Description: Homo sapiens serine palmitoyltransferase, long chain base subunit 2 (SPTLC2), mRNA. RefSeq Summary (NM_004863): 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]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. Transcript (Including UTRs) Position: hg19 chr14:77,972,340-78,083,110 Size: 110,771 Total Exon Count: 12 Strand: - Coding Region Position: hg19 chr14:77,978,627-78,082,922 Size: 104,296 Coding Exon Count: 12
ID:SPTC2_HUMAN DESCRIPTION: RecName: Full=Serine palmitoyltransferase 2; EC=2.3.1.50; AltName: Full=Long chain base biosynthesis protein 2; Short=LCB 2; AltName: Full=Long chain base biosynthesis protein 2a; Short=LCB2a; AltName: Full=Serine-palmitoyl-CoA transferase 2; Short=SPT 2; 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-SSSPTA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC2-SSSPTB complex displays a preference for C18-CoA substrate. CATALYTIC ACTIVITY: Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D- sphinganine + CO(2). COFACTOR: Pyridoxal phosphate (By similarity). PATHWAY: Lipid metabolism; sphingolipid metabolism. SUBUNIT: Heterodimer with SPTLC1. Component of the serine palmitoyltransferase (SPT) complex, composed of LCB1/SPTLC1, LCB2 (SPTLC2 or SPTLC3) and ssPT (C14orf147/SSSPTA and C3orf57/SSSPTB). SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass membrane protein (By similarity). TISSUE SPECIFICITY: Widely expressed. DISEASE: Defects in SPTLC2 are the cause of hereditary sensory and autonomic neuropathy type 1C (HSAN1C) [MIM:613640]. It is 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. SIMILARITY: Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. SEQUENCE CAUTION: Sequence=BAA25452.2; Type=Erroneous initiation;
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Genetic Association Studies of Complex Diseases and Disorders
Genetic Association Database (archive): SPTLC2 CDC HuGE Published Literature: SPTLC2 Positive Disease Associations: Cholesterol, HDL
, Tunica Media Related Studies:
Cholesterol, HDL Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics.
[PubMed 17903299]
Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on O15270
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Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
Biological Process: GO:0006629 lipid metabolic process GO:0006665 sphingolipid metabolic process GO:0006686 sphingomyelin biosynthetic process GO:0008152 metabolic process GO:0009058 biosynthetic process GO:0030148 sphingolipid biosynthetic process GO:0046511 sphinganine biosynthetic process GO:0046512 sphingosine biosynthetic process GO:0046513 ceramide biosynthetic process GO:1904504 positive regulation of lipophagy
Cellular Component: GO:0005783 endoplasmic reticulum GO:0005789 endoplasmic reticulum membrane GO:0016020 membrane GO:0016021 integral component of membrane GO:0017059 serine C-palmitoyltransferase complex
Descriptions from all associated GenBank mRNAs
AB011098 - Homo sapiens KIAA0526 mRNA for KIAA0526 protein. Y08686 - H.sapiens mRNA for serine palmitoyltransferase, subunit II. BC005123 - Homo sapiens serine palmitoyltransferase, long chain base subunit 2, mRNA (cDNA clone MGC:10362 IMAGE:3688136), complete cds. KJ898042 - Synthetic construct Homo sapiens clone ccsbBroadEn_07436 SPTLC2 gene, encodes complete protein. AB383898 - Synthetic construct DNA, clone: pF1KSDA0526, Homo sapiens SPTLC2 gene for serine palmitoyltransferase 2, complete cds, without stop codon, in Flexi system. DQ893297 - Synthetic construct clone IMAGE:100005927; FLH199491.01X; RZPDo839D1182D serine palmitoyltransferase, long chain base subunit 2 (SPTLC2) gene, encodes complete protein. DQ896786 - Synthetic construct Homo sapiens clone IMAGE:100011246; FLH199397.01L; RZPDo839D1181D serine palmitoyltransferase, long chain base subunit 2 (SPTLC2) gene, encodes complete protein. JD324819 - Sequence 305843 from Patent EP1572962. JD518147 - Sequence 499171 from Patent EP1572962. JD050845 - Sequence 31869 from Patent EP1572962. JD097441 - Sequence 78465 from Patent EP1572962. JD512516 - Sequence 493540 from Patent EP1572962. JD350968 - Sequence 331992 from Patent EP1572962. JD050844 - Sequence 31868 from Patent EP1572962. JD097440 - Sequence 78464 from Patent EP1572962. JD512515 - Sequence 493539 from Patent EP1572962. JD350967 - Sequence 331991 from Patent EP1572962. JD182498 - Sequence 163522 from Patent EP1572962. JD267322 - Sequence 248346 from Patent EP1572962. JD331765 - Sequence 312789 from Patent EP1572962. JD228947 - Sequence 209971 from Patent EP1572962. JD308755 - Sequence 289779 from Patent EP1572962. JD320590 - Sequence 301614 from Patent EP1572962. JD041118 - Sequence 22142 from Patent EP1572962. JD169103 - Sequence 150127 from Patent EP1572962. JD529072 - Sequence 510096 from Patent EP1572962. JD430098 - Sequence 411122 from Patent EP1572962. JD380566 - Sequence 361590 from Patent EP1572962. JD201244 - Sequence 182268 from Patent EP1572962. JD120865 - Sequence 101889 from Patent EP1572962. JD169102 - Sequence 150126 from Patent EP1572962. JD338924 - Sequence 319948 from Patent EP1572962. JD430097 - Sequence 411121 from Patent EP1572962. JD472357 - Sequence 453381 from Patent EP1572962. JD047519 - Sequence 28543 from Patent EP1572962. JD135738 - Sequence 116762 from Patent EP1572962. JD052723 - Sequence 33747 from Patent EP1572962. JD473574 - Sequence 454598 from Patent EP1572962. JD194662 - Sequence 175686 from Patent EP1572962. JD274680 - Sequence 255704 from Patent EP1572962. JD522224 - Sequence 503248 from Patent EP1572962. JD556267 - Sequence 537291 from Patent EP1572962. JD556266 - Sequence 537290 from Patent EP1572962. JD431213 - Sequence 412237 from Patent EP1572962. JD472269 - Sequence 453293 from Patent EP1572962. JD294060 - Sequence 275084 from Patent EP1572962. JD198980 - Sequence 180004 from Patent EP1572962. JD497714 - Sequence 478738 from Patent EP1572962. JD376022 - Sequence 357046 from Patent EP1572962. JD454101 - Sequence 435125 from Patent EP1572962. JD314426 - Sequence 295450 from Patent EP1572962. JD515877 - Sequence 496901 from Patent EP1572962. JD356105 - Sequence 337129 from Patent EP1572962. JD172002 - Sequence 153026 from Patent EP1572962. JD530965 - Sequence 511989 from Patent EP1572962. JD482571 - Sequence 463595 from Patent EP1572962. JD401904 - Sequence 382928 from Patent EP1572962. JD225214 - Sequence 206238 from Patent EP1572962. JD425287 - Sequence 406311 from Patent EP1572962. JD444033 - Sequence 425057 from Patent EP1572962. JD425286 - Sequence 406310 from Patent EP1572962. JD425289 - Sequence 406313 from Patent EP1572962. JD366337 - Sequence 347361 from Patent EP1572962. JD534774 - Sequence 515798 from Patent EP1572962. JD380482 - Sequence 361506 from Patent EP1572962. JD075897 - Sequence 56921 from Patent EP1572962. JD326891 - Sequence 307915 from Patent EP1572962. JD047708 - Sequence 28732 from Patent EP1572962. JD363144 - Sequence 344168 from Patent EP1572962. JD187310 - Sequence 168334 from Patent EP1572962. JD535496 - Sequence 516520 from Patent EP1572962. JD220318 - Sequence 201342 from Patent EP1572962. JD135309 - Sequence 116333 from Patent EP1572962. JD292470 - Sequence 273494 from Patent EP1572962. JD092063 - Sequence 73087 from Patent EP1572962. JD183891 - Sequence 164915 from Patent EP1572962. JD268435 - Sequence 249459 from Patent EP1572962. JD088858 - Sequence 69882 from Patent EP1572962. JD377765 - Sequence 358789 from Patent EP1572962. JD045152 - Sequence 26176 from Patent EP1572962. JD399816 - Sequence 380840 from Patent EP1572962. JD546417 - Sequence 527441 from Patent EP1572962. JD089586 - Sequence 70610 from Patent EP1572962. JD042381 - Sequence 23405 from Patent EP1572962. JD225582 - Sequence 206606 from Patent EP1572962. JD267511 - Sequence 248535 from Patent EP1572962. JD127411 - Sequence 108435 from Patent EP1572962. JD433806 - Sequence 414830 from Patent EP1572962. JD358987 - Sequence 340011 from Patent EP1572962. JD284509 - Sequence 265533 from Patent EP1572962. JD337307 - Sequence 318331 from Patent EP1572962. JD508593 - Sequence 489617 from Patent EP1572962. JD235343 - Sequence 216367 from Patent EP1572962. JD173840 - Sequence 154864 from Patent EP1572962. JD504381 - Sequence 485405 from Patent EP1572962. JD510385 - Sequence 491409 from Patent EP1572962. JD314460 - Sequence 295484 from Patent EP1572962. JD142128 - Sequence 123152 from Patent EP1572962. JD348843 - Sequence 329867 from Patent EP1572962. JD491610 - Sequence 472634 from Patent EP1572962. JD087727 - Sequence 68751 from Patent EP1572962. JD492509 - Sequence 473533 from Patent EP1572962. JD446963 - Sequence 427987 from Patent EP1572962. JD388265 - Sequence 369289 from Patent EP1572962. JD321086 - Sequence 302110 from Patent EP1572962. JD145448 - Sequence 126472 from Patent EP1572962. JD238034 - Sequence 219058 from Patent EP1572962. JD514762 - Sequence 495786 from Patent EP1572962. JD139088 - Sequence 120112 from Patent EP1572962. JD533679 - Sequence 514703 from Patent EP1572962. JD056827 - Sequence 37851 from Patent EP1572962. JD421878 - Sequence 402902 from Patent EP1572962. JD291723 - Sequence 272747 from Patent EP1572962. JD533161 - Sequence 514185 from Patent EP1572962. JD421602 - Sequence 402626 from Patent EP1572962. JD432533 - Sequence 413557 from Patent EP1572962. JD102066 - Sequence 83090 from Patent EP1572962. JD244411 - Sequence 225435 from Patent EP1572962. JD251394 - Sequence 232418 from Patent EP1572962. JD427473 - Sequence 408497 from Patent EP1572962. JD521696 - Sequence 502720 from Patent EP1572962. JD325258 - Sequence 306282 from Patent EP1572962. JD484484 - Sequence 465508 from Patent EP1572962. JD376933 - Sequence 357957 from Patent EP1572962. JD297034 - Sequence 278058 from Patent EP1572962. JD282245 - Sequence 263269 from Patent EP1572962. JD084065 - Sequence 65089 from Patent EP1572962. JD061518 - Sequence 42542 from Patent EP1572962. JD272801 - Sequence 253825 from Patent EP1572962. JD065218 - Sequence 46242 from Patent EP1572962. JD252341 - Sequence 233365 from Patent EP1572962. JD120011 - Sequence 101035 from Patent EP1572962. JD098532 - Sequence 79556 from Patent EP1572962. JD114708 - Sequence 95732 from Patent EP1572962. JD195026 - Sequence 176050 from Patent EP1572962. JD037925 - Sequence 18949 from Patent EP1572962. JD162697 - Sequence 143721 from Patent EP1572962. JD513459 - Sequence 494483 from Patent EP1572962. JD042337 - Sequence 23361 from Patent EP1572962. U15555 - Human serine palmitoyltransferase (LCB2) mRNA, partial cds. CU675001 - Synthetic construct Homo sapiens gateway clone IMAGE:100019878 5' read SPTLC2 mRNA. JD458230 - Sequence 439254 from Patent EP1572962. JD436550 - Sequence 417574 from Patent EP1572962. JD403141 - Sequence 384165 from Patent EP1572962. JD458544 - Sequence 439568 from Patent EP1572962. JD218871 - Sequence 199895 from Patent EP1572962. JD396368 - Sequence 377392 from Patent EP1572962. JD289332 - Sequence 270356 from Patent EP1572962. JD210592 - Sequence 191616 from Patent EP1572962.
Biochemical and Signaling Pathways
KEGG - Kyoto Encyclopedia of Genes and Genomes hsa00600 - Sphingolipid metabolism hsa01100 - Metabolic pathways
US Server
Sequence and Links to Tools and Databases 
Common Gene Haplotype Alleles 
