Incidental Mutation 'IGL00811:Sptlc1'
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Sptlc1
Ensembl Gene ENSMUSG00000021468
Gene Nameserine palmitoyltransferase, long chain base subunit 1
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #IGL00811
Quality Score
Chromosomal Location53332748-53377397 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) C to A at 53367378 bp
Amino Acid Change Alanine to Serine at position 121 (A121S)
Ref Sequence ENSEMBL: ENSMUSP00000021920 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021920]
Predicted Effect probably damaging
Transcript: ENSMUST00000021920
AA Change: A121S

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000021920
Gene: ENSMUSG00000021468
AA Change: A121S

transmembrane domain 20 40 N/A INTRINSIC
Pfam:Aminotran_1_2 98 464 9.5e-44 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000221265
Coding Region Coverage
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the class-II pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is the long chain base subunit 1 of serine palmitoyltransferase. Serine palmitoyltransferase converts L-serine and palmitoyl-CoA to 3-oxosphinganine with pyridoxal 5'-phosphate and is the key enzyme in sphingolipid biosynthesis. Mutations in this gene were identified in patients with hereditary sensory neuropathy type 1. Alternatively spliced variants encoding different isoforms have been identified. Pseudogenes of this gene have been defined on chromosomes 1, 6, 10, and 13. [provided by RefSeq, Jul 2013]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit prenatal lethality. Mice homozygous for a knock-out allele exhibit abnormal sphingolipid levels. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 24 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Agps T C 2: 75,925,972 F649L probably benign Het
Agrn A T 4: 156,168,774 D1752E possibly damaging Het
Det1 A G 7: 78,840,059 V406A probably benign Het
Dhx57 A G 17: 80,253,243 V955A probably damaging Het
Dpep1 T C 8: 123,199,615 probably benign Het
Epha7 T A 4: 28,961,285 probably benign Het
Faim G A 9: 98,992,165 G15R probably damaging Het
Fbxl5 A G 5: 43,758,225 L614P probably damaging Het
Fem1b A T 9: 62,796,919 V353D probably damaging Het
Fgf22 C T 10: 79,756,890 P140S probably damaging Het
Ifi47 T C 11: 49,095,417 F4L probably benign Het
Kmt2c A C 5: 25,374,533 S588R possibly damaging Het
Nmrk1 T A 19: 18,645,147 probably benign Het
Nomo1 C T 7: 46,083,308 A1165V possibly damaging Het
Osmr G A 15: 6,815,666 T873I probably benign Het
Pclo A G 5: 14,680,010 probably benign Het
Rims2 T A 15: 39,292,149 M115K probably damaging Het
Rora C A 9: 69,371,290 T299K probably benign Het
Sema6d C A 2: 124,658,469 P386Q probably damaging Het
Slit2 G A 5: 47,989,151 E95K possibly damaging Het
Sox18 T C 2: 181,670,420 E306G probably benign Het
Ssh2 C T 11: 77,441,926 A411V probably damaging Het
Trim13 A G 14: 61,604,857 probably null Het
Vps13c T A 9: 67,948,181 N2509K probably damaging Het
Other mutations in Sptlc1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01354:Sptlc1 APN 13 53333951 missense probably benign
IGL01773:Sptlc1 APN 13 53377298 missense probably damaging 0.96
IGL01876:Sptlc1 APN 13 53374012 missense probably benign 0.02
R0390:Sptlc1 UTSW 13 53337612 missense probably benign 0.06
R1371:Sptlc1 UTSW 13 53351624 missense probably benign
R1961:Sptlc1 UTSW 13 53358880 missense probably benign
R2179:Sptlc1 UTSW 13 53351639 missense probably damaging 1.00
R2513:Sptlc1 UTSW 13 53337640 missense possibly damaging 0.61
R4357:Sptlc1 UTSW 13 53374032 missense probably damaging 1.00
R4989:Sptlc1 UTSW 13 53351656 missense probably damaging 0.97
R5055:Sptlc1 UTSW 13 53342182 missense probably benign 0.02
R6415:Sptlc1 UTSW 13 53351692 critical splice acceptor site probably null
R6752:Sptlc1 UTSW 13 53335358 missense possibly damaging 0.67
R7283:Sptlc1 UTSW 13 53344878 missense probably benign 0.03
R7548:Sptlc1 UTSW 13 53367932 missense possibly damaging 0.84
R7731:Sptlc1 UTSW 13 53333957 missense probably benign 0.00
Posted On2012-12-06