Incidental Mutation 'R4278:Sptlc2'
ID 322775
Institutional Source Beutler Lab
Gene Symbol Sptlc2
Ensembl Gene ENSMUSG00000021036
Gene Name serine palmitoyltransferase, long chain base subunit 2
Synonyms LCB2, Spt2
MMRRC Submission 068968-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4278 (G1)
Quality Score 225
Status Not validated
Chromosome 12
Chromosomal Location 87351832-87435129 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 87382925 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Arginine at position 393 (I393R)
Ref Sequence ENSEMBL: ENSMUSP00000021424 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021424]
AlphaFold P97363
Predicted Effect probably benign
Transcript: ENSMUST00000021424
AA Change: I393R

PolyPhen 2 Score 0.040 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000021424
Gene: ENSMUSG00000021036
AA Change: I393R

DomainStartEndE-ValueType
Pfam:Aminotran_1_2 166 526 7.2e-60 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000169845
Predicted Effect noncoding transcript
Transcript: ENSMUST00000181175
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.4%
Validation Efficiency
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: 30 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Anln A G 9: 22,245,296 (GRCm39) probably null Het
Arl6ip1 AAAATAAATAAATAAATAAATAAATA AAAATAAATAAATAAATAAATAAATAAATA 7: 117,721,122 (GRCm39) probably benign Het
Bltp3b T G 10: 89,642,571 (GRCm39) probably null Het
Capza3 T A 6: 139,987,786 (GRCm39) Y128* probably null Het
Ccdc187 T A 2: 26,172,239 (GRCm39) probably benign Het
Dpp4 T C 2: 62,209,667 (GRCm39) R119G probably damaging Het
Espn T C 4: 152,218,874 (GRCm39) D308G probably damaging Het
Gm9857 T C 3: 108,847,419 (GRCm39) probably benign Het
Hhatl G A 9: 121,613,285 (GRCm39) A470V probably benign Het
Igfals A T 17: 25,100,191 (GRCm39) E427D probably benign Het
Il22ra1 C T 4: 135,478,024 (GRCm39) A365V possibly damaging Het
Kctd6 G C 14: 8,222,806 (GRCm38) R216P probably damaging Het
Lama1 A T 17: 68,098,512 (GRCm39) M1864L probably null Het
Mbd5 T G 2: 49,162,305 (GRCm39) I37S probably damaging Het
Nsf C A 11: 103,821,632 (GRCm39) A5S probably damaging Het
Nsun5 A G 5: 135,398,914 (GRCm39) Y26C probably damaging Het
Or9q1 A G 19: 13,805,793 (GRCm39) probably benign Het
Pitpnm3 C T 11: 71,965,342 (GRCm39) V164I probably damaging Het
Plk2 A G 13: 110,532,637 (GRCm39) K117R probably benign Het
Ppp1r13b G T 12: 111,796,818 (GRCm39) N908K probably damaging Het
Rapgef4 T A 2: 72,028,739 (GRCm39) N385K possibly damaging Het
Rbp3 G A 14: 33,680,607 (GRCm39) V1070I probably benign Het
Rhbdd3 C T 11: 5,055,329 (GRCm39) T226I probably benign Het
Slc27a3 C T 3: 90,296,495 (GRCm39) probably benign Het
Slc30a2 G A 4: 134,073,360 (GRCm39) E136K probably null Het
Tmem260 C T 14: 48,715,093 (GRCm39) T249M probably damaging Het
Ttn T A 2: 76,585,168 (GRCm39) I22042F probably damaging Het
Vmn1r80 G T 7: 11,927,454 (GRCm39) C188F probably benign Het
Vwa2 C A 19: 56,891,915 (GRCm39) Q283K probably benign Het
Zfp52 A G 17: 21,782,132 (GRCm39) K660R probably benign 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
R0087:Sptlc2 UTSW 12 87,415,892 (GRCm39) missense probably benign
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
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'- AAGCCTGACTCCTTATTTAGGG -3'
(R):5'- TGACCTAACCTTGGCTTTGC -3'

Sequencing Primer
(F):5'- CAGCACAATTGGCTGCTAAG -3'
(R):5'- GGCTTTGCCCTGTTTCTGGC -3'
Posted On 2015-06-20