Incidental Mutation 'R2179:Sptlc1'
ID 237076
Institutional Source Beutler Lab
Gene Symbol Sptlc1
Ensembl Gene ENSMUSG00000021468
Gene Name serine palmitoyltransferase, long chain base subunit 1
Synonyms Spt1, Lcb1
MMRRC Submission 040181-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2179 (G1)
Quality Score 225
Status Not validated
Chromosome 13
Chromosomal Location 53486784-53531433 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 53505675 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Asparagine at position 248 (Y248N)
Ref Sequence ENSEMBL: ENSMUSP00000021920 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021920]
AlphaFold O35704
Predicted Effect probably damaging
Transcript: ENSMUST00000021920
AA Change: Y248N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000021920
Gene: ENSMUSG00000021468
AA Change: Y248N

DomainStartEndE-ValueType
transmembrane domain 20 40 N/A INTRINSIC
Pfam:Aminotran_1_2 98 464 9.5e-44 PFAM
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.5%
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgb T C 10: 10,271,018 (GRCm39) D849G possibly damaging Het
Amz2 A G 11: 109,320,658 (GRCm39) H155R probably damaging Het
Cfhr4 G T 1: 139,659,279 (GRCm39) P679Q probably damaging Het
Chuk C A 19: 44,092,160 (GRCm39) C46F possibly damaging Het
Cp A T 3: 20,042,151 (GRCm39) D973V probably damaging Het
Cpm T A 10: 117,519,266 (GRCm39) D391E probably benign Het
Creb3 T C 4: 43,566,306 (GRCm39) S271P probably damaging Het
Cubn T A 2: 13,323,053 (GRCm39) H2838L possibly damaging Het
Dennd2d A G 3: 106,399,776 (GRCm39) H233R probably benign Het
Dnaaf2 C A 12: 69,245,071 (GRCm39) probably benign Het
Enpp3 T A 10: 24,681,793 (GRCm39) Q304H probably benign Het
Fermt3 C A 19: 6,991,782 (GRCm39) R143L probably benign Het
Fndc8 A C 11: 82,789,580 (GRCm39) K246T probably damaging Het
Gaa A G 11: 119,165,884 (GRCm39) probably null Het
Gucy2e A T 11: 69,119,404 (GRCm39) probably null Het
Igf1r A G 7: 67,653,698 (GRCm39) T79A probably damaging Het
Ikbkb C T 8: 23,171,769 (GRCm39) probably null Het
Il16 A T 7: 83,337,287 (GRCm39) probably null Het
Irs1 T A 1: 82,267,940 (GRCm39) H92L possibly damaging Het
Itpr2 A G 6: 146,277,464 (GRCm39) M315T probably benign Het
Lrba T G 3: 86,261,588 (GRCm39) L1514R probably damaging Het
Mcpt2 A G 14: 56,279,573 (GRCm39) probably benign Het
Metap1d A G 2: 71,283,715 (GRCm39) I5V probably benign Het
Mga T A 2: 119,790,923 (GRCm39) S2479T probably damaging Het
Mllt10 T C 2: 18,215,604 (GRCm39) V1063A probably damaging Het
Mroh2b G A 15: 4,950,928 (GRCm39) probably null Het
Mtfr1 C T 3: 19,254,308 (GRCm39) R15* probably null Het
Npm2 A G 14: 70,885,749 (GRCm39) V152A probably benign Het
Nrxn3 T A 12: 89,221,448 (GRCm39) V409D probably damaging Het
Ogdhl A G 14: 32,057,302 (GRCm39) N303D probably damaging Het
Or10g9 T C 9: 39,912,220 (GRCm39) Y101C probably benign Het
Or10q1b T C 19: 13,682,758 (GRCm39) V189A probably damaging Het
Or4d11 T C 19: 12,013,452 (GRCm39) Y218C probably damaging Het
Or6s1 A G 14: 51,308,238 (GRCm39) V204A probably benign Het
Pah T C 10: 87,403,197 (GRCm39) F191L probably damaging Het
Paics A T 5: 77,109,291 (GRCm39) I209F probably damaging Het
Pcare T C 17: 72,059,521 (GRCm39) D52G probably damaging Het
Pld6 A G 11: 59,678,184 (GRCm39) L93P probably damaging Het
Plod3 T C 5: 137,019,862 (GRCm39) F431L possibly damaging Het
Ppm1b T A 17: 85,301,862 (GRCm39) D247E probably damaging Het
Prx A G 7: 27,217,410 (GRCm39) D637G probably benign Het
Rsf1 GGCGGCGGC GGCGGCGGCCGCGGCGGC 7: 97,229,116 (GRCm39) probably benign Het
Ryr2 A T 13: 11,720,679 (GRCm39) Y2656* probably null Het
Setd2 T A 9: 110,423,756 (GRCm39) Y492* probably null Het
Shmt1 A G 11: 60,697,825 (GRCm39) W9R possibly damaging Het
Slc25a17 A G 15: 81,222,151 (GRCm39) V107A probably benign Het
Stam2 T C 2: 52,584,936 (GRCm39) T453A probably benign Het
Tango2 G T 16: 18,128,762 (GRCm39) N77K probably damaging Het
Tas2r121 A T 6: 132,677,831 (GRCm39) I47N probably damaging Het
Terb1 A T 8: 105,179,347 (GRCm39) C614S probably damaging Het
Terb1 T C 8: 105,199,369 (GRCm39) N525S probably benign Het
Ttc6 A G 12: 57,719,904 (GRCm39) D825G possibly damaging Het
U90926 A T 5: 92,357,838 (GRCm39) H104Q probably benign Het
Zfand4 G A 6: 116,291,742 (GRCm39) A559T possibly damaging Het
Zfp462 T C 4: 55,009,524 (GRCm39) S497P possibly damaging Het
Other mutations in Sptlc1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00811:Sptlc1 APN 13 53,521,414 (GRCm39) missense probably damaging 0.98
IGL01354:Sptlc1 APN 13 53,487,987 (GRCm39) missense probably benign
IGL01773:Sptlc1 APN 13 53,531,334 (GRCm39) missense probably damaging 0.96
IGL01876:Sptlc1 APN 13 53,528,048 (GRCm39) missense probably benign 0.02
R0390:Sptlc1 UTSW 13 53,491,648 (GRCm39) missense probably benign 0.06
R1371:Sptlc1 UTSW 13 53,505,660 (GRCm39) missense probably benign
R1961:Sptlc1 UTSW 13 53,512,916 (GRCm39) missense probably benign
R2513:Sptlc1 UTSW 13 53,491,676 (GRCm39) missense possibly damaging 0.61
R4357:Sptlc1 UTSW 13 53,528,068 (GRCm39) missense probably damaging 1.00
R4989:Sptlc1 UTSW 13 53,505,692 (GRCm39) missense probably damaging 0.97
R5055:Sptlc1 UTSW 13 53,496,218 (GRCm39) missense probably benign 0.02
R6415:Sptlc1 UTSW 13 53,505,728 (GRCm39) critical splice acceptor site probably null
R6752:Sptlc1 UTSW 13 53,489,394 (GRCm39) missense possibly damaging 0.67
R7283:Sptlc1 UTSW 13 53,498,914 (GRCm39) missense probably benign 0.03
R7548:Sptlc1 UTSW 13 53,521,968 (GRCm39) missense possibly damaging 0.84
R7731:Sptlc1 UTSW 13 53,487,993 (GRCm39) missense probably benign 0.00
R9268:Sptlc1 UTSW 13 53,512,872 (GRCm39) missense probably damaging 1.00
R9302:Sptlc1 UTSW 13 53,528,047 (GRCm39) missense probably benign 0.06
R9794:Sptlc1 UTSW 13 53,512,803 (GRCm39) missense possibly damaging 0.93
Predicted Primers PCR Primer
(F):5'- GAGGTCAGACTTGCCACAAG -3'
(R):5'- CTGCCTAAGAGTGAACGGAAAC -3'

Sequencing Primer
(F):5'- GACTTGCCACAAGCCCCTTC -3'
(R):5'- GAGTGAACGGAAACTGCTTTTTCTC -3'
Posted On 2014-10-02