Incidental Mutation 'R1371:Sptlc1'
ID 157334
Institutional Source Beutler Lab
Gene Symbol Sptlc1
Ensembl Gene ENSMUSG00000021468
Gene Name serine palmitoyltransferase, long chain base subunit 1
Synonyms Spt1, Lcb1
MMRRC Submission 039435-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1371 (G1)
Quality Score 123
Status Validated
Chromosome 13
Chromosomal Location 53486784-53531433 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 53505660 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 253 (T253A)
Ref Sequence ENSEMBL: ENSMUSP00000021920 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021920]
AlphaFold O35704
Predicted Effect probably benign
Transcript: ENSMUST00000021920
AA Change: T253A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000021920
Gene: ENSMUSG00000021468
AA Change: T253A

DomainStartEndE-ValueType
transmembrane domain 20 40 N/A INTRINSIC
Pfam:Aminotran_1_2 98 464 9.5e-44 PFAM
Meta Mutation Damage Score 0.0832 question?
Coding Region Coverage
  • 1x: 98.8%
  • 3x: 97.7%
  • 10x: 94.7%
  • 20x: 89.0%
Validation Efficiency 100% (55/55)
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: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca8b T A 11: 109,844,379 (GRCm39) D884V probably damaging Het
Acvr2a C T 2: 48,789,628 (GRCm39) T457M probably damaging Het
Akr1b10 C T 6: 34,369,394 (GRCm39) T208I probably benign Het
Aldh16a1 G T 7: 44,796,674 (GRCm39) T275K possibly damaging Het
Alkbh2 C T 5: 114,262,287 (GRCm39) E148K probably damaging Het
Asgr1 T G 11: 69,946,923 (GRCm39) C56W probably benign Het
Atp11b T C 3: 35,860,918 (GRCm39) I335T probably damaging Het
BC061237 A G 14: 44,741,762 (GRCm39) probably benign Het
Bdh1 G T 16: 31,275,720 (GRCm39) K280N probably benign Het
Bmp1 C T 14: 70,729,906 (GRCm39) C466Y probably damaging Het
Ccdc181 A G 1: 164,108,172 (GRCm39) E285G probably benign Het
Ces1f C T 8: 94,006,277 (GRCm39) G18R probably damaging Het
Cfap43 T A 19: 47,824,045 (GRCm39) I109L possibly damaging Het
Cma2 T C 14: 56,210,283 (GRCm39) L56S probably damaging Het
Edc4 A G 8: 106,617,382 (GRCm39) probably benign Het
F3 T C 3: 121,526,159 (GRCm39) C241R probably damaging Het
Fhdc1 T A 3: 84,352,310 (GRCm39) S972C probably damaging Het
Heatr1 T G 13: 12,432,513 (GRCm39) I1086R possibly damaging Het
Hsh2d A T 8: 72,950,738 (GRCm39) probably benign Het
Ice1 T C 13: 70,744,340 (GRCm39) Y2081C probably damaging Het
Il1rl1 A G 1: 40,481,873 (GRCm39) N194D probably damaging Het
Ip6k1 G A 9: 107,923,022 (GRCm39) V385M probably damaging Het
Lig1 G A 7: 13,022,611 (GRCm39) R147Q probably damaging Het
Lrp1b C T 2: 40,537,165 (GRCm39) V41I probably damaging Het
Macroh2a2 A T 10: 61,585,112 (GRCm39) D177E possibly damaging Het
Mst1r T A 9: 107,794,424 (GRCm39) V1201E probably damaging Het
Myof T C 19: 37,892,116 (GRCm39) probably benign Het
Nbas G T 12: 13,532,379 (GRCm39) probably benign Het
Ndst1 A G 18: 60,840,719 (GRCm39) I321T possibly damaging Het
Nek10 G A 14: 14,850,983 (GRCm38) G343R probably damaging Het
Or2a7 A T 6: 43,151,234 (GRCm39) T105S probably benign Het
Or2y1 T A 11: 49,385,650 (GRCm39) C97S probably damaging Het
Or4d2b A T 11: 87,780,122 (GRCm39) I200N probably damaging Het
Pde4d T C 13: 109,253,595 (GRCm39) S141P probably benign Het
Pigm A T 1: 172,204,381 (GRCm39) Q39L probably damaging Het
Prl7a2 T A 13: 27,846,750 (GRCm39) I88F probably benign Het
Prss16 T A 13: 22,192,856 (GRCm39) probably benign Het
Psmc4 G A 7: 27,742,222 (GRCm39) probably benign Het
Ptger3 T A 3: 157,273,365 (GRCm39) C237* probably null Het
Recql G A 6: 142,318,601 (GRCm39) T214M probably damaging Het
Rfx7 T A 9: 72,526,857 (GRCm39) V1349D probably damaging Het
Ros1 A G 10: 51,964,041 (GRCm39) S1740P probably damaging Het
Rrm2b A T 15: 37,947,053 (GRCm39) S83T probably benign Het
Sall4 A G 2: 168,598,394 (GRCm39) Y149H probably benign Het
Smad1 A G 8: 80,076,207 (GRCm39) probably benign Het
Snrnp70 T C 7: 45,030,129 (GRCm39) probably benign Het
Spef2 C A 15: 9,725,194 (GRCm39) probably benign Het
Zbbx T C 3: 74,959,784 (GRCm39) Y595C possibly damaging Het
Zfp382 T C 7: 29,833,114 (GRCm39) V255A probably benign 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
R1961:Sptlc1 UTSW 13 53,512,916 (GRCm39) missense probably benign
R2179:Sptlc1 UTSW 13 53,505,675 (GRCm39) missense probably damaging 1.00
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'- TGAGGTCAGACTTGCCACAAGC -3'
(R):5'- TGCCTAAGAGTGAACGGAAACTGC -3'

Sequencing Primer
(F):5'- TTGCCACAAGCCCCTTCAC -3'
(R):5'- GTGAACGGAAACTGCTTTTTCTC -3'
Posted On 2014-02-18