Gene Gene information from NCBI Gene database.
Entrez ID 9517
Gene name Serine palmitoyltransferase long chain base subunit 2
Gene symbol SPTLC2
Synonyms (NCBI Gene)
HSN1CLCB2LCB2ANSAN1CSPT2hLCB2a
Chromosome 14
Chromosome location 14q24.3
Summary 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.
7
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.
1174
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 (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
37
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 identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
605713 11278 ENSG00000100596
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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 associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
14
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Charcot-Marie-Tooth disease Likely pathogenic; Pathogenic rs1594986869 RCV000789584
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hereditary neuropathy or pain disorder Likely pathogenic; Pathogenic rs775437084 RCV005865350
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neuropathy, hereditary sensory and autonomic, type 1C Likely pathogenic; Pathogenic rs2140039094, rs267607089, rs864621998, rs2503570171, rs775437084, rs1594986869 RCV002249182
RCV000648366
RCV000206999
RCV003527231
RCV000576203
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE IC, SEVERE Pathogenic rs267607091 RCV000005066
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
AMYOTROPHIC LATERAL SCLEROSIS ClinGen, Disgenet, GWAS catalog
ClinGen, Disgenet, GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
HEREDITARY SENSORY AND AUTONOMIC NEUROPATHY TYPE 1 Orphanet
Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Amyotrophic Lateral Sclerosis Amyotrophic lateral sclerosis Pubtator 36966328, 38041684 Associate
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Anhidrosis Anhidrosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Attention Deficit Disorder with Hyperactivity Attention deficit hyperactivity disorder Pubtator 32730653 Associate
★☆☆☆☆
Found in Text Mining only
Charcot-Marie-Tooth Disease Charcot-Marie-Tooth Disease GENOMICS_ENGLAND_DG 20920666
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Coronary Artery Disease Coronary artery disease Pubtator 37298446 Associate
★☆☆☆☆
Found in Text Mining only
Demyelinating Diseases Demyelinating diseases Pubtator 32730653 Associate
★☆☆☆☆
Found in Text Mining only
Dysautonomia, Familial Dysautonomia GENOMICS_ENGLAND_DG 20920666
★☆☆☆☆
Found in Text Mining only
Heart Valve Diseases Heart valve disease Pubtator 37298446 Associate
★☆☆☆☆
Found in Text Mining only
Hereditary Sensory and Autonomic Neuropathies Hereditary sensory and autonomic neuropathy Pubtator 20920666, 21618344, 23658386, 24175284, 26681808, 32730653, 34090020, 34337561, 37107689 Associate
★☆☆☆☆
Found in Text Mining only
Hereditary Sensory and Autonomic Neuropathies Hereditary sensory and autonomic neuropathy BEFREE 26573920, 30866134
★☆☆☆☆
Found in Text Mining only