Incidental Mutation 'R0087:Sptlc2'
ID 19973
Institutional Source Beutler Lab
Gene Symbol Sptlc2
Ensembl Gene ENSMUSG00000021036
Gene Name serine palmitoyltransferase, long chain base subunit 2
Synonyms LCB2, Spt2
MMRRC Submission 038374-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0087 (G1)
Quality Score 225
Status Validated (trace)
Chromosome 12
Chromosomal Location 87351832-87435129 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 87415892 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Leucine at position 45 (H45L)
Ref Sequence ENSEMBL: ENSMUSP00000021424 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021424]
AlphaFold P97363
Predicted Effect probably benign
Transcript: ENSMUST00000021424
AA Change: H45L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000021424
Gene: ENSMUSG00000021036
AA Change: H45L

DomainStartEndE-ValueType
Pfam:Aminotran_1_2 166 526 7.2e-60 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000167911
Predicted Effect noncoding transcript
Transcript: ENSMUST00000221879
Meta Mutation Damage Score 0.0609 question?
Coding Region Coverage
  • 1x: 98.8%
  • 3x: 97.6%
  • 10x: 93.5%
  • 20x: 82.3%
Validation Efficiency 86% (59/69)
MGI Phenotype FUNCTION: This gene encodes a long chain base subunit of serine palmitoyltransferase. The enzyme, serine palmitoyltransferase, consists of two different subunits, and 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. A mutant allele of this gene in mice is used as a model for the human disease 'Susceptibilty to Psoriasis 1'. Mutations in the human gene are associated with hereditary sensory neuropathy type I. [provided by RefSeq, Sep 2015]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality. Mice heterozygous for this allele exhibit abnormal liver and circulating shingolipid levels. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Add3 T A 19: 53,215,038 (GRCm39) L71Q probably damaging Het
Adgrv1 T A 13: 81,535,070 (GRCm39) I5732F probably damaging Het
Adss2 A T 1: 177,598,788 (GRCm39) V330E probably benign Het
Agps T A 2: 75,739,979 (GRCm39) Y488N probably damaging Het
Ap3s1 A T 18: 46,891,106 (GRCm39) R66S probably damaging Het
Ass1 A T 2: 31,404,831 (GRCm39) N371Y probably damaging Het
Atp2a2 C T 5: 122,599,024 (GRCm39) V593I probably benign Het
Chrna6 C T 8: 27,897,014 (GRCm39) V288M probably damaging Het
Col4a2 C T 8: 11,491,296 (GRCm39) L1232F probably benign Het
Dcaf1 A G 9: 106,740,288 (GRCm39) N1225D probably damaging Het
Degs1 A G 1: 182,106,875 (GRCm39) I128T probably benign Het
Dnaaf11 T C 15: 66,341,824 (GRCm39) T91A probably benign Het
Dnah5 A T 15: 28,350,759 (GRCm39) T2594S probably damaging Het
Dnah8 G T 17: 30,974,093 (GRCm39) R2826L probably damaging Het
Elf3 A G 1: 135,184,875 (GRCm39) Y104H probably damaging Het
Fam222b C A 11: 78,044,718 (GRCm39) T93N probably benign Het
Fbxw26 A G 9: 109,554,006 (GRCm39) I211T probably benign Het
Fcho2 T C 13: 98,871,594 (GRCm39) T541A probably benign Het
Flg2 T C 3: 93,109,738 (GRCm39) S589P unknown Het
Foxj3 T A 4: 119,483,597 (GRCm39) V589E unknown Het
Gria1 A G 11: 57,208,538 (GRCm39) Y742C probably damaging Het
Inpp5d T C 1: 87,642,860 (GRCm39) S672P probably damaging Het
Lrrc19 A C 4: 94,529,009 (GRCm39) F91C probably damaging Het
Mppe1 A G 18: 67,358,775 (GRCm39) *398R probably null Het
Mroh3 T C 1: 136,118,541 (GRCm39) I561V probably benign Het
Myh11 C A 16: 14,041,883 (GRCm39) Q720H probably damaging Het
Nbea G T 3: 55,998,444 (GRCm39) T121K possibly damaging Het
Nbr1 A C 11: 101,455,519 (GRCm39) D91A probably benign Het
Ncam2 C A 16: 81,231,789 (GRCm39) N84K probably benign Het
Or4c35 T C 2: 89,808,475 (GRCm39) Y118H probably damaging Het
Or51ac3 A T 7: 103,213,569 (GRCm39) C306S probably benign Het
Or52h9 A G 7: 104,202,869 (GRCm39) I248V possibly damaging Het
Or52z13 A G 7: 103,246,928 (GRCm39) Y135C probably benign Het
Or6b6 A G 7: 106,571,323 (GRCm39) V76A probably benign Het
Pdgfrb A T 18: 61,194,585 (GRCm39) I121F probably damaging Het
Peak1 A T 9: 56,165,609 (GRCm39) I773N probably damaging Het
Pfkfb4 G T 9: 108,836,769 (GRCm39) V155F probably damaging Het
Pkm C T 9: 59,585,382 (GRCm39) R455* probably null Het
Plbd2 C A 5: 120,632,550 (GRCm39) E151* probably null Het
Pld5 G A 1: 175,812,025 (GRCm39) T353M probably damaging Het
Psme2b A T 11: 48,836,544 (GRCm39) D134E possibly damaging Het
Rida T A 15: 34,488,772 (GRCm39) D40V possibly damaging Het
Rnf126 A T 10: 79,595,068 (GRCm39) H265Q probably damaging Het
Rock2 C A 12: 16,978,967 (GRCm39) Q86K probably benign Het
Serpinb1b A T 13: 33,269,302 (GRCm39) T12S probably benign Het
Slco6c1 T A 1: 97,046,303 (GRCm39) Q277L probably benign Het
Spmap2 A T 10: 79,421,785 (GRCm39) Y144* probably null Het
Srsf4 A G 4: 131,627,641 (GRCm39) probably benign Het
Sspo A G 6: 48,454,719 (GRCm39) S2969G probably damaging Het
Steap1 C T 5: 5,786,664 (GRCm39) G258R probably damaging Het
Stk19 A T 17: 35,055,851 (GRCm39) M1K probably null Het
Stk-ps2 C A 1: 46,069,049 (GRCm39) noncoding transcript Het
Taf1c C T 8: 120,327,726 (GRCm39) R332H probably damaging Het
Thbs4 T A 13: 92,891,743 (GRCm39) T791S probably damaging Het
Tjap1 A G 17: 46,574,652 (GRCm39) L21P probably damaging Het
Tmem145 A G 7: 25,007,268 (GRCm39) Y148C probably damaging Het
Tmem267 T A 13: 120,070,810 (GRCm39) V155E probably benign Het
Tns1 T A 1: 73,956,076 (GRCm39) H549L possibly damaging Het
Tyro3 T G 2: 119,632,182 (GRCm39) I83S probably benign Het
Ubxn4 G A 1: 128,190,641 (GRCm39) E256K probably benign Het
Vmn1r53 A T 6: 90,200,413 (GRCm39) C304S probably benign Het
Vwf G A 6: 125,622,917 (GRCm39) M1761I probably benign Het
Zfp276 T C 8: 123,991,786 (GRCm39) Y445H probably damaging Het
Zfp407 A T 18: 84,578,536 (GRCm39) I859N probably damaging Het
Other mutations in Sptlc2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00757:Sptlc2 APN 12 87,415,842 (GRCm39) missense probably damaging 0.99
IGL02458:Sptlc2 APN 12 87,356,667 (GRCm39) utr 3 prime probably benign
IGL02734:Sptlc2 APN 12 87,402,444 (GRCm39) missense probably damaging 0.97
IGL03252:Sptlc2 APN 12 87,402,431 (GRCm39) missense probably benign 0.00
lopsided UTSW 12 87,388,339 (GRCm39) missense probably benign 0.27
shinola UTSW 12 87,397,069 (GRCm39) missense possibly damaging 0.64
R0116:Sptlc2 UTSW 12 87,403,454 (GRCm39) missense probably benign 0.00
R0492:Sptlc2 UTSW 12 87,393,580 (GRCm39) splice site probably null
R1353:Sptlc2 UTSW 12 87,388,520 (GRCm39) missense probably damaging 1.00
R1470:Sptlc2 UTSW 12 87,402,414 (GRCm39) missense probably benign 0.00
R1470:Sptlc2 UTSW 12 87,402,414 (GRCm39) missense probably benign 0.00
R3417:Sptlc2 UTSW 12 87,393,582 (GRCm39) splice site probably benign
R3735:Sptlc2 UTSW 12 87,388,339 (GRCm39) missense probably benign 0.27
R3736:Sptlc2 UTSW 12 87,388,339 (GRCm39) missense probably benign 0.27
R4278:Sptlc2 UTSW 12 87,382,925 (GRCm39) missense probably benign 0.04
R5252:Sptlc2 UTSW 12 87,382,829 (GRCm39) missense possibly damaging 0.49
R5593:Sptlc2 UTSW 12 87,415,857 (GRCm39) missense probably benign 0.11
R5656:Sptlc2 UTSW 12 87,393,535 (GRCm39) missense probably damaging 1.00
R5801:Sptlc2 UTSW 12 87,388,545 (GRCm39) splice site probably null
R6256:Sptlc2 UTSW 12 87,402,305 (GRCm39) missense probably damaging 1.00
R6280:Sptlc2 UTSW 12 87,434,905 (GRCm39) missense probably benign
R6520:Sptlc2 UTSW 12 87,402,436 (GRCm39) missense probably benign
R6808:Sptlc2 UTSW 12 87,397,069 (GRCm39) missense possibly damaging 0.64
R7133:Sptlc2 UTSW 12 87,397,151 (GRCm39) missense probably benign 0.00
R7274:Sptlc2 UTSW 12 87,388,380 (GRCm39) missense probably benign 0.24
R7366:Sptlc2 UTSW 12 87,360,823 (GRCm39) critical splice donor site probably null
R7602:Sptlc2 UTSW 12 87,388,463 (GRCm39) missense probably damaging 0.99
R9085:Sptlc2 UTSW 12 87,382,839 (GRCm39) missense probably benign 0.00
R9710:Sptlc2 UTSW 12 87,359,533 (GRCm39) missense probably benign 0.44
Z1177:Sptlc2 UTSW 12 87,415,818 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- GCACTTTTCAATTCTCCAATGCCTCAA -3'
(R):5'- TCACTGAGGGAAGGCAATAAAACCTG -3'

Sequencing Primer
(F):5'- TGCCTCAAGAAATCTCGAAGATATCC -3'
(R):5'- GCATGTTCCCTGAAGTTATAATGCG -3'
Posted On 2013-04-11