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
GO:0004758 Function Serine C-palmitoyltransferase activity IDA 25332431, 25691431
GO:0004758 Function Serine C-palmitoyltransferase activity IDA 19416851, 20920666, 26573920
GO:0004758 Function Serine C-palmitoyltransferase activity IEA
GO:0004758 Function Serine C-palmitoyltransferase activity 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
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Associated diseases Disease associations categorized as Causal (pathogenic variants), Unknown (uncertain genetic evidence), or Text Mining (literature-based associations)
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Disease merge term Disease name dbSNP ID References
Hereditary sensory and autonomic neuropathy Neuropathy, hereditary sensory and autonomic, type 1C, NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE IC, SEVERE rs775437084, rs1594986869, rs267607089, rs267607091, rs864621998 N/A
Charcot-Marie-Tooth Disease Charcot-Marie-Tooth Disease rs1594986869 N/A
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Disease merge term Disease name Evidence References Source
Colorectal Cancer Colorectal cancer N/A N/A GWAS
Sensory And Autonomic Neuropathy hereditary sensory and autonomic neuropathy type 1 N/A N/A GenCC
Associations from Text Mining Disease associations identified through Pubtator
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