Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
9517
Gene name Gene Name - the full gene name approved by the HGNC.
Serine palmitoyltransferase long chain base subunit 2
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
SPTLC2
Synonyms (NCBI Gene) Gene synonyms aliases
HSN1C, LCB2, LCB2A, NSAN1C, SPT2, hLCB2a
Chromosome Chromosome number
14
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
14q24.3
Summary Summary of gene provided in NCBI Entrez 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 conde
SNPs SNP information provided by dbSNP.
SNP ID Visualize variation Clinical significance Consequence
rs199867946 A>G Conflicting-interpretations-of-pathogenicity, likely-benign Intron variant
rs267607089 C>A Pathogenic, likely-pathogenic Coding sequence variant, missense variant
rs267607090 C>T Pathogenic Coding sequence variant, missense variant
rs267607091 T>A Pathogenic Coding sequence variant, missense variant, genic downstream transcript variant
rs775437084 G>A Pathogenic Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
miRTarBase ID miRNA Experiments Reference
MIRT638218 hsa-miR-4797-5p HITS-CLIP 23824327
MIRT638217 hsa-miR-5007-5p HITS-CLIP 23824327
MIRT638216 hsa-miR-1228-3p HITS-CLIP 23824327
MIRT638215 hsa-miR-6892-3p HITS-CLIP 23824327
MIRT638214 hsa-miR-2276-5p HITS-CLIP 23824327
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0004758 Function Serine C-palmitoyltransferase activity IBA 21873635
GO:0004758 Function Serine C-palmitoyltransferase activity IDA 19416851, 20920666, 26573920
GO:0004758 Function Serine C-palmitoyltransferase activity IDA 25332431, 25691431
GO:0005789 Component Endoplasmic reticulum membrane TAS
GO:0006686 Process Sphingomyelin biosynthetic process IEA
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM HGNC e!Ensembl
605713 11278 ENSG00000100596
Protein
UniProt ID O15270
Protein name Serine palmitoyltransferase 2 (EC 2.3.1.50) (Long chain base biosynthesis protein 2) (LCB 2) (Long chain base biosynthesis protein 2a) (LCB2a) (Serine-palmitoyl-CoA transferase 2) (SPT 2)
Protein function Component of the serine palmitoyltransferase multisubunit enzyme (SPT) that catalyzes the initial and rate-limiting step in sphingolipid biosynthesis by condensing L-serine and activated acyl-CoA (most commonly palmitoyl-CoA) to form long-chain
PDB 6M4N , 6M4O , 7CQI , 7CQK , 7K0I , 7K0J , 7K0K , 7K0L , 7K0M , 7K0N , 7K0O , 7K0P , 7K0Q , 7YIU , 7YIY , 7YJ1 , 7YJ2
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00155 Aminotran_1_2 168 528 Aminotransferase class I and II Domain
Tissue specificity TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:17023427}.
Sequence
Sequence length 562
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG   Reactome
  Sphingolipid metabolism
Metabolic pathways
Sphingolipid signaling pathway
  Sphingolipid de novo biosynthesis
Associated diseases Disease information provided by ClinVar, GenCC, and GWAS databases.
Causal
Disease term Disease name dbSNP ID References
Charcot-marie-tooth disease Charcot-Marie-Tooth Disease rs137852739, rs137852737, rs118203972, rs118203974, rs267607183, rs267606878, rs121908287, rs1562648373, rs121908288, rs1368013631, rs28940291, rs28940292, rs28940293, rs28940294, rs28940295
View all (1137 more)
20920666
Dysautonomia Dysautonomia, Familial rs111033171, rs137853022, rs28939712, rs754348901, rs749052963, rs1057517169, rs1057516865, rs763445509, rs767527819, rs781333644, rs1239081703, rs1554696574, rs539544212, rs1201626345, rs774890086
View all (27 more)
20920666
Hereditary sensory and autonomic neuropathy Hereditary Sensory Autonomic Neuropathy, Type 1 rs137852739, rs137852737, rs28940291, rs28940294, rs267607089, rs267607091, rs119482081, rs119482083, rs119482082, rs267607087, rs111033592, rs111033590, rs111033591, rs387906331, rs387906332
View all (41 more)
26681808, 23658386, 20920666
Neuropathy NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE IC rs121913593, rs121913595, rs751050956, rs878853221, rs768554986, rs1553259568, rs1567973091, rs1560046845, rs1567969825, rs1567973088, rs756896276 23658386, 24175284, 29042446, 26350204, 26681808, 26573920, 20920666
Unknown
Disease term Disease name Evidence References Source
Osteomyelitis Osteomyelitis ClinVar
Sensory And Autonomic Neuropathy hereditary sensory and autonomic neuropathy type 1 GenCC
Colorectal Cancer Colorectal Cancer In summary, our data strongly demonstrated that upregulation of GRB7 conferred MEKi resistance in CRC cells with KRAS mutations by mediating RTK signaling through the recruitment of PLK1. GWAS, CBGDA
Associations from Text Mining
Disease Name Relationship Type References
Amyotrophic Lateral Sclerosis Associate 36966328, 38041684
Attention Deficit Disorder with Hyperactivity Associate 32730653
Charcot Marie Tooth Disease Associate 27025386
Coronary Artery Disease Associate 37298446
Demyelinating Diseases Associate 32730653
Disease Progression Stimulate 33031402
Fasciculation Associate 38041684
Heart Valve Diseases Associate 37298446
Hereditary Sensory and Autonomic Neuropathies Associate 20920666, 21618344, 23658386, 24175284, 26681808, 32730653, 34090020, 34337561, 37107689
Inherited Peripheral Neuropathy Associate 27025386