Incidental Mutation 'R5656:Sptlc2'
ID 442345
Institutional Source Beutler Lab
Gene Symbol Sptlc2
Ensembl Gene ENSMUSG00000021036
Gene Name serine palmitoyltransferase, long chain base subunit 2
Synonyms LCB2
MMRRC Submission 043302-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5656 (G1)
Quality Score 225
Status Not validated
Chromosome 12
Chromosomal Location 87305058-87388355 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to T at 87346761 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Leucine to Glutamine at position 264 (L264Q)
Ref Sequence ENSEMBL: ENSMUSP00000021424 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021424]
AlphaFold P97363
Predicted Effect probably damaging
Transcript: ENSMUST00000021424
AA Change: L264Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000021424
Gene: ENSMUSG00000021036
AA Change: L264Q

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
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.9%
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: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933405L10Rik A G 8: 105,709,512 (GRCm38) S139G probably benign Het
Adrb3 T C 8: 27,227,377 (GRCm38) D348G probably damaging Het
Atg2b A G 12: 105,621,328 (GRCm38) V1959A probably benign Het
Bicral G A 17: 46,808,369 (GRCm38) T742M probably damaging Het
Bub1b T A 2: 118,605,431 (GRCm38) I60N probably damaging Het
Ccdc162 A G 10: 41,569,934 (GRCm38) V414A probably benign Het
Cd22 T G 7: 30,869,773 (GRCm38) Y612S probably damaging Het
Cd68 T A 11: 69,664,421 (GRCm38) I320F probably damaging Het
Clca3a2 A T 3: 144,797,632 (GRCm38) N852K probably benign Het
Cpa6 T A 1: 10,329,514 (GRCm38) H363L probably benign Het
Ddx18 A T 1: 121,561,358 (GRCm38) L320Q probably damaging Het
Dnah5 A G 15: 28,421,064 (GRCm38) D3849G probably benign Het
Eci1 T A 17: 24,437,309 (GRCm38) N164K probably damaging Het
Efs T C 14: 54,917,127 (GRCm38) T552A probably damaging Het
Fbp1 C A 13: 62,875,196 (GRCm38) V96L probably damaging Het
Gtf3c1 T A 7: 125,662,654 (GRCm38) N1139I probably benign Het
Gucy1b2 T C 14: 62,422,981 (GRCm38) Y152C probably damaging Het
Gxylt1 A T 15: 93,245,661 (GRCm38) L362Q probably damaging Het
Iqcd A G 5: 120,605,126 (GRCm38) probably null Het
Klhl41 T A 2: 69,683,532 (GRCm38) I585N possibly damaging Het
Map6 A G 7: 99,336,298 (GRCm38) K470E probably damaging Het
Mast3 T C 8: 70,786,221 (GRCm38) T496A probably damaging Het
Mbd6 A T 10: 127,285,286 (GRCm38) probably benign Het
Melk A G 4: 44,312,237 (GRCm38) K183R possibly damaging Het
Mta1 T C 12: 113,123,139 (GRCm38) V152A probably damaging Het
Naa35 G A 13: 59,622,866 (GRCm38) probably benign Het
Nav3 A C 10: 109,764,633 (GRCm38) S1378A probably damaging Het
Ncapd3 T A 9: 27,051,645 (GRCm38) D415E possibly damaging Het
Nlrp4f G A 13: 65,190,871 (GRCm38) R651* probably null Het
Or1e1f T A 11: 73,964,710 (GRCm38) M34K probably damaging Het
Or5b121 A G 19: 13,530,380 (GRCm38) T280A probably benign Het
Or5p72 A G 7: 108,422,618 (GRCm38) I16V probably benign Het
P2rx7 A T 5: 122,673,717 (GRCm38) R364W probably damaging Het
Phactr2 T C 10: 13,388,703 (GRCm38) D2G probably benign Het
Phc3 G T 3: 30,965,866 (GRCm38) S28R probably damaging Het
Ppfia1 A T 7: 144,519,974 (GRCm38) probably null Het
Prdm10 C T 9: 31,353,417 (GRCm38) T667M probably benign Het
Pwwp2b T A 7: 139,255,971 (GRCm38) S443T possibly damaging Het
Pzp T C 6: 128,490,072 (GRCm38) T1113A probably damaging Het
Rapgef6 A G 11: 54,636,136 (GRCm38) E551G possibly damaging Het
Sec23ip A G 7: 128,776,784 (GRCm38) Y774C probably damaging Het
Setdb2 T C 14: 59,419,118 (GRCm38) D266G probably damaging Het
Shank1 T C 7: 44,352,886 (GRCm38) V1343A probably benign Het
Slf2 T A 19: 44,973,235 (GRCm38) D1064E probably benign Het
Slu7 A G 11: 43,443,418 (GRCm38) K424E probably benign Het
Smg1 A T 7: 118,154,664 (GRCm38) probably benign Het
Sra1 A G 18: 36,678,407 (GRCm38) S93P probably damaging Het
Sult1c1 T C 17: 53,964,652 (GRCm38) E169G probably benign Het
Sv2a A G 3: 96,185,572 (GRCm38) D196G probably damaging Het
Tbc1d22b A G 17: 29,594,780 (GRCm38) I362M probably damaging Het
Tenm3 T C 8: 48,228,762 (GRCm38) D2611G probably damaging Het
Tmem43 T C 6: 91,480,708 (GRCm38) F191L probably benign Het
Trbv13-2 T A 6: 41,121,694 (GRCm38) Y68N probably benign Het
Ttn T G 2: 76,774,654 (GRCm38) D18312A possibly damaging Het
Ublcp1 A G 11: 44,465,606 (GRCm38) V95A probably damaging Het
Usp17ld A G 7: 103,250,840 (GRCm38) V295A probably damaging Het
Vmn1r29 T A 6: 58,308,167 (GRCm38) L291M possibly damaging Het
Vsig10l C T 7: 43,464,151 (GRCm38) R176* probably null Het
Zbtb46 A G 2: 181,423,417 (GRCm38) probably null Het
Zfp644 A G 5: 106,637,982 (GRCm38) V233A probably benign Het
Other mutations in Sptlc2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00757:Sptlc2 APN 12 87,369,068 (GRCm38) missense probably damaging 0.99
IGL02458:Sptlc2 APN 12 87,309,893 (GRCm38) utr 3 prime probably benign
IGL02734:Sptlc2 APN 12 87,355,670 (GRCm38) missense probably damaging 0.97
IGL03252:Sptlc2 APN 12 87,355,657 (GRCm38) missense probably benign 0.00
lopsided UTSW 12 87,341,565 (GRCm38) missense probably benign 0.27
shinola UTSW 12 87,350,295 (GRCm38) missense possibly damaging 0.64
R0087:Sptlc2 UTSW 12 87,369,118 (GRCm38) missense probably benign
R0116:Sptlc2 UTSW 12 87,356,680 (GRCm38) missense probably benign 0.00
R0492:Sptlc2 UTSW 12 87,346,806 (GRCm38) splice site probably null
R1353:Sptlc2 UTSW 12 87,341,746 (GRCm38) missense probably damaging 1.00
R1470:Sptlc2 UTSW 12 87,355,640 (GRCm38) missense probably benign 0.00
R1470:Sptlc2 UTSW 12 87,355,640 (GRCm38) missense probably benign 0.00
R3417:Sptlc2 UTSW 12 87,346,808 (GRCm38) splice site probably benign
R3735:Sptlc2 UTSW 12 87,341,565 (GRCm38) missense probably benign 0.27
R3736:Sptlc2 UTSW 12 87,341,565 (GRCm38) missense probably benign 0.27
R4278:Sptlc2 UTSW 12 87,336,151 (GRCm38) missense probably benign 0.04
R5252:Sptlc2 UTSW 12 87,336,055 (GRCm38) missense possibly damaging 0.49
R5593:Sptlc2 UTSW 12 87,369,083 (GRCm38) missense probably benign 0.11
R5801:Sptlc2 UTSW 12 87,341,771 (GRCm38) splice site probably null
R6256:Sptlc2 UTSW 12 87,355,531 (GRCm38) missense probably damaging 1.00
R6280:Sptlc2 UTSW 12 87,388,131 (GRCm38) missense probably benign
R6520:Sptlc2 UTSW 12 87,355,662 (GRCm38) missense probably benign
R6808:Sptlc2 UTSW 12 87,350,295 (GRCm38) missense possibly damaging 0.64
R7133:Sptlc2 UTSW 12 87,350,377 (GRCm38) missense probably benign 0.00
R7274:Sptlc2 UTSW 12 87,341,606 (GRCm38) missense probably benign 0.24
R7366:Sptlc2 UTSW 12 87,314,049 (GRCm38) critical splice donor site probably null
R7602:Sptlc2 UTSW 12 87,341,689 (GRCm38) missense probably damaging 0.99
R9085:Sptlc2 UTSW 12 87,336,065 (GRCm38) missense probably benign 0.00
R9710:Sptlc2 UTSW 12 87,312,759 (GRCm38) missense probably benign 0.44
Z1177:Sptlc2 UTSW 12 87,369,044 (GRCm38) missense probably benign 0.01
Predicted Primers PCR Primer

Sequencing Primer
Posted On 2016-11-09