Incidental Mutation 'IGL03278:Sptlc3'
ID 415486
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Sptlc3
Ensembl Gene ENSMUSG00000039092
Gene Name serine palmitoyltransferase, long chain base subunit 3
Synonyms C130053K05Rik
Accession Numbers
Essential gene? Probably non essential (E-score: 0.122) question?
Stock # IGL03278
Quality Score
Status
Chromosome 2
Chromosomal Location 139335833-139478981 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 139431579 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glycine to Aspartic acid at position 367 (G367D)
Ref Sequence ENSEMBL: ENSMUSP00000105710 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047370] [ENSMUST00000110083]
AlphaFold Q8BG54
Predicted Effect probably damaging
Transcript: ENSMUST00000047370
AA Change: G367D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: G367D

DomainStartEndE-ValueType
transmembrane domain 60 79 N/A INTRINSIC
Pfam:Aminotran_1_2 160 520 4.8e-59 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000110083
AA Change: G367D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: G367D

DomainStartEndE-ValueType
transmembrane domain 60 79 N/A INTRINSIC
Pfam:Aminotran_1_2 160 520 4.8e-59 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134801
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184747
Coding Region Coverage
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: 39 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2700049A03Rik T A 12: 71,205,599 (GRCm39) probably benign Het
Acss2 A G 2: 155,403,921 (GRCm39) D676G possibly damaging Het
Antxr1 A G 6: 87,181,439 (GRCm39) probably benign Het
Ccdc134 C T 15: 82,015,682 (GRCm39) A54V possibly damaging Het
Ccdc40 A T 11: 119,133,336 (GRCm39) I465F probably damaging Het
Cdk5rap1 A T 2: 154,212,622 (GRCm39) S79T probably benign Het
Col6a6 T C 9: 105,586,651 (GRCm39) E1790G probably benign Het
Cops8 C A 1: 90,532,087 (GRCm39) probably null Het
Dnah7a T C 1: 53,536,124 (GRCm39) T2640A probably benign Het
F2 G A 2: 91,465,527 (GRCm39) A86V probably benign Het
Fhip1b C A 7: 105,034,331 (GRCm39) M433I possibly damaging Het
Gabrb1 T G 5: 72,026,939 (GRCm39) D113E probably damaging Het
Git2 C A 5: 114,883,640 (GRCm39) probably benign Het
Git2 A T 5: 114,883,641 (GRCm39) probably null Het
Gm4847 A T 1: 166,462,605 (GRCm39) I295N probably benign Het
H2-M10.6 C A 17: 37,124,715 (GRCm39) H211N probably damaging Het
Hmgcr A G 13: 96,793,270 (GRCm39) probably benign Het
Larp1 T C 11: 57,934,882 (GRCm39) probably benign Het
Lrguk A G 6: 34,093,381 (GRCm39) E634G possibly damaging Het
Nanog A G 6: 122,688,704 (GRCm39) Y95C probably damaging Het
Nelfcd G A 2: 174,268,625 (GRCm39) A559T possibly damaging Het
Nfe2l1 C A 11: 96,713,018 (GRCm39) R55L probably benign Het
Or1f19 C T 16: 3,410,971 (GRCm39) A237V possibly damaging Het
Pkmyt1 A G 17: 23,953,221 (GRCm39) E259G probably damaging Het
Pld4 A G 12: 112,733,165 (GRCm39) N247S probably damaging Het
Prdm4 A T 10: 85,743,622 (GRCm39) M211K probably damaging Het
Rab37 A C 11: 115,050,517 (GRCm39) I121L possibly damaging Het
Rabl6 T C 2: 25,473,834 (GRCm39) probably benign Het
Slc34a3 A T 2: 25,122,059 (GRCm39) V154E probably benign Het
Slc38a9 T G 13: 112,826,052 (GRCm39) probably benign Het
Stk24 T C 14: 121,540,182 (GRCm39) K139R possibly damaging Het
Tacc2 T C 7: 130,335,298 (GRCm39) probably null Het
Tap1 A T 17: 34,410,457 (GRCm39) K378M probably damaging Het
Tfr2 A T 5: 137,569,298 (GRCm39) R10* probably null Het
Trim38 A G 13: 23,974,979 (GRCm39) D306G possibly damaging Het
Ttc6 A T 12: 57,668,812 (GRCm39) K418I probably damaging Het
Ush2a T A 1: 188,581,313 (GRCm39) L3731Q probably damaging Het
Vmn2r89 A T 14: 51,692,557 (GRCm39) Y120F probably damaging Het
Vps35 A T 8: 86,021,590 (GRCm39) 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
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
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
Posted On 2016-08-02