Incidental Mutation 'R5801:Sptlc2'
ID 448372
Institutional Source Beutler Lab
Gene Symbol Sptlc2
Ensembl Gene ENSMUSG00000021036
Gene Name serine palmitoyltransferase, long chain base subunit 2
Synonyms LCB2, Spt2
MMRRC Submission 043390-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5801 (G1)
Quality Score 225
Status Validated
Chromosome 12
Chromosomal Location 87351832-87435129 bp(-) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) T to C at 87388545 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000021424 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021424]
AlphaFold P97363
Predicted Effect probably null
Transcript: ENSMUST00000021424
SMART Domains Protein: ENSMUSP00000021424
Gene: ENSMUSG00000021036

DomainStartEndE-ValueType
Pfam:Aminotran_1_2 166 526 7.2e-60 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000167911
Predicted Effect noncoding transcript
Transcript: ENSMUST00000169845
Predicted Effect noncoding transcript
Transcript: ENSMUST00000170110
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.8%
  • 10x: 97.5%
  • 20x: 95.9%
Validation Efficiency 100% (75/75)
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: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
AAdacl4fm3 T A 4: 144,430,206 (GRCm39) D261V probably damaging Het
Adam15 C T 3: 89,249,668 (GRCm39) V667I probably damaging Het
Adamts14 T C 10: 61,038,775 (GRCm39) S912G probably damaging Het
Adamts20 C A 15: 94,245,551 (GRCm39) E584* probably null Het
Ago3 A T 4: 126,265,561 (GRCm39) N284K possibly damaging Het
Alx3 T A 3: 107,512,257 (GRCm39) Y298* probably null Het
Arhgap32 A G 9: 32,167,084 (GRCm39) I574V probably benign Het
Bsn C T 9: 107,990,208 (GRCm39) R1848Q possibly damaging Het
Caskin2 T C 11: 115,694,299 (GRCm39) D400G probably damaging Het
Cdc73 T A 1: 143,484,281 (GRCm39) H525L probably benign Het
Cep135 A G 5: 76,778,523 (GRCm39) E674G probably damaging Het
Cic G A 7: 24,970,863 (GRCm39) R198Q possibly damaging Het
Col5a2 T C 1: 45,428,641 (GRCm39) probably null Het
Col6a5 A G 9: 105,825,566 (GRCm39) V9A unknown Het
Cpsf7 A T 19: 10,516,996 (GRCm39) D366V probably benign Het
Cuedc2 T C 19: 46,319,796 (GRCm39) E173G probably damaging Het
D5Ertd579e T C 5: 36,761,913 (GRCm39) E1318G probably damaging Het
Ddx55 T C 5: 124,704,560 (GRCm39) probably null Het
Dennd1b T A 1: 138,967,727 (GRCm39) probably null Het
Dpy19l3 T C 7: 35,424,723 (GRCm39) T111A probably benign Het
Edn1 C A 13: 42,460,282 (GRCm39) A179E probably benign Het
Eif2b1 T C 5: 124,712,775 (GRCm39) probably null Het
Epha5 A G 5: 84,479,085 (GRCm39) probably null Het
Erc1 T A 6: 119,750,783 (GRCm39) N466I probably damaging Het
Ermp1 A G 19: 29,590,228 (GRCm39) F825L probably damaging Het
Fbh1 T C 2: 11,774,637 (GRCm39) D36G probably damaging Het
Fbxo41 G T 6: 85,461,515 (GRCm39) F64L probably damaging Het
Gabrb2 T C 11: 42,312,216 (GRCm39) S14P probably benign Het
Gm6505 A T 3: 28,819,116 (GRCm39) noncoding transcript Het
Ighv1-18 T A 12: 114,646,328 (GRCm39) D91V probably damaging Het
Imp3 A G 9: 56,845,086 (GRCm39) D99G probably benign Het
Iqub T C 6: 24,449,768 (GRCm39) K699R probably benign Het
Itpk1 A G 12: 102,540,204 (GRCm39) V293A probably damaging Het
Lrrc49 A T 9: 60,509,916 (GRCm39) F157L probably damaging Het
Mapk1ip1 T A 7: 138,438,239 (GRCm39) T64S possibly damaging Het
Mrpl9 T C 3: 94,355,103 (GRCm39) L225P possibly damaging Het
Ms4a14 A G 19: 11,279,150 (GRCm39) L1136S possibly damaging Het
Ms4a14 A T 19: 11,279,246 (GRCm39) I1104K possibly damaging Het
Nkain2 T C 10: 32,278,264 (GRCm39) T54A probably damaging Het
Ociad2 A G 5: 73,483,642 (GRCm39) F60S probably damaging Het
Or1e1f T C 11: 73,855,772 (GRCm39) F113L probably benign Het
Polk T A 13: 96,620,094 (GRCm39) H723L probably damaging Het
Prickle4 C A 17: 47,999,698 (GRCm39) R285L possibly damaging Het
Psmd2 A G 16: 20,473,672 (GRCm39) N121S probably damaging Het
Rab11fip5 T A 6: 85,314,582 (GRCm39) S1212C probably damaging Het
Rasgef1c T G 11: 49,860,883 (GRCm39) M266R probably damaging Het
Rpusd4 A G 9: 35,181,369 (GRCm39) E155G possibly damaging Het
Rrbp1 A G 2: 143,831,703 (GRCm39) S155P probably damaging Het
Safb2 T C 17: 56,870,103 (GRCm39) Y991C possibly damaging Het
Shank1 G A 7: 44,006,240 (GRCm39) E1986K possibly damaging Het
Slc22a14 A G 9: 119,001,149 (GRCm39) F482L probably benign Het
Slc35e3 T A 10: 117,581,767 (GRCm39) M109L probably benign Het
Slco4c1 T C 1: 96,799,809 (GRCm39) N9S probably damaging Het
Slco6b1 C T 1: 96,875,356 (GRCm39) noncoding transcript Het
Sptan1 A G 2: 29,920,613 (GRCm39) probably null Het
Stk10 C T 11: 32,546,748 (GRCm39) P335L probably benign Het
Strip1 A C 3: 107,528,757 (GRCm39) L391R possibly damaging Het
Tacr1 T A 6: 82,534,134 (GRCm39) S387T probably benign Het
Thbs2 A T 17: 14,908,125 (GRCm39) F213I probably damaging Het
Thbs3 A T 3: 89,131,704 (GRCm39) Y692F probably benign Het
Tktl2 C A 8: 66,966,299 (GRCm39) A619E probably benign Het
Tmc3 A T 7: 83,271,686 (GRCm39) E946V possibly damaging Het
Tmem132d A G 5: 127,861,964 (GRCm39) V719A possibly damaging Het
Trpa1 T C 1: 14,968,302 (GRCm39) H488R probably damaging Het
Tsfm TCACTCC TCACTCCACTCC 10: 126,858,706 (GRCm39) probably null Het
Wdr35 A G 12: 9,056,723 (GRCm39) T503A possibly damaging Het
Zfp109 T C 7: 23,928,126 (GRCm39) K436E probably damaging Het
Zfp423 A G 8: 88,585,990 (GRCm39) Y78H probably damaging Het
Zfp970 A G 2: 177,165,151 (GRCm39) K26E 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
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
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
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'- TACATCCTCAGGATCCAGGC -3'
(R):5'- CAAGGCATTCATAATGAGCATAGAG -3'

Sequencing Primer
(F):5'- TCAGGATCCAGGCCAAAGTAATC -3'
(R):5'- AGAGTGCTTTCCTGGCATATTCAAG -3'
Posted On 2016-12-15