Incidental Mutation 'R2972:Sptlc3'
ID 255236
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 # R2972 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 139335833-139478981 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 139431581 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 368 (T368A)
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: T368A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: T368A

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: T368A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: T368A

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
Meta Mutation Damage Score 0.9207 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.5%
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: 25 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
BC048507 T C 13: 68,011,749 (GRCm39) I42T probably benign Het
Card9 C T 2: 26,247,222 (GRCm39) R309H probably damaging Het
Clec14a T A 12: 58,314,360 (GRCm39) R421W probably damaging Het
Crnkl1 A G 2: 145,774,181 (GRCm39) L94P probably benign Het
D930007J09Rik C T 13: 32,986,742 (GRCm39) probably benign Het
Dhrs7c T A 11: 67,706,697 (GRCm39) I285N possibly damaging Het
Golga2 A G 2: 32,195,671 (GRCm39) N752S probably benign Het
Klrb1-ps1 A G 6: 129,096,719 (GRCm39) noncoding transcript Het
Nin G A 12: 70,109,487 (GRCm39) R151C probably damaging Het
Nsun6 A C 2: 15,042,883 (GRCm39) probably null Het
Nyap2 C T 1: 81,169,485 (GRCm39) R81* probably null Het
Or1n2 G A 2: 36,797,416 (GRCm39) V153M probably benign Het
Or4a69 G T 2: 89,313,120 (GRCm39) R120S possibly damaging Het
Pkhd1l1 T A 15: 44,410,644 (GRCm39) M2717K possibly damaging Het
Ralgapa1 T C 12: 55,867,540 (GRCm39) K5E possibly damaging Het
Rnf130 T A 11: 49,984,627 (GRCm39) L309* probably null Het
Rsf1 ATGGCG ATGGCGACGGTGGCG 7: 97,229,111 (GRCm39) probably benign Het
Rxrg G A 1: 167,466,715 (GRCm39) R422H probably damaging Het
Serpinb9e T A 13: 33,439,126 (GRCm39) V184E probably benign Het
Slc10a5 A T 3: 10,399,517 (GRCm39) I381N probably damaging Het
Slit1 G A 19: 41,599,455 (GRCm39) P1032L probably benign Het
Ubr4 T C 4: 139,133,847 (GRCm39) Y748H probably benign Het
Ugt8a T C 3: 125,708,957 (GRCm39) H51R probably benign Het
Vmn2r117 A G 17: 23,678,830 (GRCm39) V798A probably damaging Het
Vmn2r77 T C 7: 86,452,893 (GRCm39) Y537H 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
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
Predicted Primers PCR Primer
(F):5'- TGTGCTAGCATGGAAGGTTC -3'
(R):5'- CTCCCAGGTACTCTACACAGTTTG -3'

Sequencing Primer
(F):5'- CCATTGTGAACCTTGCCCAGATAG -3'
(R):5'- CCAGGTACTCTACACAGTTTGTTATG -3'
Posted On 2014-12-29