Incidental Mutation 'R3726:Sptssa'
ID 270804
Institutional Source Beutler Lab
Gene Symbol Sptssa
Ensembl Gene ENSMUSG00000044408
Gene Name serine palmitoyltransferase, small subunit A
Synonyms 1110002B05Rik
MMRRC Submission 040717-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3726 (G1)
Quality Score 180
Status Validated
Chromosome 12
Chromosomal Location 54692177-54703358 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 54703180 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 30 (E30G)
Ref Sequence ENSEMBL: ENSMUSP00000053671 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056228] [ENSMUST00000218147]
AlphaFold Q8R207
Predicted Effect probably damaging
Transcript: ENSMUST00000056228
AA Change: E30G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000053671
Gene: ENSMUSG00000044408
AA Change: E30G

DomainStartEndE-ValueType
Pfam:DUF3317 10 63 9.9e-21 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000218147
AA Change: E30G

PolyPhen 2 Score 0.290 (Sensitivity: 0.91; Specificity: 0.88)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220090
Predicted Effect noncoding transcript
Transcript: ENSMUST00000223505
Meta Mutation Damage Score 0.5458 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 97.2%
  • 20x: 94.9%
Validation Efficiency 100% (49/49)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Serine palmitoyltransferase (SPT; EC 2.3.1.50) catalyzes the first committed and rate-limiting step in sphingolipid biosynthesis. SSSPTA is a small SPT subunit that stimulates SPT activity and confers acyl-CoA preference to the SPT catalytic heterodimer of SPTLC1 (MIM 605712) and either SPTLC2 (MIM 605713) or SPTLC3 (MIM 611120) (Han et al., 2009 [PubMed 19416851]).[supplied by OMIM, Nov 2010]
Allele List at MGI
Other mutations in this stock
Total: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930402K13Rik AGAGGAG AGAG X: 8,971,342 (GRCm39) probably benign Het
Caap1 A T 4: 94,389,380 (GRCm39) V318D probably damaging Het
Camsap3 T C 8: 3,653,785 (GRCm39) L485P probably damaging Het
Ccsap T C 8: 124,586,100 (GRCm39) E17G possibly damaging Het
Cdk5rap2 C A 4: 70,153,674 (GRCm39) K1716N possibly damaging Het
Coq3 T C 4: 21,892,941 (GRCm39) probably benign Het
Daam2 T A 17: 49,776,766 (GRCm39) D773V probably damaging Het
F11 A G 8: 45,701,675 (GRCm39) S353P probably damaging Het
Fam209 T C 2: 172,315,915 (GRCm39) S97P probably benign Het
Fam50b G A 13: 34,930,869 (GRCm39) R115H probably damaging Het
Fbxo31 A G 8: 122,305,248 (GRCm39) F83L probably damaging Het
Fsip2 G T 2: 82,819,311 (GRCm39) A5015S possibly damaging Het
Galnt13 A G 2: 54,988,669 (GRCm39) H497R probably damaging Het
Ggnbp2 A G 11: 84,744,920 (GRCm39) C201R possibly damaging Het
Gm8730 T C 8: 103,591,664 (GRCm39) noncoding transcript Het
Gsr A G 8: 34,161,565 (GRCm39) K124R probably benign Het
Hdgf T C 3: 87,821,804 (GRCm39) S140P probably benign Het
Iqcg C T 16: 32,849,411 (GRCm39) E292K probably damaging Het
Lamb1 C T 12: 31,371,074 (GRCm39) A1375V probably null Het
Lct T C 1: 128,231,963 (GRCm39) M629V probably damaging Het
Lonp1 A G 17: 56,925,310 (GRCm39) probably benign Het
Mrc2 G A 11: 105,239,257 (GRCm39) probably null Het
Or6c212 A T 10: 129,558,984 (GRCm39) V143D probably damaging Het
Pcdhb9 T C 18: 37,534,654 (GRCm39) L216P possibly damaging Het
Ppp3cb A G 14: 20,581,010 (GRCm39) probably null Het
Ptprm G A 17: 67,263,855 (GRCm39) P464L possibly damaging Het
Rars2 A G 4: 34,645,787 (GRCm39) T235A probably benign Het
Rimkla A T 4: 119,334,986 (GRCm39) probably null Het
Rnf216 A T 5: 143,013,701 (GRCm39) I708N probably damaging Het
Six5 T A 7: 18,830,855 (GRCm39) V494E possibly damaging Het
Slc43a2 A G 11: 75,433,980 (GRCm39) probably benign Het
Slmap C A 14: 26,148,397 (GRCm39) R671S probably damaging Het
Smarcal1 T C 1: 72,665,755 (GRCm39) F751S possibly damaging Het
Sptan1 G A 2: 29,908,431 (GRCm39) D1711N possibly damaging Het
Taf1c A G 8: 120,329,809 (GRCm39) F111L probably damaging Het
Thbs1 A G 2: 117,945,191 (GRCm39) I255V probably benign Het
Tmem19 A G 10: 115,195,675 (GRCm39) probably benign Het
Tmem59l A G 8: 70,939,951 (GRCm39) L6S unknown Het
Tmod1 T C 4: 46,097,026 (GRCm39) V273A probably benign Het
Trpm8 A T 1: 88,255,918 (GRCm39) Y191F probably benign Het
Ube4a T C 9: 44,844,621 (GRCm39) I934V probably damaging Het
Vpreb3 G A 10: 75,779,125 (GRCm39) probably null Het
Vwf G T 6: 125,654,911 (GRCm39) probably benign Het
Wdr53 T C 16: 32,075,538 (GRCm39) C248R probably benign Het
Zfp217 A G 2: 169,961,130 (GRCm39) V399A probably damaging Het
Zfp980 G A 4: 145,428,653 (GRCm39) G461S probably benign Het
Other mutations in Sptssa
AlleleSourceChrCoordTypePredicted EffectPPH Score
R2913:Sptssa UTSW 12 54,703,267 (GRCm39) start codon destroyed probably null 0.86
R3725:Sptssa UTSW 12 54,703,180 (GRCm39) missense probably damaging 1.00
R6645:Sptssa UTSW 12 54,693,275 (GRCm39) missense probably damaging 1.00
R7743:Sptssa UTSW 12 54,703,201 (GRCm39) missense possibly damaging 0.68
R8771:Sptssa UTSW 12 54,703,211 (GRCm39) missense probably damaging 1.00
X0026:Sptssa UTSW 12 54,703,189 (GRCm39) missense probably damaging 0.97
Predicted Primers PCR Primer
(F):5'- AATCAGGATGCCTCCACCTTG -3'
(R):5'- CTTGGCCAATAAGCGCAAG -3'

Sequencing Primer
(F):5'- CCTTGGGCAGGGGAATTGC -3'
(R):5'- TTGGGCGTACACGGTGAC -3'
Posted On 2015-03-18