Serine palmitoyltransferase (SPT) (PubMed:19416851). The heterodimer formed with SPTLC2 or SPTLC3 constitutes the catalytic core (PubMed:19416851). The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference (PubMed:19416851). The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA (PubMed:19416851). The SPTLC1-SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate, while the SPTLC1-SPTLC3-SPTSSB isozyme displays an ability to use a broader range of acyl-CoAs, without apparent preference (PubMed:19416851). Required for adipocyte cell viability and metabolic homeostasis (By similarity).

Gene Wiki entry for SPTLC1 Gene

Additional gene information for SPTLC1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPTLC1 Gene

Genomics for SPTLC1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for SPTLC1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPTLC1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SPTLC1

Top Transcription factor binding sites by QIAGEN in the SPTLC1 gene promoter:
  • aMEF-2
  • AML1a
  • c-Myc
  • COMP1
  • E47
  • HSF1 (long)
  • HSF1short
  • Max1
  • MEF-2A

Genomic Locations for SPTLC1 Gene

Latest Assembly
chr9:92,000,087-92,115,413
(GRCh38/hg38)
Size:
115,327 bases
Orientation:
Minus strand

Previous Assembly
chr9:94,793,429-94,877,695
(GRCh37/hg19 by Entrez Gene)
Size:
84,267 bases
Orientation:
Minus strand

chr9:94,794,281-94,877,666
(GRCh37/hg19 by Ensembl)
Size:
83,386 bases
Orientation:
Minus strand

Genomic View for SPTLC1 Gene

Genes around SPTLC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPTLC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPTLC1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SPTLC1 Gene

Proteins for SPTLC1 Gene

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  • Protein details for SPTLC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15269-SPTC1_HUMAN
    Recommended name:
    Serine palmitoyltransferase 1
    Protein Accession:
    O15269
    Secondary Accessions:
    • A8K681
    • Q5VWB4
    • Q96IX6

    Protein attributes for SPTLC1 Gene

    Size:
    473 amino acids
    Molecular mass:
    52744 Da
    Cofactor:
    Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Heterodimer with SPTLC2 or SPTLC3. Component of the serine palmitoyltransferase (SPT) complex, composed of SPTLC1, either SPTLC2 or SPTLC3, and either SPTSSA or SPTSSB. The composition of the complex will define the substrate specificity. Interacts with SPTSSA and SPTSSB; the interaction is direct (PubMed:19416851). Interacts with ORMDL3 (PubMed:20182505). Interacts with RTN4 (isoform B) (By similarity).

    Alternative splice isoforms for SPTLC1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPTLC1 Gene

Protein Expression for SPTLC1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for SPTLC1 Gene

O15269:
  • NPRVKAAA
  • FSKTYKLQERSDLT
  • DVHLDLE
  • DHQRLSGQGYCFSASLPPLLAAAAIEALNIMEENP
  • HPALNYNIVSGPP
  • ASAIPAYSKRGDI
  • HLQLEESTGSRE
  • NFASFNFL
  • CGPRGFYGT
  • DLERLLKEQEIEDQKNPRKARVTRRFI
  • TEEAIIYSYGF
  • AACFAIQKGLQASRSDIK
  • CPLPELVKLKYKYKARIFLEESLSFGVLGEHGRGVTEH

Post-translational modifications for SPTLC1 Gene

  • Phosphorylation at Tyr-164 inhibits activity and promotes cell survival.
  • Ubiquitination at Lys57, Lys197, and Lys375
  • Modification sites at PhosphoSitePlus

Other Protein References for SPTLC1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for SPTLC1 Gene

Gene Families for SPTLC1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted membrane proteins

Protein Domains for SPTLC1 Gene

InterPro:
Blocks:
  • Aminotransferase, class I and II
  • Aminotransferase, class-II

Suggested Antigen Peptide Sequences for SPTLC1 Gene

GenScript: Design optimal peptide antigens:
  • SPTLC1 protein (Q6NUL7_HUMAN)
  • Serine-palmitoyl-CoA transferase 1 (SPTC1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O15269

UniProtKB/Swiss-Prot:

SPTC1_HUMAN :
  • Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.
Family:
  • Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.
genes like me logo Genes that share domains with SPTLC1: view

Function for SPTLC1 Gene

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  6. Cell Lines for research

Molecular function for SPTLC1 Gene

UniProtKB/Swiss-Prot Function:
Serine palmitoyltransferase (SPT) (PubMed:19416851). The heterodimer formed with SPTLC2 or SPTLC3 constitutes the catalytic core (PubMed:19416851). The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference (PubMed:19416851). The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA (PubMed:19416851). The SPTLC1-SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate, while the SPTLC1-SPTLC3-SPTSSB isozyme displays an ability to use a broader range of acyl-CoAs, without apparent preference (PubMed:19416851). Required for adipocyte cell viability and metabolic homeostasis (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H(+) + hexadecanoyl-CoA + L-serine = 3-oxosphinganine + CO2 + CoA; Xref=Rhea:RHEA:14761, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:33384, ChEBI:CHEBI:57287, ChEBI:CHEBI:57379, ChEBI:CHEBI:58299; EC=2.3.1.50; Evidence={ECO:0000269|PubMed:19416851};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H(+) + L-serine + octadecanoyl-CoA = 3-oxoeicosasphinganine + CO2 + CoA; Xref=Rhea:RHEA:33683, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:33384, ChEBI:CHEBI:57287, ChEBI:CHEBI:57394, ChEBI:CHEBI:65073; Evidence={ECO:0000269|PubMed:19416851};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H(+) + L-serine + tetradecanoyl-CoA = 3-oxohexadecasphinganine + CO2 + CoA; Xref=Rhea:RHEA:35675, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:33384, ChEBI:CHEBI:57287, ChEBI:CHEBI:57385, ChEBI:CHEBI:71007; Evidence={ECO:0000269|PubMed:19416851};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=dodecanoyl-CoA + H(+) + L-serine = 3-oxotetradecasphinganine + CO2 + CoA; Xref=Rhea:RHEA:35679, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:33384, ChEBI:CHEBI:57287, ChEBI:CHEBI:57375, ChEBI:CHEBI:71008; Evidence={ECO:0000269|PubMed:19416851};.
UniProtKB/Swiss-Prot Induction:
Expression at protein level is highly increased in brains of patients with Alzheimer disease. No changes are observed at mRNA level.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=0.75 mM for serine {ECO:0000269|PubMed:20504773}; Vmax=1350 pmol/min/mg enzyme {ECO:0000269|PubMed:20504773};

Enzyme Numbers (IUBMB) for SPTLC1 Gene

Phenotypes From GWAS Catalog for SPTLC1 Gene

Gene Ontology (GO) - Molecular Function for SPTLC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0004758 contributes_to serine C-palmitoyltransferase activity TAS,IDA 25332431
GO:0005515 protein binding IPI 19416851
GO:0016740 transferase activity IEA --
GO:0016746 transferase activity, transferring acyl groups IEA --
genes like me logo Genes that share ontologies with SPTLC1: view
genes like me logo Genes that share phenotypes with SPTLC1: view

Human Phenotype Ontology for SPTLC1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SPTLC1 Gene

MGI Knock Outs for SPTLC1:

Animal Models for research

  • Taconic Biosciences Mouse Models for SPTLC1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPTLC1

Clone products for research

No data available for Transcription Factor Targets and HOMER Transcription for SPTLC1 Gene

Localization for SPTLC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPTLC1 Gene

Endoplasmic reticulum membrane. Single-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SPTLC1 gene
Compartment Confidence
endoplasmic reticulum 5
cytosol 3
plasma membrane 2
extracellular 2
mitochondrion 2
nucleus 2
golgi apparatus 2
cytoskeleton 1
peroxisome 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SPTLC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IBA,IDA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0017059 serine C-palmitoyltransferase complex IDA 19416851
genes like me logo Genes that share ontologies with SPTLC1: view

Pathways & Interactions for SPTLC1 Gene

genes like me logo Genes that share pathways with SPTLC1: view

Pathways by source for SPTLC1 Gene

2 BioSystems pathways for SPTLC1 Gene

UniProtKB/Swiss-Prot O15269-SPTC1_HUMAN

  • Pathway: Lipid metabolism; sphingolipid metabolism.

SIGNOR curated interactions for SPTLC1 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for SPTLC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006665 sphingolipid metabolic process TAS 9363775
GO:0009058 biosynthetic process IEA --
GO:0030148 sphingolipid biosynthetic process IDA,TAS 19416851
GO:0046512 sphingosine biosynthetic process IBA 21873635
genes like me logo Genes that share ontologies with SPTLC1: view

Drugs & Compounds for SPTLC1 Gene

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(9) Drugs for SPTLC1 Gene - From: DrugBank, DGIdb, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Pyridoxal Phosphate Approved, Investigational Nutra Target, cofactor 18
Carbon dioxide Approved, Investigational, Vet_approved Pharma 0
Vitamin E Approved, Vet_approved Nutra 553,561
Serine Investigational Nutra Target Weak endogenous glycine receptor agonist 1286
Coenzyme A Investigational Nutra 0

(3) Additional Compounds for SPTLC1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
3-Dehydrosphinganine
  • 3-Dehydro-D-sphinganine
  • 3-Ketodihydrosphingosine
  • 3-Ketosphinganine
  • (2S)-2-Amino-1-hydroxyoctadecan-3-one
  • 1-Hydroxy-2-amino-3-oxo-octadecane
 16105-69-4
hexadecanoyl-CoA
  • coenzyme A, S-Hexadecanoate
  • Palmitoyl coenzyme A
  • S-Palmitoylcoenzyme A
  • coenzyme A, S-Hexadecanoic acid
  • Hexadecanoyl-CoA
Palmityl-CoA
  • Hexadecanoyl CoA
  • Hexadecanoyl coenzyme A
  • Palmitoyl CoA
  • Palmitoyl coenzyme A
  • Palmitoyl-CoA
 1763-10-6
genes like me logo Genes that share compounds with SPTLC1: view

Transcripts for SPTLC1 Gene

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mRNA/cDNA for SPTLC1 Gene

5 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPTLC1

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for SPTLC1 Gene

No ASD Table

Relevant External Links for SPTLC1 Gene

GeneLoc Exon Structure for
SPTLC1

Expression for SPTLC1 Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SPTLC1 Gene

mRNA expression in normal human tissues for SPTLC1 Gene
mRNA expression by BioGPS for SPTLC1 GenemRNA expression by GTEx for SPTLC1 Gene

Protein differential expression in normal tissues from HIPED for SPTLC1 Gene

This gene is overexpressed in Bone (22.9) and Peripheral blood mononuclear cells (9.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SPTLC1 Gene



Protein tissue co-expression partners for SPTLC1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPTLC1

SOURCE GeneReport for Unigene cluster for SPTLC1 Gene:

Hs.90458

mRNA Expression by UniProt/SwissProt for SPTLC1 Gene:

O15269-SPTC1_HUMAN
Tissue specificity: Widely expressed. Not detected in small intestine.

Evidence on tissue expression from TISSUES for SPTLC1 Gene

  • Nervous system(4.9)
  • Kidney(4.5)
  • Intestine(3.9)
  • Spleen(2.5)
  • Skin(2.5)
  • Muscle(2.3)
  • Liver(2.3)
  • Blood(2.1)
  • Heart(2.1)
  • Lung(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SPTLC1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • cardiovascular
  • immune
  • integumentary
  • lymphatic
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • bone marrow
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • sweat gland
  • vertebrae
genes like me logo Genes that share expression patterns with SPTLC1: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for SPTLC1 Gene

Orthologs for SPTLC1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SPTLC1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia SPTLC1 29 30
  • 99.4 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia SPTLC1 29 30
  • 91.97 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia SPTLC1 29 30
  • 91.68 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Sptlc1 29 16 30
  • 84.57 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Sptlc1 29
  • 84 (n)
Oppossum
(Monodelphis domestica)
 Mammalia SPTLC1 30
  • 83 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves SPTLC1 29 30
  • 79.8 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia SPTLC1 30
  • 87 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia sptlc1 29
  • 76.86 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.7364 29
Zebrafish
(Danio rerio)
 Actinopterygii sptlc1 29 30
  • 72.45 (n)
 OneToOne
-- 29
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.9491 29
Fruit Fly
(Drosophila melanogaster)
 Insecta Spt-I 29 30 31
  • 54.4 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP010427 29
  • 53.52 (n)
Worm
(Caenorhabditis elegans)
 Secernentea sptl-1 29 30
  • 57.06 (n)
 OneToOne
C23H3.4 31
  • 49 (a)
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes LCB1 29 30 32
  • 47.12 (n)
 OneToOne
K. Lactis Yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0A09955g 29
  • 46.28 (n)
A. gosspyii yeast
(Eremothecium gossypii)
 Saccharomycetes AGOS_ABR145C 29
  • 45.52 (n)
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons LCB1 29
  • 52.49 (n)
Rice
(Oryza sativa)
 Liliopsida Os02g0806900 29
  • 53.75 (n)
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 30
  • 61 (a)
 OneToMany
-- 30
  • 56 (a)
 OneToMany
Fission Yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes SPBC18E5.02c 29
  • 49.88 (n)
Bread mold
(Neurospora crassa)
 Ascomycetes NCU06870 29
  • 46.73 (n)
Species where no ortholog for SPTLC1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SPTLC1 Gene

ENSEMBL:
Gene Tree for SPTLC1 (if available)
TreeFam:
Gene Tree for SPTLC1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPTLC1: view image
Alliance of Genome Resources:
Additional Orthologs for SPTLC1

Paralogs for SPTLC1 Gene

Variants for SPTLC1 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SPTLC1 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
1002990 Uncertain Significance: Hereditary sensory and autonomic neuropathy type 1 92,047,271(-) G/A
NM_006415.4(SPTLC1):c.985-3C>T 		INTRON
1008500 Uncertain Significance: Hereditary sensory and autonomic neuropathy type 1 92,034,879(-) A/C
NM_006415.4(SPTLC1):c.1259T>G (p.Met420Arg) 		MISSENSE
1016208 Uncertain Significance: Hereditary sensory and autonomic neuropathy type 1 92,038,286(-) C/T
NM_006415.4(SPTLC1):c.1216G>A (p.Glu406Lys) 		MISSENSE
1020665 Uncertain Significance: Hereditary sensory and autonomic neuropathy type 1 92,055,473(-) T/C
NM_006415.4(SPTLC1):c.712A>G (p.Thr238Ala) 		MISSENSE
1021849 Uncertain Significance: Hereditary sensory and autonomic neuropathy type 1 92,080,076(-) C/T
NM_006415.4(SPTLC1):c.367G>A (p.Ala123Thr) 		MISSENSE_VARIANT,FIVE_PRIME_UTR

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SPTLC1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SPTLC1 Gene

Variant ID Type Subtype PubMed ID
nsv1046733 CNV gain 25217958
nsv1151320 CNV duplication 26484159
nsv831653 CNV gain 17160897
nsv950891 CNV duplication 24416366
nsv950892 CNV duplication 24416366
nsv972418 CNV duplication 23825009

Variation tolerance for SPTLC1 Gene

Residual Variation Intolerance Score: 20.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.92; 48.92% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPTLC1 Gene

Human Gene Mutation Database (HGMD)
SPTLC1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPTLC1
Leiden Open Variation Database (LOVD)
SPTLC1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPTLC1 Gene

Disorders for SPTLC1 Gene

MalaCards: The human disease database

(35) MalaCards diseases for SPTLC1 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

Disorder Aliases PubMed IDs
neuropathy, hereditary sensory and autonomic, type ia
  • hsan1a
hereditary sensory and autonomic neuropathy type 1
  • hereditary sensory and autonomic neuropathy type i
neuropathy, hereditary sensory, type ie
  • hsn1e
charcot-marie-tooth disease
  • cmt - charcot-marie-tooth disease
hereditary sensory neuropathy
  • familial dysautonomia, type ii
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SPTC1_HUMAN
  • Neuropathy, hereditary sensory and autonomic, 1A (HSAN1A) [MIM:162400]: A form of hereditary sensory and autonomic neuropathy, a genetically and clinically heterogeneous group of disorders characterized by degeneration of dorsal root and autonomic ganglion cells, and by prominent sensory abnormalities with a variable degree of motor and autonomic dysfunction. The neurological phenotype is often complicated by severe infections, osteomyelitis, and amputations. HSAN1A is an autosomal dominant axonal form with onset in the second or third decades. Initial symptoms are loss of pain, touch, heat, and cold sensation over the feet, followed by distal muscle wasting and weakness. Loss of pain sensation leads to chronic skin ulcers and distal amputations. {ECO:0000269 PubMed:11242114, ECO:0000269 PubMed:19132419, ECO:0000269 PubMed:19651702, ECO:0000269 PubMed:20504773, ECO:0000269 PubMed:21618344, ECO:0000269 PubMed:22302274, ECO:0000269 PubMed:24247255, ECO:0000269 PubMed:30420926}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Note=SPTLC1 mutations at Ser-331 are responsible for severe hereditary motor and sensory neuropathy (HMSN) forms, whose core features are severe, diffuse muscle wasting and hypotonia, motor and sensory disturbances, foot ulcers, amputations and/or burns, joint hypermobility, cataracts and considerable growth retardation. {ECO:0000269 PubMed:23454272}.

Additional Disease Information for SPTLC1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SPTLC1: view

No data available for Genatlas for SPTLC1 Gene

Publications for SPTLC1 Gene

  1. Genes for hereditary sensory and autonomic neuropathies: a genotype-phenotype correlation. (PMID: 19651702) Rotthier A … Timmerman V (Brain : a journal of neurology 2009) 3 4 22 40
  2. Mutations in SPTLC1, encoding serine palmitoyltransferase, long chain base subunit-1, cause hereditary sensory neuropathy type I. (PMID: 11242114) Dawkins JL … Nicholson GA (Nature genetics 2001) 3 4 22 72
  3. Human and murine serine-palmitoyl-CoA transferase--cloning, expression and characterization of the key enzyme in sphingolipid synthesis. (PMID: 9363775) Weiss B … Stoffel W (European journal of biochemistry 1997) 2 3 4 22
  4. A systematic comparison of all mutations in hereditary sensory neuropathy type I (HSAN I) reveals that the G387A mutation is not disease associated. (PMID: 19132419) Hornemann T … von Eckardstein A (Neurogenetics 2009) 3 4 72
  5. SPTLC1 mutation in twin sisters with hereditary sensory neuropathy type I. (PMID: 15037712) Verhoeven K … De Jonghe P (Neurology 2004) 3 4 22

ExternalLinks

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