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This gene encodes a long chain base subunit of serine palmitoyltransferase. Serine palmitoyltransferase, which consists of two different subunits, is the key enzyme in sphingolipid biosynthesis. It catalyzes the pyridoxal-5-prime-phosphate-dependent condensation of L-serine and palmitoyl-CoA to 3-oxosphinganine. Mutations in this gene were identified in patients with hereditary... See more...
Aliases for SPTLC2 Gene
Aliases for SPTLC2 Gene
External Ids for SPTLC2 Gene
- HGNC: 11278
- NCBI Entrez Gene: 9517
- Ensembl: ENSG00000100596
- OMIM®: 605713
- UniProtKB/Swiss-Prot: O15270
Previous GeneCards Identifiers for SPTLC2 Gene
- GC14M075479
- GC14M071790
- GC14M075963
- GC14M077043
- GC14M077973
- GC14M058139
Summaries for SPTLC2 Gene
-
This gene encodes a long chain base subunit of serine palmitoyltransferase. Serine palmitoyltransferase, which consists of two different subunits, is the key enzyme in sphingolipid biosynthesis. It catalyzes the pyridoxal-5-prime-phosphate-dependent condensation of L-serine and palmitoyl-CoA to 3-oxosphinganine. Mutations in this gene were identified in patients with hereditary sensory neuropathy type I. [provided by RefSeq, Mar 2011]
GeneCards Summary for SPTLC2 Gene
SPTLC2 (Serine Palmitoyltransferase Long Chain Base Subunit 2) is a Protein Coding gene. Diseases associated with SPTLC2 include Neuropathy, Hereditary Sensory And Autonomic, Type Ic 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 SPTLC3.
UniProtKB/Swiss-Prot Summary for SPTLC2 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. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC2-SPTSSB complex displays a preference for C18-CoA substrate. Plays an important role in de novo sphyngolipid biosynthesis which is crucial for adipogenesis (By similarity).
Additional gene information for SPTLC2 Gene
- HGNC (11278)
- NCBI Entrez Gene (9517)
- Ensembl (ENSG00000100596)
- OMIM® (605713)
- UniProtKB/Swiss-Prot (O15270)
- Open Targets Platform(ENSG00000100596)
- Monarch Initiative
- Alliance of Genome Resources
- Search for SPTLC2 at DataMed
- Search for SPTLC2 at HumanCyc
No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPTLC2 Gene
Genomics for SPTLC2 Gene
GeneHancer (GH) Regulatory Elements Pubs
Promoters and enhancers for SPTLC2 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 SPTLC2 on the GeneHancer Hub at the UCSC Golden Path
Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SPTLC2
- Top Transcription factor binding sites by QIAGEN in the SPTLC2 gene promoter:
-
- C/EBPalpha
- C/EBPbeta
- Elk-1
- Lhx3a
- LHX3b
- Pax-6
- RORalpha1
- STAT1
- ZID
Genomic Locations for SPTLC2 Gene
Latest Assembly
- chr14:77,505,997-77,616,663
- (GRCh38/hg38)
- Size:
- 110,667 bases
- Orientation:
- Minus strand
Previous Assembly
- chr14:77,972,340-78,082,980
- (GRCh37/hg19 by Entrez Gene)
- Size:
- 110,641 bases
- Orientation:
- Minus strand
Genomic View for SPTLC2 Gene
Genes around SPTLC2 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 14q24.3 by HGNC
- 14q24.3 by Entrez Gene
- 14q24.3 by Ensembl
SPTLC2 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene Density
RefSeq DNA sequence for SPTLC2 Gene
Proteins for SPTLC2 Gene
-
Protein details for SPTLC2 Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- O15270-SPTC2_HUMAN
- Recommended name:
- Serine palmitoyltransferase 2
- Protein Accession:
- O15270
- Q16685
Protein attributes for SPTLC2 Gene
- Size:
- 562 amino acids
- Molecular mass:
- 62924 Da
- Cofactor:
- Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
- Quaternary structure:
-
- Heterodimer with SPTLC1. 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=BAA25452.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
Protein Expression for SPTLC2 Gene
Selected DME Specific Peptides for SPTLC2 Gene
- O15270:
-
- RNLYMRIRD
- LFGYLRDF
- YGQPRTRR
- VVVVGFPAT
- VINMGSYN
- EGIYSMEG
- HSHSAVYA
- SLVLGARLSGATIRIFKHNN
- DSPVVPL
- ALKKKYKAYLY
- SDELNHAS
- YSMEGSIV
- MGTFTKSF
- SYNYLGFA
- GMGFATNSMNIPALVGKGCLILSDELNH
- LYQDFENFY
Post-translational modifications for SPTLC2 Gene
Other Protein References for SPTLC2 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibodies for research
- LifeSpan BioSciences SPTLC2 / LCB2 Antibody (LS-B9514) and SPTLC2 / LCB2 Antibody (LS-B1616)
- G Biosciences Immunotag™ SPTLC2 Antibody
-
Custom Antibody ServicesOriGene Antibodies for SPTLC2
- Novus Biologicals Antibodies for SPTLC2
-
Abcam antibodies for SPTLC2
- Invitrogen Antibodies for SPTLC2 (AFLGC-SPTLC2)
-
Boster Bio Antibodies for SPTLC2
-
Santa Cruz Biotechnology (SCBT) Antibodies for SPTLC2
- Sino Biological Antibodies for SPTLC2
Protein products for research
-
OriGene Purified Proteins for SPTLC2
- Search Origene for MassSpec and Protein Over-expression Lysates for SPTLC2
- Origene Custom Protein Services for SPTLC2
- antibodies-online: Show 7 available SPTLC2 Proteins ranked by validation data
- Compare Top SPTLC2 Proteins
-
Quality Products:
-
Abcam proteins for SPTLC2
Assay products for research
- antibodies-online: Show 7 available SPTLC2 Elisa Kits ranked by validation data
- Compare Top SPTLC2 Elisa Kits
-
Quality Products:
Domains & Families for SPTLC2 Gene
Gene Families for SPTLC2 Gene
- Human Protein Atlas (HPA):
-
- Disease related genes
- Enzymes
- Plasma proteins
- Potential drug targets
- Predicted membrane proteins
Protein Domains for SPTLC2 Gene
- InterPro:
- Blocks:
-
- Aminotransferase, class-II
Suggested Antigen Peptide Sequences for SPTLC2 Gene
- GenScript: Design optimal peptide antigens:
-
- Serine-palmitoyl-CoA transferase 2 (SPTC2_HUMAN)
Graphical View of Domain Structure for InterPro Entry
O15270UniProtKB/Swiss-Prot:
SPTC2_HUMAN :- Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.
- Family:
-
- Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.
Function for SPTLC2 Gene
Molecular function for SPTLC2 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. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC2-SPTSSB complex displays a preference for C18-CoA substrate. Plays an important role in de novo sphyngolipid biosynthesis which is crucial for adipogenesis (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 Induction:
- Expression at protein level is highly increased in brains of patients with Alzheimer disease. No changes are observed at mRNA level.
Enzyme Numbers (IUBMB) for SPTLC2 Gene
Phenotypes From GWAS Catalog for SPTLC2 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:0016740 | transferase activity | IEA | -- |
| GO:0016746 | transferase activity, transferring acyl groups | IEA | -- |
| GO:0030170 | pyridoxal phosphate binding | IEA | -- |
Phenotypes for SPTLC2 Gene
- MGI mutant phenotypes for SPTLC2:
- inferred from 4 alleles
- GenomeRNAi human phenotypes for SPTLC2:
-
- shRNA abundance <= 50%
- Increased shRNA abundance (Z-score > 2)
- no effect
- Inconclusive
- Decreased viability
- Increased ionizing radiation sensitivity
- Decreased shRNA abundance (Z-score < -2)
- Moderately decreased NFAT1-GFP nuclear translocation
- Negative genetic interaction between KRASG13D/+ and KRAS+/-
- Increased cell number in G1, average or increased nuclei size in G1
Animal Models for SPTLC2 Gene
- MGI Knock Outs for SPTLC2:
-
- Sptlc2 Sptlc2<tm1Jia>
Animal Models for research
-
Taconic Biosciences Mouse Models for SPTLC2
CRISPR products for research
- Applied Biological Materials (abm): CRISPR Clones for SPTLC2 - Starting at $85 >
- * SPTLC2 CRISPR as ready-to-use vector or virus: Non-viral | Lenti- | Adeno- | AAV- | siRNA - Browse All
- * Cas9 Nucleases, Nickases, Null Mutants, and GFP tag also available.
-
OriGene CRISPR knockouts for SPTLC2
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for SPTLC2
-
Santa Cruz Biotechnology (SCBT) CRISPR for SPTLC2
miRNA for SPTLC2 Gene
- miRTarBase miRNAs that target SPTLC2
-
- hsa-miR-3187-3p (MIRT519461)
- hsa-miR-4435 (MIRT519462)
- hsa-miR-588 (MIRT519463)
- hsa-miR-4701-5p (MIRT519464)
- hsa-miR-548s (MIRT519465)
- hsa-miR-6788-3p (MIRT519466)
- hsa-miR-6832-5p (MIRT519467)
- hsa-miR-6086 (MIRT519468)
- hsa-miR-377-5p (MIRT519469)
- hsa-miR-655-5p (MIRT519470)
- hsa-miR-6088 (MIRT519471)
- hsa-miR-4770 (MIRT519472)
- hsa-miR-143-3p (MIRT519473)
- hsa-miR-4716-5p (MIRT519474)
- hsa-miR-4494 (MIRT519475)
- hsa-miR-4781-3p (MIRT519476)
- hsa-miR-4639-5p (MIRT532602)
- hsa-miR-5581-3p (MIRT532603)
- hsa-miR-340-5p (MIRT532604)
- hsa-miR-210-5p (MIRT532605)
- hsa-miR-4749-3p (MIRT532606)
- hsa-miR-6810-3p (MIRT532607)
- hsa-miR-6801-3p (MIRT532608)
- hsa-miR-6872-3p (MIRT532609)
- hsa-miR-330-3p (MIRT532610)
- hsa-miR-5590-3p (MIRT532611)
- hsa-miR-142-5p (MIRT532612)
- hsa-miR-548p (MIRT532613)
- hsa-miR-93-5p (MIRT532614)
- hsa-miR-526b-3p (MIRT532615)
- hsa-miR-519d-3p (MIRT532616)
- hsa-miR-20b-5p (MIRT532617)
- hsa-miR-20a-5p (MIRT532618)
- hsa-miR-17-5p (MIRT532619)
- hsa-miR-106b-5p (MIRT532620)
- hsa-miR-106a-5p (MIRT532621)
- hsa-miR-6507-3p (MIRT532622)
- hsa-miR-887-5p (MIRT545707)
- hsa-miR-6780a-5p (MIRT545708)
- hsa-miR-6779-5p (MIRT545709)
- hsa-miR-3689c (MIRT545710)
- hsa-miR-3689b-3p (MIRT545711)
- hsa-miR-3689a-3p (MIRT545712)
- hsa-miR-30b-3p (MIRT545713)
- hsa-miR-1273h-5p (MIRT545714)
- hsa-miR-6788-5p (MIRT545715)
- hsa-miR-30c-2-3p (MIRT545716)
- hsa-miR-30c-1-3p (MIRT545717)
- hsa-miR-6505-5p (MIRT545718)
- hsa-miR-466 (MIRT545719)
- hsa-miR-4672 (MIRT545720)
- hsa-miR-3941 (MIRT545721)
- hsa-miR-8085 (MIRT545722)
- hsa-miR-6731-5p (MIRT545723)
- hsa-miR-6878-5p (MIRT545724)
- hsa-miR-3189-3p (MIRT545725)
- hsa-miR-4801 (MIRT545726)
- hsa-miR-4731-3p (MIRT545727)
- hsa-miR-548ao-3p (MIRT545728)
- hsa-miR-3667-5p (MIRT545729)
- hsa-miR-4694-3p (MIRT545730)
- hsa-miR-129-5p (MIRT638203)
- hsa-miR-8055 (MIRT638204)
- hsa-miR-6864-3p (MIRT638205)
- hsa-miR-3672 (MIRT638206)
- hsa-miR-6867-3p (MIRT638207)
- hsa-miR-642a-5p (MIRT638208)
- hsa-miR-4524a-3p (MIRT638209)
- hsa-miR-4685-3p (MIRT638210)
- hsa-miR-4287 (MIRT638211)
- hsa-miR-7113-3p (MIRT638212)
- hsa-miR-4469 (MIRT638213)
- hsa-miR-2276-5p (MIRT638214)
- hsa-miR-6892-3p (MIRT638215)
- hsa-miR-1228-3p (MIRT638216)
- hsa-miR-5007-5p (MIRT638217)
- hsa-miR-4797-5p (MIRT638218)
- hsa-miR-215-3p (MIRT763848)
- hsa-miR-5586-3p (MIRT774779)
- hsa-miR-5693 (MIRT775045)
- hsa-miR-6499-3p (MIRT776375)
- hsa-miR-6773-3p (MIRT778718)
- hsa-miR-891a-3p (MIRT782624)
- hsa-miR-1200 (MIRT783122)
- hsa-miR-183-3p (MIRT783974)
- hsa-miR-3663-5p (MIRT785067)
- hsa-miR-378a-5p (MIRT785384)
- hsa-miR-4452 (MIRT785909)
- hsa-miR-4635 (MIRT786242)
- hsa-miR-4755-3p (MIRT786626)
- hsa-miR-6131 (MIRT788078)
- hsa-miR-6513-3p (MIRT788310)
- hsa-miR-6790-3p (MIRT788742)
- hsa-miR-6807-5p (MIRT788859)
- hsa-miR-6821-3p (MIRT788955)
miRNA products for research
Inhibitory RNAs for research
- Origene shrna, sirna, and RNAi products in human, mouse, rat for SPTLC2
- Browse OriGene Inhibitory RNA Products For SPTLC2
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPTLC2
Clone products for research
- Applied Biological Materials (abm): Clones for SPTLC2 - Starting at $45 >
- * SPTLC2 as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Retro- | Protein Vector - Browse All
- * Viral Packaging Services and High Titer Production Services also available.
- Sino Biological Human cDNA Clone for SPTLC2
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for SPTLC2
Cell Lines for research
-
Horizon Cell Lines for SPTLC2
No data available for Transcription Factor Targets and HOMER Transcription for SPTLC2 Gene
Localization for SPTLC2 Gene
Subcellular locations from UniProtKB/Swiss-Prot for SPTLC2 Gene
- Endoplasmic reticulum membrane. Single-pass membrane protein.
| Compartment | Confidence |
|---|---|
| mitochondrion | 4 |
| plasma membrane | 2 |
| nucleus | 2 |
| endoplasmic reticulum | 2 |
| cytosol | 2 |
| golgi apparatus | 2 |
| extracellular | 1 |
| cytoskeleton | 1 |
| peroxisome | 1 |
| endosome | 1 |
| lysosome | 1 |
- Mitochondria (2)
| 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 | 19416851 |
Pathways & Interactions for SPTLC2 Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | Sphingolipid metabolism | ||
| 2 | Metabolism |
.40
|
|
| 3 | Sphingolipid signaling pathway | ||
Pathways by source for SPTLC2 Gene
2 BioSystems pathways for SPTLC2 Gene
4 Reactome pathways for SPTLC2 Gene
3 KEGG pathways for SPTLC2 Gene
UniProtKB/Swiss-Prot O15270-SPTC2_HUMAN
- Pathway: Lipid metabolism; sphingolipid metabolism.
Interacting Proteins for SPTLC2 Gene
GPS-Prot Interaction Network for SPTLC2
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0006629 | lipid metabolic process | IEA | -- |
| GO:0006665 | sphingolipid metabolic process | IEA | -- |
| GO:0006686 | sphingomyelin biosynthetic process | IEA | -- |
| GO:0009058 | biosynthetic process | IEA | -- |
| GO:0030148 | sphingolipid biosynthetic process | TAS | 19416851 |
No data available for SIGNOR curated interactions for SPTLC2 Gene
Drugs & Compounds for SPTLC2 Gene
| 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 | |||
| Serine | Investigational | Nutra | Target | Weak endogenous glycine receptor agonist | 1286 | |
| Coenzyme A | Investigational | Nutra | 0 | |||
| Myriocin | Pharma | 0 |
| Name | Synonyms | Role | CAS Number | PubChem IDs | PubMed IDs | |
|---|---|---|---|---|---|---|
| 3-Dehydrosphinganine |
|
16105-69-4 |
|
|||
| hexadecanoyl-CoA |
|
|
||||
| Palmityl-CoA |
|
1763-10-6 |
|
Transcripts for SPTLC2 Gene
mRNA/cDNA for SPTLC2 Gene
- 1 REFSEQ mRNAs :
- 8 NCBI additional mRNA sequence :
- 6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
-
- ENST00000216484 8034 nts (view in UCSC)
- ENST00000554365 604 nts (view in UCSC)
- ENST00000554901 1518 nts (view in UCSC)
- ENST00000556264 263 nts (view in UCSC)
- ENST00000556607 460 nts (view in UCSC)
CRISPR products for research
- Applied Biological Materials (abm): CRISPR Clones for SPTLC2 - Starting at $85 >
- * SPTLC2 CRISPR as ready-to-use vector or virus: Non-viral | Lenti- | Adeno- | AAV- | siRNA - Browse All
- * Cas9 Nucleases, Nickases, Null Mutants, and GFP tag also available.
-
OriGene CRISPR knockouts for SPTLC2
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for SPTLC2
-
Santa Cruz Biotechnology (SCBT) CRISPR for SPTLC2
miRNA products for research
Inhibitory RNAs for research
- Origene shrna, sirna, and RNAi products in human, mouse, rat for SPTLC2
- Browse OriGene Inhibitory RNA Products For SPTLC2
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPTLC2
Clone products for research
- Applied Biological Materials (abm): Clones for SPTLC2 - Starting at $45 >
- * SPTLC2 as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Retro- | Protein Vector - Browse All
- * Viral Packaging Services and High Titer Production Services also available.
- Sino Biological Human cDNA Clone for SPTLC2
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for SPTLC2
Relevant External Links for SPTLC2 Gene
- GeneLoc Exon Structure for
- SPTLC2
Expression for SPTLC2 Gene
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
- Brain (Nervous System)
- Lung (Respiratory System)
- Neural Tube (Nervous System)
mRNA differential expression in normal tissues according to GTEx for SPTLC2 Gene
This gene is overexpressed in Whole Blood (x6.1).
This gene is overexpressed in Bone (15.0), Peripheral blood mononuclear cells (13.8), and Breast (7.6).
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SPTLC2 Gene
Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPTLC2
SOURCE GeneReport for Unigene cluster for SPTLC2 Gene:
Hs.435661mRNA Expression by UniProt/SwissProt for SPTLC2 Gene:
O15270-SPTC2_HUMAN
Tissue specificity:
Widely expressed.
Evidence on tissue expression from TISSUES for SPTLC2 Gene
- Nervous system(4.8)
- Pancreas(4.3)
- Lung(2.5)
- Kidney(2.2)
- Spleen(2.2)
- Intestine(2.1)
- Liver(2.1)
- Skin(2)
- Blood(2)
Phenotype-based relationships between genes and organs from Gene ORGANizer for SPTLC2 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
Primer products for research
-
OriGene qPCR primer pairs for SPTLC2
-
OriGene qPCR primer pairs and template standards for SPTLC2
Gene Expression Assays for research
Orthologs for SPTLC2 Gene
This gene was present in the common ancestor of eukaryotes.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| Chimpanzee (Pan troglodytes) |
Mammalia | SPTLC2 29 30 |
|
OneToOne | |
| Oppossum (Monodelphis domestica) |
Mammalia | SPTLC2 30 |
|
OneToOne | |
| Dog (Canis familiaris) |
Mammalia | SPTLC2 29 30 |
|
OneToOne | |
| Mouse (Mus musculus) |
Mammalia | Sptlc2 29 16 30 |
|
OneToOne | |
| Cow (Bos Taurus) |
Mammalia | SPTLC2 29 30 |
|
OneToOne | |
| Rat (Rattus norvegicus) |
Mammalia | Sptlc2 29 |
|
||
| Platypus (Ornithorhynchus anatinus) |
Mammalia | SPTLC2 30 |
|
OneToOne | |
| Chicken (Gallus gallus) |
Aves | SPTLC2 29 30 |
|
OneToOne | |
| Lizard (Anolis carolinensis) |
Reptilia | SPTLC2 30 |
|
OneToOne | |
| Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | sptlc2 29 |
|
||
| African clawed frog (Xenopus laevis) |
Amphibia | Xl.2338 29 |
|
||
| Zebrafish (Danio rerio) |
Actinopterygii | sptlc2b 30 |
|
OneToMany | |
| sptlc2a 29 30 |
|
OneToMany | |||
| Dr.16885 29 |
|
||||
| African malaria mosquito (Anopheles gambiae) |
Insecta | AgaP_AGAP007941 29 |
|
||
| Fruit Fly (Drosophila melanogaster) |
Insecta | lace 29 30 31 |
|
OneToMany | |
| Worm (Caenorhabditis elegans) |
Secernentea | sptl-2 29 30 |
|
ManyToMany | |
| F43H9.2a 31 |
|
|
|||
| F43H9.2b 31 |
|
|
|||
| T22G5.5 31 |
|
|
|||
| sptl-3 30 |
|
ManyToMany | |||
| K. Lactis Yeast (Kluyveromyces lactis) |
Saccharomycetes | KLLA0D02134g 29 |
|
||
| Baker's yeast (Saccharomyces cerevisiae) |
Saccharomycetes | LCB2 29 30 32 |
|
OneToMany | |
| A. gosspyii yeast (Eremothecium gossypii) |
Saccharomycetes | AGOS_AGR127C 29 |
|
||
| Thale Cress (Arabidopsis thaliana) |
eudicotyledons | LCB2 29 |
|
||
| Alicante grape (Vitis vinifera) |
eudicotyledons | Vvi.2016 29 |
|
||
| Rice (Oryza sativa) |
Liliopsida | Os01g0928800 29 |
|
||
| Barley (Hordeum vulgare) |
Liliopsida | Hv.11007 29 |
|
||
| Wheat (Triticum aestivum) |
Liliopsida | Ta.2702 29 |
|
||
| Corn (Zea mays) |
Liliopsida | Zm.13752 29 |
|
||
| Sea Squirt (Ciona savignyi) |
Ascidiacea | -- 30 |
|
OneToMany | |
| Bread mold (Neurospora crassa) |
Ascomycetes | NCU00447 29 |
|
||
| Fission Yeast (Schizosaccharomyces pombe) |
Schizosaccharomycetes | lcb2 29 |
|
||
| Sea Vase (Ciona intestinalis) |
Ascidiacea | Cin.835 29 |
|
- Species where no ortholog for SPTLC2 was found in the sources mined by GeneCards:
-
- Actinobacteria (Mycobacterium tuberculosis)
- Alpha proteobacteria (Wolbachia pipientis)
- Amoeba (Dictyostelium discoideum)
- Archea (Pyrococcus horikoshii)
- Beta proteobacteria (Neisseria meningitidis)
- Chromalveolata (Phytophthora infestans)
- Common water flea (Daphnia pulex)
- 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)
- Rainbow Trout (Oncorhynchus mykiss)
- Rice Blast Fungus (Magnaporthe grisea)
- Schistosome Parasite (Schistosoma mansoni)
- Sea Anemone (Nematostella vectensis)
- 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)
Evolution for SPTLC2 Gene
- ENSEMBL:
- Gene Tree for SPTLC2 (if available)
- TreeFam:
- Gene Tree for SPTLC2 (if available)
- Aminode:
- Evolutionary constrained regions (ECRs) for SPTLC2: view image
- Alliance of Genome Resources:
- Additional Orthologs for SPTLC2
Paralogs for SPTLC2 Gene
(1) SIMAP similar genes for SPTLC2 Gene using alignment to 4 proteins:
- SPTC2_HUMAN
- H0YJ96_HUMAN
- H0YJV2_HUMAN
- L8E997_HUMAN
Pseudogenes.org Pseudogenes for SPTLC2 Gene
Variants for SPTLC2 Gene
Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SPTLC2 Gene
| SNP ID | Clinical significance and condition | Chr 14 pos | Variation | AA Info | Type |
|---|---|---|---|---|---|
| 1003505 | Uncertain Significance: Hereditary sensory and autonomic neuropathy type IC | 77,555,416(-) |
G/A NM_004863.4(SPTLC2):c.1060C>T (p.Pro354Ser) |
MISSENSE | |
| 1005402 | Uncertain Significance: Hereditary sensory and autonomic neuropathy type IC | 77,616,572(-) |
G/A NM_004863.4(SPTLC2):c.8C>T (p.Pro3Leu) |
MISSENSE | |
| 1009829 | Uncertain Significance: Hereditary sensory and autonomic neuropathy type IC | 77,578,970(-) |
T/C NM_004863.4(SPTLC2):c.467A>G (p.Tyr156Cys) |
MISSENSE | |
| 1010136 | Uncertain Significance: Hereditary sensory and autonomic neuropathy type IC | 77,518,160(-) |
C/A NM_004863.4(SPTLC2):c.1447G>T (p.Gly483Ter) |
NONSENSE | |
| 1011602 | Uncertain Significance: Hereditary sensory and autonomic neuropathy type IC | 77,555,425(-) |
C/A NM_004863.4(SPTLC2):c.1051G>T (p.Ala351Ser) |
MISSENSE |
All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).
| Variant ID | Type | Subtype | PubMed ID |
|---|---|---|---|
| esv2759998 | CNV | gain | 17122850 |
| esv3309823 | CNV | mobile element insertion | 20981092 |
| esv3340561 | CNV | insertion | 20981092 |
| esv3358343 | CNV | insertion | 20981092 |
| esv3635007 | CNV | loss | 21293372 |
| esv7096 | OTHER | inversion | 19470904 |
| nsv1051554 | CNV | loss | 25217958 |
| nsv1053810 | CNV | gain | 25217958 |
| nsv1118537 | CNV | duplication | 24896259 |
| nsv832835 | CNV | gain | 17160897 |
| nsv85432 | CNV | deletion | 16902084 |
Residual Variation Intolerance Score:
17.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
1.73;
32.79% of all genes are more intolerant (likely to be disease-causing)
Additional Variant Information for SPTLC2 Gene
SNP Genotyping and Copy Number Assays for research
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPTLC2 Gene
Disorders for SPTLC2 Gene
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| neuropathy, hereditary sensory and autonomic, type ic |
|
|
| hereditary sensory and autonomic neuropathy type 1 |
|
|
| charcot-marie-tooth disease, demyelinating, type 1c |
|
|
| hereditary sensory neuropathy |
|
|
| autonomic neuropathy |
|
|
Search SPTLC2 in MalaCards
View complete list of genes associated with diseases
UniProtKB/Swiss-Prot
SPTC2_HUMAN- Neuropathy, hereditary sensory and autonomic, 1C (HSAN1C) [MIM:613640]: 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. HSAN1C symptoms include loss of touch and vibration in the feet, dysesthesia and severe panmodal sensory loss in the upper and lower limbs, distal lower limb sensory loss with ulceration and osteomyelitis, and distal muscle weakness. {ECO:0000269 PubMed:20920666, ECO:0000269 PubMed:23658386, ECO:0000269 PubMed:26573920}. Note=The disease is caused by variants affecting the gene represented in this entry. SPTLC2 disease mutations cause a shift in the substrate specificity of SPT resulting in the alternative use of L-alanine and L-glycine over its canonical substrate L-serine. This leads to the production of 1-deoxysphingolipids that cannot be correctly metabolized (PubMed:23658386). {ECO:0000269 PubMed:23658386, ECO:0000269 PubMed:26573920}.
Additional Disease Information for SPTLC2
- Human Genome Epidemiology Navigator
- (HuGE)
- Atlas
- ATLAS of Genetics and Cytogenetics in Oncology and Haematology
- Open Targets Platform
- Open Targets Platform
No data available for Genatlas for SPTLC2 Gene
Publications for SPTLC2 Gene
- 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
- Sphingolipid synthesis: identification and characterization of mammalian cDNAs encoding the Lcb2 subunit of serine palmitoyltransferase. (PMID: 8921873) Nagiec MM … Dickson RC (Gene 1996) 2 3 4 22
- The Variant p.(Arg183Trp) in SPTLC2 Causes Late-Onset Hereditary Sensory Neuropathy. (PMID: 26573920) Suriyanarayanan S … Ylikallio E (Neuromolecular medicine 2016) 3 4 72
- Mutations in the SPTLC2 subunit of serine palmitoyltransferase cause hereditary sensory and autonomic neuropathy type I. (PMID: 20920666) Rotthier A … Timmerman V (American journal of human genetics 2010) 3 4 72
- Hereditary sensory and autonomic neuropathy type 1 (HSANI) caused by a novel mutation in SPTLC2. (PMID: 23658386) Murphy SM … Reilly MM (Neurology 2013) 3 4
ExternalLinks
Products for SPTLC2 Gene
- Custom Antibody ServicesOriGene Antibodies for SPTLC2
- Browse OriGene ELISA Kits
- Custom Assay Services
- OriGene Purified Proteins for SPTLC2
- Search Origene for MassSpec and Protein Over-expression Lysates for SPTLC2
- Origene Custom Protein Services for SPTLC2
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- Sino Biological Human cDNA Clone for SPTLC2
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- Sino Biological Antibodies for SPTLC2
- Browse Sino Biological Assays
- Browse Antibodies
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- High-throughput Antibody Production Service
- Protein Production Service
- Epitope Tag Antibodies & Reporter Protein Antibodies
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- Novus Biologicals Antibodies for SPTLC2
- Novus Biologicals proteins and lysates for SPTLC2
- Browse Antibodies
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- Abcam proteins for SPTLC2
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- Browse Primary Antibodies
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- Taconic Biosciences Mouse Models for SPTLC2
- Find your next knockout model in the Taconic Knockout Repository
- Genetically Engineered Models Available Immediately
- Humanized Mice
- Invitrogen Antibodies for SPTLC2 (AFLGC-SPTLC2)
- VectorBuilder Custom and pre-made DNA vectors for SPTLC2 (ie. gene expression, shRNA knockdown, CRISPR)
- VectorBuilder Viral vectors for SPTLC2 (ie. lentivirus, AAV, adenovirus)
- VectorBuilder CRISPR vectors for SPTLC2 (ie. knockout, knockin, CRISPRa, CRISPRi)
- VectorBuilder Virus packaging for SPTLC2 CRISPR vectors (ie. lentivirus, AAV, adenovirus)
- VectorBuilder Stable cell line generation for SPTLC2
- antibodies-online: Show 23 available SPTLC2 Antibodies ranked by validation data
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- antibodies-online: Show 7 available SPTLC2 Elisa Kits ranked by validation data
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- Quality Products:
- antibodies-online: Show 7 available SPTLC2 Proteins ranked by validation data
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- Quality Products:
- Santa Cruz Biotechnology (SCBT) Antibodies for SPTLC2
- Search Santa Cruz Biotechnology (SCBT) for SPTLC2 siRNA/shRNA
- Santa Cruz Biotechnology (SCBT) CRISPR for SPTLC2
- Horizon Cell Lines for SPTLC2
- Browse GeneCopoeia Cell Lines
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for SPTLC2
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for SPTLC2
- Search GeneCopoeia for miRNA 3'UTR Target clone products for SPTLC2
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPTLC2
- Boster Bio Antibodies for SPTLC2
- Browse Boster Bio ELISA Kits
Sources for SPTLC2 Gene
- (1) GeneCards
- (2) HGNC
- (3) NCBI Entrez Gene
- (4) UniProtKB/Swiss-Prot
- (5) Ensembl
- (6) OMIM® (Updated: 05-Apr-2021)
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) Cell Signaling Technology
- (12) GO
- (13) UniProtKB/TrEMBL
- (14) InterPro
- (15) Blocks
- (16) MGI
- (17) IUBMB
- (18) KEGG
- (19) MINT
- (20) STRING
- (21) IntAct
- (22) Novoseek
- (23) PharmGKB
- (24) DrugBank
- (25) HMDB
- (26) ASD
- (27) SAGE
- (28) SOURCE
- (29) HomoloGene
- (30) PanEnsembl
- (31) euGenes
- (32) SGD
- (33) FlyBase
- (34) WormBase
- (35) Pseudogene
- (36) DGV
- (37) dbSNP
- (38) GenAtlas
- (39) HGMD
- (40) GAD
- (41) BGMUT
- (42) HuGE
- (43) Atlas
- (44) GenBank
- (45) HORDE
- (46) HUGE
- (47) IMGT
- (48) Leiden
- (49) miRBase
- (50) DME
- (51) OriGene
- (52) PubMed
- (53) R&D Systems
- (54) Tocris
- (55) Abcam
- (56) Novus Biologicals
- (57) ProSpec
- (58) Sino Biological
- (59) GenScript
- (60) Qiagen
- (61) OCA
- (62) Proteopedia
- (63) MOPED
- (64) neXtProt
- (65) Reactome
- (66) GeneGo (Thomson Reuters)
- (67) DISEASES
- (68) SIMAP
- (69) GenomeRNAi
- (70) LifeMap
- (71) miRTarBase
- (72) MalaCards
- (73) Invitrogen
- (74) BitterDB
- (75) ESI-BIO
- (76) RefSeq
- (77) BioSystems
- (78) MaxQB
- (79) IUPHAR
- (80) BioGPS
- (81) Illumina
- (82) COMPARTMENTS
- (83) HOMER
- (84) PaxDb
- (85) ApexBio
- (86) Addgene
- (87) antibodies-online
- (88) CYP
- (89) NONCODE
- (90) TreeFam
- (91) PathCards
- (92) GeneReviews
- (93) GeneTex
- (94) Taconic Biosciences
- (95) GTEx
- (96) ProteomicsDB
- (97) SCBT
- (98) DGIdb
- (99) ClinicalTrials
- (100) RVIS
- (101) SIGNOR
- (102) diseasecard
- (103) NIH Rare Diseases
- (104) Orphanet
- (105) UMLS
- (106) GTR
- (107) Disease Ontology
- (108) MedlinePlus Genetics
- (109) MeSH
- (110) MedlinePlus
- (111) CDC
- (112) NINDS
- (113) NCBI Bookshelf
- (114) ClinVar
- (115) Gene Damage Index
- (116) HPO
- (117) UDN
- (118) VISTA
- (119) FANTOM5
- (120) ENCODE
- (121) ProSci
- (122) Horizon
- (123) The Signaling Pathways Project (SPP)
- (124) IID
- (125) VectorBuilder
- (126) SNPedia
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- (128) CIViC
- (129) ProteoGenix
- (130) dbSUPER
- (131) TISSUES
- (132) Gene ORGANizer
- (133) abm
- (134) Human Protein Atlas
- (135) GWAS Catalog
- (136) Monarch Initiative
- (137) DataMed
- (138) HumanCyc
- (139) UCNEbase
- (140) EPDnew
- (141) Applied Biosystems
- (142) GlyConnect
- (143) Aminode
- (144) GeneCopoeia
- (145) GPS-Prot
- (146) RNAcentral
- (147) LncRNADisease
- (148) LOVD
- (149) miR2Disease
- (150) DiseaseEnhancer
- (151) Boster Bio
- (152) Biorbyt
- (153) Biocompare
- (154) Mastermind
- (155) CTD^2 Dashboard
- (156) CraniofacialAtlas
- (157) GeneImprint
- (158) Synthego
- (159) ENA
- (160) GtRNAdb
- (161) LncBase
- (162) LncBook
- (163) LNCipedia
- (164) Modomics
- (165) PDBe
- (166) Rfam
- (167) SILVA
- (168) snOPY
- (169) SRPDB
- (170) GENCODE
- (171) TarBase
- (172) Open Targets Platform
- (173) 5SRRNADB
- (174) snoDB
- (175) MirGeneDB
- (176) Alliance of Genome Resources