Incidental Mutation 'R7516:Sptlc3'
ID 582438
Institutional Source Beutler Lab
Gene Symbol Sptlc3
Ensembl Gene ENSMUSG00000039092
Gene Name serine palmitoyltransferase, long chain base subunit 3
Synonyms C130053K05Rik
MMRRC Submission 045589-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.122) question?
Stock # R7516 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 139335833-139478981 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 139431438 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Aspartic acid at position 320 (A320D)
Ref Sequence ENSEMBL: ENSMUSP00000048313 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047370] [ENSMUST00000110083]
AlphaFold Q8BG54
Predicted Effect probably benign
Transcript: ENSMUST00000047370
AA Change: A320D

PolyPhen 2 Score 0.113 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: A320D

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: A320D

PolyPhen 2 Score 0.113 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: A320D

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: 99.2%
Validation Efficiency
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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam28 T A 14: 68,868,125 (GRCm39) I407F probably damaging Het
Agbl1 A G 7: 76,075,669 (GRCm39) Y437C probably damaging Het
Alkbh5 T C 11: 60,429,979 (GRCm39) V244A probably damaging Het
Arap1 T C 7: 101,058,538 (GRCm39) F1390L probably benign Het
Asph T C 4: 9,630,940 (GRCm39) D136G possibly damaging Het
Atp8a2 A T 14: 60,094,516 (GRCm39) Y841N probably damaging Het
Cald1 A T 6: 34,686,492 (GRCm39) probably benign Het
Capn11 A G 17: 45,949,766 (GRCm39) I400T possibly damaging Het
Cdh18 T A 15: 23,259,684 (GRCm39) probably null Het
Ces2h T A 8: 105,743,458 (GRCm39) L204Q probably damaging Het
Chrna3 G A 9: 54,922,653 (GRCm39) A385V probably benign Het
Clca4a A T 3: 144,672,009 (GRCm39) L311Q probably damaging Het
Clip1 A G 5: 123,721,448 (GRCm39) V1149A probably benign Het
Clip3 T A 7: 29,998,268 (GRCm39) V238D possibly damaging Het
Col12a1 A G 9: 79,520,192 (GRCm39) probably null Het
Coro2a A G 4: 46,562,992 (GRCm39) V54A probably benign Het
Crem T C 18: 3,299,141 (GRCm39) probably null Het
Dennd5b T C 6: 148,969,878 (GRCm39) I192V probably benign Het
Dst A G 1: 34,209,560 (GRCm39) N1209S probably benign Het
Ero1a T A 14: 45,525,480 (GRCm39) M385L probably benign Het
Fam13a A T 6: 58,932,248 (GRCm39) V375D probably damaging Het
Fgfbp3 T A 19: 36,896,324 (GRCm39) Y98F possibly damaging Het
Frem3 T C 8: 81,338,712 (GRCm39) V335A probably damaging Het
Gm19410 T A 8: 36,263,433 (GRCm39) D951E probably benign Het
Gpatch1 T C 7: 35,007,625 (GRCm39) D145G probably benign Het
H60c G T 10: 3,209,746 (GRCm39) C180* probably null Het
Hmcn1 T C 1: 150,498,718 (GRCm39) T4054A probably benign Het
Hrg A G 16: 22,780,048 (GRCm39) Y442C unknown Het
Hspg2 C T 4: 137,269,931 (GRCm39) R2327C possibly damaging Het
Klhl31 G T 9: 77,558,429 (GRCm39) A382S probably damaging Het
Knl1 T C 2: 118,901,179 (GRCm39) V960A probably damaging Het
Lztr1 C T 16: 17,327,525 (GRCm39) A76V possibly damaging Het
Me3 G T 7: 89,497,183 (GRCm39) E395* probably null Het
Morc2b G A 17: 33,356,435 (GRCm39) H446Y probably benign Het
Mroh7 A T 4: 106,548,316 (GRCm39) M1054K probably benign Het
Ms4a6b T C 19: 11,506,907 (GRCm39) V232A probably benign Het
Nmt2 C A 2: 3,313,767 (GRCm39) D224E probably damaging Het
Nox4 C A 7: 86,970,905 (GRCm39) R261S probably benign Het
Obscn T A 11: 59,015,416 (GRCm39) K1019* probably null Het
Or4a15 T A 2: 89,193,719 (GRCm39) N18I probably benign Het
Or4g7 T A 2: 111,309,282 (GRCm39) V51D probably benign Het
Or5p67 G A 7: 107,922,223 (GRCm39) S220F probably damaging Het
Or8k24 C T 2: 86,216,328 (GRCm39) V145I probably benign Het
Pcdha11 A T 18: 37,144,671 (GRCm39) N254I probably damaging Het
Pck2 T A 14: 55,779,913 (GRCm39) I54N probably benign Het
Pkd1l3 T A 8: 110,361,861 (GRCm39) W978R probably damaging Het
Plxna4 T C 6: 32,214,703 (GRCm39) T593A probably benign Het
Podn G A 4: 107,879,321 (GRCm39) R266W probably damaging Het
Ptpn22 A G 3: 103,792,854 (GRCm39) D335G probably benign Het
Pxn A G 5: 115,644,922 (GRCm39) D3G unknown Het
Rapgefl1 T G 11: 98,736,960 (GRCm39) V320G probably benign Het
Rel A G 11: 23,692,785 (GRCm39) I416T probably benign Het
Sema5b A G 16: 35,471,540 (GRCm39) N378D probably benign Het
Sh3bp4 C A 1: 89,073,368 (GRCm39) L739M probably damaging Het
Skint2 A T 4: 112,483,168 (GRCm39) D191V probably damaging Het
Slc3a1 T C 17: 85,371,190 (GRCm39) Y581H probably damaging Het
Smcr8 G T 11: 60,670,814 (GRCm39) C654F probably benign Het
Spta1 A C 1: 174,025,349 (GRCm39) Q738P probably damaging Het
Thnsl2 T A 6: 71,108,990 (GRCm39) K274* probably null Het
Tmed2 T A 5: 124,685,055 (GRCm39) I68K possibly damaging Het
Tmtc4 G A 14: 123,180,735 (GRCm39) A326V possibly damaging Het
Tnks2 T A 19: 36,849,064 (GRCm39) S179T possibly damaging Het
Trim34b G T 7: 103,978,918 (GRCm39) C55F probably damaging Het
Trpm4 T A 7: 44,954,444 (GRCm39) E1129V probably damaging Het
Tvp23b T C 11: 62,782,867 (GRCm39) S188P possibly damaging Het
Usp1 A G 4: 98,822,356 (GRCm39) T557A probably damaging Het
Vmn2r66 C T 7: 84,661,176 (GRCm39) C18Y possibly damaging Het
Vmn2r85 T A 10: 130,254,852 (GRCm39) T611S probably damaging Het
Vps13c T C 9: 67,862,289 (GRCm39) S2969P possibly damaging Het
Wdr74 T A 19: 8,713,554 (GRCm39) C62* probably null Het
Wfikkn1 A T 17: 26,097,020 (GRCm39) C435S probably damaging Het
Zbtb45 A T 7: 12,740,269 (GRCm39) F449I probably damaging 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
R7026:Sptlc3 UTSW 2 139,379,608 (GRCm39) missense probably benign
R7412:Sptlc3 UTSW 2 139,431,537 (GRCm39) missense possibly damaging 0.75
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'- AGTAGACACCCAGAGAAATGTTAC -3'
(R):5'- TATATCCTCCTGAGCCCGAGAAG -3'

Sequencing Primer
(F):5'- CAAGACTGAAATGTTGTCTTTGCTG -3'
(R):5'- AGAAGCTCTTGGTGAATGTACCC -3'
Posted On 2019-10-17