Incidental Mutation 'R7026:Sptlc3'
ID 545947
Institutional Source Beutler Lab
Gene Symbol Sptlc3
Ensembl Gene ENSMUSG00000039092
Gene Name serine palmitoyltransferase, long chain base subunit 3
Synonyms C130053K05Rik
MMRRC Submission 045127-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.122) question?
Stock # R7026 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 139335833-139478981 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 139379608 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Leucine at position 83 (M83L)
Ref Sequence ENSEMBL: ENSMUSP00000105710 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047370] [ENSMUST00000110083]
AlphaFold Q8BG54
Predicted Effect probably benign
Transcript: ENSMUST00000047370
AA Change: M83L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: M83L

DomainStartEndE-ValueType
transmembrane domain 60 79 N/A INTRINSIC
Pfam:Aminotran_1_2 160 520 4.8e-59 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000110083
AA Change: M83L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: M83L

DomainStartEndE-ValueType
transmembrane domain 60 79 N/A INTRINSIC
Pfam:Aminotran_1_2 160 520 4.8e-59 PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 98.9%
Validation Efficiency 99% (69/70)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The SPTLC3 gene encodes an isoform of the third subunit of serine palmitoyltransferase (SPT; EC 2.3.1.50), which catalyzes the rate-limiting step of the de novo synthesis of sphingolipids (Hornemann et al., 2006 [PubMed 17023427]). SPT contains 2 main subunits: the common SPTLC1 subunit (MIM 605712) and either SPTLC2 (MIM 605713) or its isoform SPTLC2L (SPTLC3), depending on the tissue in which biosynthesis occurs (Hornemann et al., 2006 [PubMed 17023427]). There are also 2 highly related isoforms of a third subunit, SSSPTA (MIM 613540) and SSSPTB (MIM 610412), that confer acyl-CoA preference of the SPT enzyme and are essential for maximal enzyme activity (Han et al., 2009 [PubMed 19416851]).[supplied by OMIM, Nov 2010]
Allele List at MGI
Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc2 A T 19: 43,805,392 (GRCm39) M749L probably benign Het
Abcc2 A G 19: 43,818,974 (GRCm39) N1321S probably benign Het
Acsm2 T A 7: 119,191,450 (GRCm39) V506E probably damaging Het
Add2 G A 6: 86,063,965 (GRCm39) R88Q probably benign Het
Adgra3 A G 5: 50,118,083 (GRCm39) V1155A probably benign Het
Ahsg T A 16: 22,710,963 (GRCm39) D33E probably damaging Het
Alox12b A T 11: 69,048,131 (GRCm39) D20V possibly damaging Het
Alppl2 A G 1: 87,017,420 (GRCm39) probably null Het
Ankfn1 A G 11: 89,530,403 (GRCm39) *49Q probably null Het
Bcl11b T C 12: 107,882,851 (GRCm39) D488G probably damaging Het
Bcl2l10 T A 9: 75,258,364 (GRCm39) F175L probably benign Het
C2cd3 T A 7: 100,081,299 (GRCm39) D127E probably damaging Het
Cacna1c C T 6: 118,614,732 (GRCm39) V1311I probably damaging Het
Cd55b A T 1: 130,316,427 (GRCm39) I374K probably benign Het
Cfap36 T C 11: 29,172,565 (GRCm39) T267A probably benign Het
Cibar2 G A 8: 120,895,324 (GRCm39) H193Y probably damaging Het
Cog1 T C 11: 113,540,415 (GRCm39) L10P probably damaging Het
Dnah7a T A 1: 53,543,448 (GRCm39) M2241L probably benign Het
Dock10 G T 1: 80,479,504 (GRCm39) A1809E probably benign Het
Dock7 A T 4: 98,967,156 (GRCm39) D255E probably benign Het
Exph5 T C 9: 53,251,728 (GRCm39) F123L probably benign Het
Fbxw27 C A 9: 109,617,146 (GRCm39) K118N possibly damaging Het
Fscb C A 12: 64,518,391 (GRCm39) S1025I unknown Het
Get4 C T 5: 139,238,358 (GRCm39) R47W possibly damaging Het
Gm3676 G A 14: 41,366,072 (GRCm39) S81F probably benign Het
Gulp1 C T 1: 44,820,245 (GRCm39) P251S possibly damaging Het
Hhatl T C 9: 121,617,339 (GRCm39) D298G probably benign Het
Hsf2bp T A 17: 32,252,254 (GRCm39) K60N possibly damaging Het
Ints4 T A 7: 97,168,361 (GRCm39) V625D possibly damaging Het
Iqch T A 9: 63,432,421 (GRCm39) K286* probably null Het
Irak1bp1 T A 9: 82,712,084 (GRCm39) S2T possibly damaging Het
Kdm3b G A 18: 34,955,517 (GRCm39) V1135I possibly damaging Het
Lama3 C A 18: 12,649,605 (GRCm39) N181K probably damaging Het
Lrfn2 T G 17: 49,404,005 (GRCm39) S709R probably benign Het
Lrp12 T C 15: 39,743,566 (GRCm39) H123R probably damaging Het
Lrp1b A G 2: 41,159,234 (GRCm39) S1569P probably damaging Het
Lrp2 T G 2: 69,352,131 (GRCm39) Q635P probably damaging Het
Mboat2 T C 12: 24,998,381 (GRCm39) probably null Het
Mctp1 A G 13: 76,954,378 (GRCm39) T596A probably benign Het
Mroh9 T A 1: 162,888,251 (GRCm39) M275L probably benign Het
Ms4a10 A C 19: 10,944,869 (GRCm39) probably null Het
Myo9a C T 9: 59,722,617 (GRCm39) R560C probably damaging Het
Or11h4b A G 14: 50,918,716 (GRCm39) I125T probably damaging Het
Or5b107 A G 19: 13,142,779 (GRCm39) T134A probably benign Het
Or6z1 T A 7: 6,504,820 (GRCm39) H135L probably damaging Het
Ormdl3 A G 11: 98,474,808 (GRCm39) V45A possibly damaging Het
Parp4 T C 14: 56,858,049 (GRCm39) Y894H probably benign Het
Pigo G A 4: 43,023,380 (GRCm39) Q259* probably null Het
Prrc2a G A 17: 35,380,803 (GRCm39) P70S unknown Het
Rab3ip A G 10: 116,773,441 (GRCm39) I124T probably benign Het
Rap1b A G 10: 117,654,384 (GRCm39) I21T probably benign Het
Rasgrf2 T A 13: 92,131,732 (GRCm39) S642C probably damaging Het
Rb1 T C 14: 73,535,539 (GRCm39) E106G probably benign Het
Reps1 C A 10: 17,983,437 (GRCm39) R427S probably damaging Het
Rnf213 A C 11: 119,370,481 (GRCm39) H4760P possibly damaging Het
Rtl1 A G 12: 109,559,595 (GRCm39) I748T probably damaging Het
Sco1 A T 11: 66,944,683 (GRCm39) K102M probably damaging Het
Sec16b T C 1: 157,362,281 (GRCm39) M44T possibly damaging Het
Slc7a10 T C 7: 34,898,139 (GRCm39) M297T probably damaging Het
Smchd1 T C 17: 71,656,662 (GRCm39) H1935R probably benign Het
Sowaha G A 11: 53,370,050 (GRCm39) R229W probably damaging Het
Tbc1d9 T C 8: 83,968,192 (GRCm39) V431A probably benign Het
Tmem98 A G 11: 80,712,214 (GRCm39) E217G possibly damaging Het
Trim13 T A 14: 61,842,562 (GRCm39) L193* probably null Het
Trp53bp2 T C 1: 182,270,300 (GRCm39) S367P probably benign Het
Tsc2 T G 17: 24,845,713 (GRCm39) I202L probably damaging Het
Twf2 T A 9: 106,092,079 (GRCm39) V312E probably damaging Het
Usp34 G T 11: 23,311,622 (GRCm39) L471F probably damaging Het
Vps37c A G 19: 10,683,632 (GRCm39) D18G probably damaging Het
Zfp1010 T A 2: 176,957,361 (GRCm39) I46F probably benign Het
Other mutations in Sptlc3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01392:Sptlc3 APN 2 139,388,341 (GRCm39) missense possibly damaging 0.55
IGL01537:Sptlc3 APN 2 139,431,615 (GRCm39) missense possibly damaging 0.95
IGL01996:Sptlc3 APN 2 139,423,424 (GRCm39) splice site probably benign
IGL02512:Sptlc3 APN 2 139,389,123 (GRCm39) missense probably damaging 1.00
IGL03278:Sptlc3 APN 2 139,431,579 (GRCm39) missense probably damaging 1.00
IGL03286:Sptlc3 APN 2 139,431,579 (GRCm39) missense probably damaging 1.00
R0266:Sptlc3 UTSW 2 139,437,957 (GRCm39) missense possibly damaging 0.93
R0362:Sptlc3 UTSW 2 139,388,475 (GRCm39) splice site probably benign
R1464:Sptlc3 UTSW 2 139,389,154 (GRCm39) missense probably benign 0.00
R1464:Sptlc3 UTSW 2 139,389,154 (GRCm39) missense probably benign 0.00
R1494:Sptlc3 UTSW 2 139,431,480 (GRCm39) missense possibly damaging 0.58
R1847:Sptlc3 UTSW 2 139,467,843 (GRCm39) missense probably benign 0.08
R1919:Sptlc3 UTSW 2 139,408,595 (GRCm39) missense possibly damaging 0.66
R2093:Sptlc3 UTSW 2 139,467,794 (GRCm39) missense possibly damaging 0.89
R2396:Sptlc3 UTSW 2 139,408,506 (GRCm39) missense probably benign 0.44
R2972:Sptlc3 UTSW 2 139,431,581 (GRCm39) missense probably damaging 1.00
R2973:Sptlc3 UTSW 2 139,431,581 (GRCm39) missense probably damaging 1.00
R2974:Sptlc3 UTSW 2 139,431,581 (GRCm39) missense probably damaging 1.00
R4601:Sptlc3 UTSW 2 139,478,600 (GRCm39) missense probably benign 0.01
R4602:Sptlc3 UTSW 2 139,478,600 (GRCm39) missense probably benign 0.01
R4610:Sptlc3 UTSW 2 139,478,600 (GRCm39) missense probably benign 0.01
R4745:Sptlc3 UTSW 2 139,389,087 (GRCm39) missense probably damaging 1.00
R4779:Sptlc3 UTSW 2 139,431,509 (GRCm39) missense probably benign 0.04
R4992:Sptlc3 UTSW 2 139,437,923 (GRCm39) missense probably benign 0.04
R5162:Sptlc3 UTSW 2 139,473,263 (GRCm39) missense probably benign 0.11
R5401:Sptlc3 UTSW 2 139,478,643 (GRCm39) missense possibly damaging 0.75
R5406:Sptlc3 UTSW 2 139,388,398 (GRCm39) missense probably benign 0.26
R5642:Sptlc3 UTSW 2 139,388,328 (GRCm39) missense probably damaging 0.96
R5840:Sptlc3 UTSW 2 139,389,126 (GRCm39) missense probably damaging 1.00
R6057:Sptlc3 UTSW 2 139,423,533 (GRCm39) missense probably damaging 0.99
R6376:Sptlc3 UTSW 2 139,478,692 (GRCm39) missense probably benign 0.21
R6852:Sptlc3 UTSW 2 139,408,506 (GRCm39) missense probably benign 0.44
R7412:Sptlc3 UTSW 2 139,431,537 (GRCm39) missense possibly damaging 0.75
R7516:Sptlc3 UTSW 2 139,431,438 (GRCm39) missense probably benign 0.11
R7733:Sptlc3 UTSW 2 139,473,288 (GRCm39) missense possibly damaging 0.77
R7826:Sptlc3 UTSW 2 139,389,115 (GRCm39) missense probably benign 0.44
R7949:Sptlc3 UTSW 2 139,467,795 (GRCm39) missense possibly damaging 0.81
R9224:Sptlc3 UTSW 2 139,336,154 (GRCm39) missense probably benign 0.17
R9237:Sptlc3 UTSW 2 139,408,605 (GRCm39) missense probably benign 0.40
R9319:Sptlc3 UTSW 2 139,478,730 (GRCm39) missense possibly damaging 0.65
R9330:Sptlc3 UTSW 2 139,388,423 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- CCTTCTCAGTGATCAAATTCCAATG -3'
(R):5'- ATGGTGAATGGTTCCTGGAC -3'

Sequencing Primer
(F):5'- CAAATTCCAATGTCTTTCAAGCAG -3'
(R):5'- TGAATGGTTCCTGGACATATCC -3'
Posted On 2019-05-13