Incidental Mutation 'R4601:Sptlc3'
ID 345601
Institutional Source Beutler Lab
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 # R4601 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 139335833-139478981 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 139478600 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Isoleucine at position 520 (V520I)
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: V520I

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: V520I

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: V520I

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: V520I

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
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.1%
  • 20x: 94.5%
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: 91 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aars2 T A 17: 45,827,847 (GRCm39) D555E probably damaging Het
Abca16 T G 7: 120,035,920 (GRCm39) F334L probably damaging Het
Abcc4 T A 14: 118,869,575 (GRCm39) M186L probably benign Het
Agap3 T C 5: 24,681,406 (GRCm39) L120P probably damaging Het
Ak7 G A 12: 105,679,834 (GRCm39) V123M probably benign Het
Aldh1a7 A T 19: 20,693,343 (GRCm39) V192D probably damaging Het
Ankrd36 A G 11: 5,520,102 (GRCm39) D59G probably benign Het
Arsi G A 18: 61,049,723 (GRCm39) G202E probably benign Het
Cacna1e A G 1: 154,347,359 (GRCm39) V936A probably benign Het
Camkv T C 9: 107,823,295 (GRCm39) V107A probably damaging Het
Camp T C 9: 109,677,730 (GRCm39) E80G probably damaging Het
Cblif A C 19: 11,729,554 (GRCm39) D171A probably damaging Het
Ccdc66 T C 14: 27,222,377 (GRCm39) N122S probably damaging Het
Cd101 G A 3: 100,901,204 (GRCm39) T960M possibly damaging Het
Cdk18 A G 1: 132,044,657 (GRCm39) V323A possibly damaging Het
Celf2 G T 2: 6,590,831 (GRCm39) N279K possibly damaging Het
Cemip T C 7: 83,600,826 (GRCm39) I932V probably damaging Het
Cep250 C A 2: 155,803,973 (GRCm39) Q28K probably benign Het
Ces2f T C 8: 105,676,596 (GRCm39) C97R probably damaging Het
Cfap126 G T 1: 170,941,627 (GRCm39) G41C possibly damaging Het
Cfap96 A T 8: 46,423,505 (GRCm39) I69N probably damaging Het
Chat T C 14: 32,146,112 (GRCm39) M354V probably benign Het
Clca4b A T 3: 144,632,945 (GRCm39) D168E possibly damaging Het
Cpxm1 T A 2: 130,235,496 (GRCm39) M499L possibly damaging Het
Dennd3 T A 15: 73,439,009 (GRCm39) W1126R probably damaging Het
Dgkb T C 12: 38,652,819 (GRCm39) S735P probably damaging Het
Dlec1 T C 9: 118,976,202 (GRCm39) probably null Het
Dnajc6 T C 4: 101,468,461 (GRCm39) F166L probably damaging Het
Dph5 A G 3: 115,693,426 (GRCm39) N115D possibly damaging Het
Ercc3 G A 18: 32,378,624 (GRCm39) A202T probably benign Het
Erich3 A T 3: 154,470,375 (GRCm39) D136V unknown Het
Exoc2 T C 13: 31,066,251 (GRCm39) N475S probably benign Het
Fam217a T C 13: 35,095,285 (GRCm39) D310G probably damaging Het
Fam53a C T 5: 33,758,007 (GRCm39) S372N probably benign Het
Fbn2 C G 18: 58,186,805 (GRCm39) G1699R probably damaging Het
Fbxo46 T C 7: 18,869,489 (GRCm39) V36A probably benign Het
Fhip1a T C 3: 85,648,487 (GRCm39) M26V probably damaging Het
G6pc1 A G 11: 101,263,567 (GRCm39) Y127C probably damaging Het
Gba2 A G 4: 43,573,810 (GRCm39) F161L probably damaging Het
Gja1 T C 10: 56,264,325 (GRCm39) L228P probably damaging Het
Gm20834 A G Y: 10,323,178 (GRCm39) V86A probably benign Het
Hmcn1 A T 1: 150,614,396 (GRCm39) C1337S probably damaging Het
Il1rl1 T A 1: 40,480,460 (GRCm39) S30T possibly damaging Het
Itgb4 A G 11: 115,896,548 (GRCm39) T1436A probably damaging Het
Itk T A 11: 46,227,342 (GRCm39) Q427L probably benign Het
Klhdc4 T C 8: 122,526,266 (GRCm39) E291G probably damaging Het
Map4 T A 9: 109,881,887 (GRCm39) S250R possibly damaging Het
Mnt T A 11: 74,727,285 (GRCm39) V57E possibly damaging Het
Mrc2 G A 11: 105,239,257 (GRCm39) probably null Het
Mslnl G A 17: 25,961,908 (GRCm39) V128M probably damaging Het
Mtcl2 T C 2: 156,881,844 (GRCm39) K736R probably benign Het
Musk A T 4: 58,301,625 (GRCm39) I128F probably damaging Het
Myh4 G A 11: 67,141,136 (GRCm39) A733T possibly damaging Het
Myo5a T A 9: 75,043,670 (GRCm39) F220I probably damaging Het
Npas3 A G 12: 54,091,361 (GRCm39) H305R probably damaging Het
Nrcam A T 12: 44,637,839 (GRCm39) Y1132F probably damaging Het
Nt5c3b A C 11: 100,323,744 (GRCm39) D189E probably benign Het
Nuf2 A G 1: 169,333,683 (GRCm39) L331P probably damaging Het
Nup214 C T 2: 31,887,977 (GRCm39) T646I probably benign Het
Or14j9 T C 17: 37,875,076 (GRCm39) N42S probably damaging Het
Pcdh18 T C 3: 49,699,174 (GRCm39) E1096G probably damaging Het
Pgm2 T A 5: 64,265,070 (GRCm39) F364I probably benign Het
Pikfyve A G 1: 65,273,421 (GRCm39) N612S probably damaging Het
Pla2g4e T G 2: 120,016,863 (GRCm39) H226P possibly damaging Het
Ppp3cb T C 14: 20,570,714 (GRCm39) N339S possibly damaging Het
Prkd2 G T 7: 16,577,573 (GRCm39) probably benign Het
Rnf133 T C 6: 23,649,041 (GRCm39) E296G possibly damaging Het
Sav1 A T 12: 70,031,095 (GRCm39) D142E probably benign Het
Scn3b C A 9: 40,199,719 (GRCm39) P212T probably damaging Het
Sel1l A T 12: 91,799,827 (GRCm39) probably null Het
Septin9 A G 11: 117,251,310 (GRCm39) K543E probably damaging Het
Serpinb12 T A 1: 106,876,883 (GRCm39) D66E probably benign Het
Slc35e2 T C 4: 155,702,106 (GRCm39) F290S probably benign Het
Snrpa A G 7: 26,894,958 (GRCm39) M1T probably null Het
Srpk3 A G X: 72,818,547 (GRCm39) H79R possibly damaging Het
Stox2 A G 8: 47,645,970 (GRCm39) S497P probably damaging Het
Stradb G A 1: 59,032,731 (GRCm39) S361N probably damaging Het
Sult3a2 T C 10: 33,658,083 (GRCm39) K10R probably benign Het
Susd4 A G 1: 182,686,025 (GRCm39) N192D probably damaging Het
Tcp10a T A 17: 7,593,374 (GRCm39) D32E probably benign Het
Tdpoz4 T A 3: 93,704,339 (GRCm39) V212D probably damaging Het
Tdrd5 T A 1: 156,111,944 (GRCm39) T479S probably benign Het
Tex10 T C 4: 48,452,946 (GRCm39) D671G probably benign Het
Tex55 A G 16: 38,648,380 (GRCm39) V243A probably benign Het
Traj37 T C 14: 54,418,996 (GRCm39) probably benign Het
Ttc7b G A 12: 100,466,376 (GRCm39) R79C probably damaging Het
Vmn2r115 T A 17: 23,565,373 (GRCm39) L420Q probably benign Het
Wdr24 T A 17: 26,047,181 (GRCm39) probably null Het
Wdr81 T A 11: 75,336,484 (GRCm39) Q516L probably damaging Het
Zfp516 A G 18: 82,974,164 (GRCm39) T121A probably benign Het
Zmat1 A T X: 133,873,694 (GRCm39) S566T probably damaging Homo
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
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
Predicted Primers PCR Primer
(F):5'- ACACTCACAATGTTGAGTTAGAGC -3'
(R):5'- TGAAATTGTCCTCAGAAGGGG -3'

Sequencing Primer
(F):5'- ATTACTGGAGCATACTGGCC -3'
(R):5'- TTGTCCTCAGAAGGGGTAAAATAC -3'
Posted On 2015-09-25