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] See more...

Aliases for SPTLC3 Gene

Aliases for SPTLC3 Gene

  • Serine Palmitoyltransferase Long Chain Base Subunit 3 2 3 5
  • Serine Palmitoyltransferase, Long Chain Base Subunit 2-Like (Aminotransferase 2) 2 3
  • Long Chain Base Biosynthesis Protein 2b 3 4
  • Long Chain Base Biosynthesis Protein 3 3 4
  • Serine-Palmitoyl-CoA Transferase 3 3 4
  • Serine Palmitoyltransferase 3 3 4
  • EC 2.3.1.50 4 50
  • C20orf38 3 4
  • SPTLC2L 3 4
  • HLCB2b 2 3
  • LCB 3 3 4
  • LCB2B 2 3
  • SPT 3 3 4
  • Chromosome 20 Open Reading Frame 38 2
  • DJ718P11.1 3
  • DJ718P11 3
  • FLJ11112 2
  • EC 2.3.1 50
  • SPTLC3 5
  • LCB2b 4
  • LCB3 3
  • SPT3 3

External Ids for SPTLC3 Gene

Previous HGNC Symbols for SPTLC3 Gene

  • C20orf38
  • SPTLC2L

Previous GeneCards Identifiers for SPTLC3 Gene

  • GC20P012938

Summaries for SPTLC3 Gene

Entrez Gene Summary for SPTLC3 Gene

  • 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]

GeneCards Summary for SPTLC3 Gene

SPTLC3 (Serine Palmitoyltransferase Long Chain Base Subunit 3) is a Protein Coding gene. Diseases associated with SPTLC3 include Sensory Peripheral Neuropathy and Neuropathy. Among its related pathways are Sphingolipid metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include pyridoxal phosphate binding and transaminase activity. An important paralog of this gene is SPTLC2.

UniProtKB/Swiss-Prot Summary for SPTLC3 Gene

  • Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. SPT complexes containing SPTLC3 generate shorter chain sphingoid bases compared to complexes containing SPTLC2. The SPTLC1-SPTLC3-SPTSSA isozyme uses C12-CoA, C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA. On the other hand, the SPTLC1-SPTLC3-SPTSSB has the ability to use a broader range of acyl-CoAs without apparent preference.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPTLC3 Gene

Genomics for SPTLC3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SPTLC3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J013008 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 260.9 +1.2 1201 3.3 BCLAF1 CHD4 YY1 BCL11A HOMEZ CTCF MAFF SAP130 IRF4 JUND SPTLC3 NONHSAG031294.2 NDUFAF5 lnc-TASP1-15 ISM1
GH20J013059 Enhancer 1.2 Ensembl ENCODE dbSUPER 33.3 +50.3 50329 2.2 ZMYM3 KLF9 CEBPA CHD4 MXD4 KLF11 HOMEZ KMT2B THAP11 FOXA2 SPTLC3 ENSG00000271426 lnc-TASP1-15 HSALNG0128746-001 ISM1
GH20J012976 Enhancer 1.2 Ensembl ENCODE dbSUPER 21.7 -31.6 -31588 2 CEBPA HOMEZ KMT2B THAP11 FOXA2 KDM6A MAFF SMAD4 RXRA ZNF511 SPTLC3 ISM1 HSALNG0128742 HSALNG0128743 LINC01723
GH20J012979 Enhancer 1 ENCODE dbSUPER 22.7 -29.8 -29751 0.4 CEBPA MXD4 KLF11 HOMEZ KMT2B THAP11 FOXA2 KDM6A SMAD4 ZNF511 SPTLC3 HSALNG0128742 HSALNG0128743 LINC01723
GH20J013027 Enhancer 0.9 Ensembl ENCODE 16.7 +20.6 20550 3.5 CEBPA ZIC2 CEBPB FEZF1 MAX EP300 DMAP1 TEAD3 FOSL2 JUND SPTLC3 lnc-TASP1-15 NONHSAG031294.2 ENSG00000271426 ISM1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPTLC3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SPTLC3

Top Transcription factor binding sites by QIAGEN in the SPTLC3 gene promoter:
  • AML1a
  • AREB6
  • C/EBPalpha
  • Lmo2
  • Nkx2-2
  • Pax-4a
  • Pax-6
  • SRY
  • TBP
  • TFIID

Genomic Locations for SPTLC3 Gene

Latest Assembly
chr20:13,008,972-13,169,103
(GRCh38/hg38)
Size:
160,132 bases
Orientation:
Plus strand

Previous Assembly
chr20:12,989,620-13,149,750
(GRCh37/hg19 by Entrez Gene)
Size:
160,131 bases
Orientation:
Plus strand

chr20:12,989,627-13,147,411
(GRCh37/hg19 by Ensembl)
Size:
157,785 bases
Orientation:
Plus strand

Genomic View for SPTLC3 Gene

Genes around SPTLC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPTLC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPTLC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPTLC3 Gene

Proteins for SPTLC3 Gene

  • Protein details for SPTLC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NUV7-SPTC3_HUMAN
    Recommended name:
    Serine palmitoyltransferase 3
    Protein Accession:
    Q9NUV7
    Secondary Accessions:
    • A2A2I4
    • B9EK64
    • Q05DQ8
    • Q5T1U4
    • Q9H1L1
    • Q9H1Z0

    Protein attributes for SPTLC3 Gene

    Size:
    552 amino acids
    Molecular mass:
    62049 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.
    SequenceCaution:
    • Sequence=AAH05205.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};

    Alternative splice isoforms for SPTLC3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPTLC3 Gene

Selected DME Specific Peptides for SPTLC3 Gene

Q9NUV7:
  • RNLYMRIRD
  • VVVVGFPAT
  • MGTFTKSF
  • GMGFATNSMNIPALVGKGCLILSDELNH
  • LFGYLRDF
  • LYIDEAH
  • YGQPRTRR
  • VINMGSYN
  • HSHSAVYA
  • SLVLGARLSGATIRIFKHNN
  • ALKKKYKAYLY
  • YSMEGSIV
  • LYQDFENFY

Post-translational modifications for SPTLC3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for SPTLC3 Gene

Gene Families for SPTLC3 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for SPTLC3 Gene

GenScript: Design optimal peptide antigens:
  • Serine palmitoyltransferase, long chain base subunit 2-like (Aminotransferase 2) (B1AKI8_HUMAN)
  • Serine palmitoyltransferase, long chain base subunit 2-like (Aminotransferase 2) (B1AKS3_HUMAN)
  • Serine-palmitoyl-CoA transferase 3 (SPTC3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NUV7

UniProtKB/Swiss-Prot:

SPTC3_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 SPTLC3: view

Function for SPTLC3 Gene

Molecular function for SPTLC3 Gene

UniProtKB/Swiss-Prot Function:
Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. SPT complexes containing SPTLC3 generate shorter chain sphingoid bases compared to complexes containing SPTLC2. The SPTLC1-SPTLC3-SPTSSA isozyme uses C12-CoA, C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA. On the other hand, the SPTLC1-SPTLC3-SPTSSB has the ability to use a broader range of acyl-CoAs without apparent preference.
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:17023427, ECO:0000269|PubMed:19416851, ECO:0000269|PubMed:19648650};.
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, ECO:0000269|PubMed:19648650};.
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, ECO:0000269|PubMed:19648650};.
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 BiophysicochemicalProperties:
Kinetic parameters: KM=0.04 mM for hexadecanoyl-CoA {ECO:0000269|PubMed:19648650}; KM=0.03 mM for tetradecanoyl-CoA {ECO:0000269|PubMed:19648650}; Vmax=120 pmol/min/mg enzyme toward hexadecanoyl-CoA {ECO:0000269|PubMed:19648650}; Vmax=60 pmol/min/mg enzyme toward tetradecanoyl-CoA {ECO:0000269|PubMed:19648650};

Enzyme Numbers (IUBMB) for SPTLC3 Gene

Phenotypes From GWAS Catalog for SPTLC3 Gene

Gene Ontology (GO) - Molecular Function for SPTLC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0004758 serine C-palmitoyltransferase activity IBA,IDA 19416851
GO:0005515 protein binding IPI 19416851
GO:0008483 transaminase activity IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with SPTLC3: view
genes like me logo Genes that share phenotypes with SPTLC3: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPTLC3

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SPTLC3 Gene

Localization for SPTLC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPTLC3 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 SPTLC3 gene
Compartment Confidence
mitochondrion 3
nucleus 3
endoplasmic reticulum 2
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
peroxisome 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SPTLC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0017059 serine C-palmitoyltransferase complex IBA,IDA 17331073
genes like me logo Genes that share ontologies with SPTLC3: view

Pathways & Interactions for SPTLC3 Gene

genes like me logo Genes that share pathways with SPTLC3: view

Pathways by source for SPTLC3 Gene

UniProtKB/Swiss-Prot Q9NUV7-SPTC3_HUMAN

  • Pathway: Lipid metabolism; sphingolipid metabolism.

Gene Ontology (GO) - Biological Process for SPTLC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006665 sphingolipid metabolic process IEA --
GO:0009058 biosynthetic process IEA --
GO:0030148 sphingolipid biosynthetic process TAS 19416851
GO:0046512 sphingosine biosynthetic process IBA 21873635
genes like me logo Genes that share ontologies with SPTLC3: view

No data available for SIGNOR curated interactions for SPTLC3 Gene

Drugs & Compounds for SPTLC3 Gene

(5) Drugs for SPTLC3 Gene - From: DrugBank, DGIdb, and HMDB

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
Coenzyme A Investigational Nutra 0
Serine Investigational Nutra Weak endogenous glycine receptor agonist 1286
Myriocin Pharma 0

(2) Additional Compounds for SPTLC3 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
genes like me logo Genes that share compounds with SPTLC3: view

Transcripts for SPTLC3 Gene

mRNA/cDNA for SPTLC3 Gene

2 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
6 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 SPTLC3

Alternative Splicing Database (ASD) splice patterns (SP) for SPTLC3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4
SP1: -
SP2: -
SP3:

Relevant External Links for SPTLC3 Gene

GeneLoc Exon Structure for
SPTLC3

Expression for SPTLC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SPTLC3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SPTLC3 Gene

This gene is overexpressed in Skin - Sun Exposed (Lower leg) (x7.1) and Skin - Not Sun Exposed (Suprapubic) (x6.6).

Protein differential expression in normal tissues from HIPED for SPTLC3 Gene

This gene is overexpressed in Placenta (66.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SPTLC3 Gene



Protein tissue co-expression partners for SPTLC3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPTLC3

SOURCE GeneReport for Unigene cluster for SPTLC3 Gene:

Hs.425023

mRNA Expression by UniProt/SwissProt for SPTLC3 Gene:

Q9NUV7-SPTC3_HUMAN
Tissue specificity: Expressed in most tissues, except peripheral blood cells and bone marrow, with highest levels in heart, kidney, liver, uterus and skin.

Evidence on tissue expression from TISSUES for SPTLC3 Gene

  • Nervous system(4.4)
  • Liver(2.3)
  • Kidney(2.2)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with SPTLC3: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SPTLC3 Gene

Orthologs for SPTLC3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SPTLC3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SPTLC3 29 30
  • 99.46 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SPTLC3 29 30
  • 89.01 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SPTLC3 29 30
  • 85.61 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SPTLC3 30
  • 82 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SPTLC3 30
  • 78 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sptlc3 29
  • 77.37 (n)
Mouse
(Mus musculus)
Mammalia Sptlc3 29 16 30
  • 76.53 (n)
OneToOne
Chicken
(Gallus gallus)
Aves SPTLC3 29 30
  • 74 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 82 (a)
OneToMany
-- 30
  • 68 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sptlc3 29
  • 71.61 (n)
Zebrafish
(Danio rerio)
Actinopterygii sptlc3 29 30
  • 67.41 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta lace 30
  • 44 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea sptl-2 30
  • 44 (a)
ManyToMany
sptl-3 30
  • 42 (a)
ManyToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LCB2 30
  • 40 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 52 (a)
OneToMany
Species where no ortholog for SPTLC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • 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)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SPTLC3 Gene

ENSEMBL:
Gene Tree for SPTLC3 (if available)
TreeFam:
Gene Tree for SPTLC3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPTLC3: view image
Alliance of Genome Resources:
Additional Orthologs for SPTLC3

Paralogs for SPTLC3 Gene

Paralogs for SPTLC3 Gene

(2) SIMAP similar genes for SPTLC3 Gene using alignment to 5 proteins:

  • SPTC3_HUMAN
  • B1AKS2_HUMAN
  • B1AKS3_HUMAN
  • C9JC36_HUMAN
  • H0Y733_HUMAN
genes like me logo Genes that share paralogs with SPTLC3: view

Variants for SPTLC3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SPTLC3 Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
rs755919784 Likely Pathogenic: Sensory neuropathy; Peripheral neuropathy 13,072,400(+) T/C
NM_018327.4(SPTLC3):c.448T>C (p.Trp150Arg)
MISSENSE
rs243887 -- p.Leu140Val

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SPTLC3 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 SPTLC3 Gene

Variant ID Type Subtype PubMed ID
dgv4247n100 CNV gain 25217958
esv2017186 CNV deletion 18987734
esv2722196 CNV deletion 23290073
esv2722197 CNV deletion 23290073
esv2722198 CNV deletion 23290073
esv3645279 CNV loss 21293372
esv3893288 CNV gain 25118596
nsv1073045 CNV deletion 25765185
nsv1123455 CNV deletion 24896259
nsv518184 CNV gain 19592680
nsv833923 CNV gain+loss 17160897
nsv833924 CNV gain 17160897

Variation tolerance for SPTLC3 Gene

Residual Variation Intolerance Score: 9.58% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.16; 51.68% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPTLC3 Gene

Human Gene Mutation Database (HGMD)
SPTLC3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPTLC3
Leiden Open Variation Database (LOVD)
SPTLC3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPTLC3 Gene

Disorders for SPTLC3 Gene

MalaCards: The human disease database

(10) MalaCards diseases for SPTLC3 Gene - From: CVR, COP, and GCD

Disorder Aliases PubMed IDs
sensory peripheral neuropathy
  • peripheral sensory neuropathy
neuropathy
  • peripheral neuropathy
peripheral nervous system disease
  • peripheral nerve disease
neuritis
  • peripheral neuritis
neuropathy, hereditary sensory and autonomic, type ia
  • hsan1a
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SPTLC3

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 SPTLC3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SPTLC3 Gene

Publications for SPTLC3 Gene

  1. Cloning and initial characterization of a new subunit for mammalian serine-palmitoyltransferase. (PMID: 17023427) Hornemann T … von Eckardstein A (The Journal of biological chemistry 2006) 2 3 4
  2. Genome-wide association study of personality traits in bipolar patients. (PMID: 21368711) Alliey-Rodriguez N … Gershon ES (Psychiatric genetics 2011) 3 40
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 40
  4. A genome-wide perspective of genetic variation in human metabolism. (PMID: 20037589) Illig T … Suhre K (Nature genetics 2010) 3 40
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 40

Products for SPTLC3 Gene

Sources for SPTLC3 Gene