Incidental Mutation 'R2513:Sptlc1'
ID 253680
Institutional Source Beutler Lab
Gene Symbol Sptlc1
Ensembl Gene ENSMUSG00000021468
Gene Name serine palmitoyltransferase, long chain base subunit 1
Synonyms Spt1, Lcb1
MMRRC Submission 040419-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2513 (G1)
Quality Score 225
Status Not validated
Chromosome 13
Chromosomal Location 53486784-53531433 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 53491676 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Asparagine at position 408 (D408N)
Ref Sequence ENSEMBL: ENSMUSP00000021920 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021920]
AlphaFold O35704
Predicted Effect possibly damaging
Transcript: ENSMUST00000021920
AA Change: D408N

PolyPhen 2 Score 0.605 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000021920
Gene: ENSMUSG00000021468
AA Change: D408N

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: 98.6%
  • 10x: 97.4%
  • 20x: 95.4%
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: 90 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
3425401B19Rik T C 14: 32,383,809 (GRCm39) T719A possibly damaging Het
Abcc1 A G 16: 14,290,873 (GRCm39) probably null Het
Aftph C T 11: 20,658,676 (GRCm39) probably null Het
Als2 C A 1: 59,254,276 (GRCm39) K360N probably benign Het
Atg2a T A 19: 6,308,076 (GRCm39) probably null Het
Axl T C 7: 25,486,941 (GRCm39) D22G probably benign Het
Baiap2 G A 11: 119,890,052 (GRCm39) A438T probably benign Het
Bean1 G C 8: 104,908,643 (GRCm39) A7P probably benign Het
Birc6 C G 17: 74,954,724 (GRCm39) P3431R probably damaging Het
Camk1d A G 2: 5,719,047 (GRCm39) M1T probably null Het
Carmil3 T C 14: 55,741,295 (GRCm39) Y1027H probably damaging Het
Ccdc6 G A 10: 70,023,658 (GRCm39) probably benign Het
Cemip C A 7: 83,591,233 (GRCm39) V1280L probably benign Het
Cfap58 C A 19: 47,950,981 (GRCm39) N447K probably benign Het
Chd3 A G 11: 69,251,471 (GRCm39) L520P probably damaging Het
Col1a2 T A 6: 4,531,223 (GRCm39) probably null Het
Cpne7 A C 8: 123,844,406 (GRCm39) probably null Het
Ctla4 T C 1: 60,951,723 (GRCm39) V84A probably damaging Het
Dap3 A G 3: 88,835,565 (GRCm39) V263A probably benign Het
Dhx57 T A 17: 80,549,378 (GRCm39) probably null Het
Dlg5 C A 14: 24,214,593 (GRCm39) K663N probably damaging Het
Dsg3 C A 18: 20,656,719 (GRCm39) F196L possibly damaging Het
Eif2ak4 C A 2: 118,257,064 (GRCm39) D402E probably damaging Het
Fance T C 17: 28,537,068 (GRCm39) V24A probably benign Het
Fasn A T 11: 120,705,574 (GRCm39) L1149Q probably damaging Het
Fcgbpl1 C G 7: 27,831,060 (GRCm39) S91C probably damaging Het
Flg T A 3: 93,187,093 (GRCm39) S182T possibly damaging Het
Gm128 T A 3: 95,147,293 (GRCm39) S334C possibly damaging Het
Gm3727 A C 14: 7,264,561 (GRCm38) H31Q probably damaging Het
Gm4841 T G 18: 60,403,977 (GRCm39) T39P probably damaging Het
Golgb1 G T 16: 36,735,513 (GRCm39) V1587L possibly damaging Het
Golm1 G A 13: 59,790,072 (GRCm39) P243S probably benign Het
Gstcd C A 3: 132,788,081 (GRCm39) A206S possibly damaging Het
Gstcd C A 3: 132,788,082 (GRCm39) K205N possibly damaging Het
Gtf3c1 A G 7: 125,280,345 (GRCm39) V355A probably benign Het
Hhatl T C 9: 121,618,236 (GRCm39) D173G probably benign Het
Kcnu1 T A 8: 26,395,994 (GRCm39) C660S probably benign Het
Kctd8 T C 5: 69,267,988 (GRCm39) D374G probably benign Het
Kif21a T C 15: 90,878,594 (GRCm39) I229V possibly damaging Het
L3mbtl1 A T 2: 162,809,505 (GRCm39) I702F probably benign Het
Lce1d T C 3: 92,593,066 (GRCm39) probably benign Het
Lrig1 C T 6: 94,594,347 (GRCm39) probably null Het
Lrp12 A T 15: 39,739,507 (GRCm39) D563E probably damaging Het
Lrp2 C T 2: 69,336,718 (GRCm39) probably null Het
Map3k5 G A 10: 19,970,201 (GRCm39) V703I possibly damaging Het
Mecr A G 4: 131,581,076 (GRCm39) R110G probably benign Het
Mtrr T A 13: 68,715,092 (GRCm39) K445* probably null Het
Nanos1 T A 19: 60,744,990 (GRCm39) L96Q probably benign Het
Or13a24 T G 7: 140,154,069 (GRCm39) M1R probably null Het
Or51t4 T A 7: 102,598,700 (GRCm39) F333I probably benign Het
Or6c214 T A 10: 129,591,021 (GRCm39) L99F probably damaging Het
Otog T C 7: 45,955,014 (GRCm39) probably null Het
Pcdhb3 G T 18: 37,434,294 (GRCm39) V87F probably benign Het
Pcdhb3 T A 18: 37,434,292 (GRCm39) L86* probably null Het
Pcdhb3 A T 18: 37,434,293 (GRCm39) L86F probably damaging Het
Pdgfd A G 9: 6,359,894 (GRCm39) K322E probably damaging Het
Picalm T C 7: 89,846,217 (GRCm39) S648P probably damaging Het
Pigr T C 1: 130,774,357 (GRCm39) S446P possibly damaging Het
Pik3cb A C 9: 98,943,895 (GRCm39) L636W probably damaging Het
Pla2g2f A T 4: 138,481,473 (GRCm39) L92Q probably damaging Het
Plod3 G C 5: 137,017,000 (GRCm39) A50P probably benign Het
Prkar2b C T 12: 32,025,928 (GRCm39) V191I possibly damaging Het
Prune1 C A 3: 95,165,430 (GRCm39) A281S probably benign Het
Ptges3l A T 11: 101,314,868 (GRCm39) C42S possibly damaging Het
Reg3b A T 6: 78,348,802 (GRCm39) I33L probably benign Het
Rel A G 11: 23,695,823 (GRCm39) I188T probably damaging Het
Rif1 GCCACCA GCCA 2: 52,000,336 (GRCm39) probably benign Het
Ripor1 G T 8: 106,344,254 (GRCm39) V463L probably benign Het
Rrm1 T A 7: 102,109,896 (GRCm39) D510E probably damaging Het
Setd7 A G 3: 51,440,436 (GRCm39) S202P probably damaging Het
Shank3 T A 15: 89,432,889 (GRCm39) D1211E probably benign Het
Slc30a1 A T 1: 191,639,674 (GRCm39) T186S possibly damaging Het
Slc4a4 G A 5: 89,304,257 (GRCm39) V523I probably benign Het
Slc9a2 T A 1: 40,781,768 (GRCm39) probably null Het
Smg6 A G 11: 74,820,502 (GRCm39) T258A probably damaging Het
Tasor2 G T 13: 3,632,150 (GRCm39) L784I possibly damaging Het
Tbl3 T C 17: 24,923,524 (GRCm39) probably null Het
Tdo2 T C 3: 81,876,812 (GRCm39) D139G possibly damaging Het
Ticam1 T A 17: 56,578,612 (GRCm39) H161L possibly damaging Het
Tnfaip3 T A 10: 18,881,407 (GRCm39) D293V probably benign Het
Trim72 G A 7: 127,603,878 (GRCm39) V75M possibly damaging Het
Trip11 T A 12: 101,803,986 (GRCm39) N1632I possibly damaging Het
Tspan18 A T 2: 93,050,440 (GRCm39) M61K possibly damaging Het
Tuba8 A T 6: 121,202,932 (GRCm39) E415V probably damaging Het
Ung A G 5: 114,275,253 (GRCm39) H214R probably benign Het
Uqcrc1 T C 9: 108,765,836 (GRCm39) L17P probably damaging Het
Usp24 A G 4: 106,236,602 (GRCm39) probably null Het
Vps39 A C 2: 120,169,268 (GRCm39) Y245D probably damaging Het
Whrn T A 4: 63,353,649 (GRCm39) T373S probably benign Het
Zc2hc1a C T 3: 7,581,596 (GRCm39) probably null 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
R2179:Sptlc1 UTSW 13 53,505,675 (GRCm39) missense probably damaging 1.00
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'- ACAAGGTGAGAGAAGCCCTC -3'
(R):5'- TGCAATGTCAGCATGATGCCC -3'

Sequencing Primer
(F):5'- TGAGAGAAGCCCTCAGCCTG -3'
(R):5'- ATGTCAGCATGATGCCCTAACTC -3'
Posted On 2014-12-04