Incidental Mutation 'R2913:Sptssa'
ID 334565
Institutional Source Beutler Lab
Gene Symbol Sptssa
Ensembl Gene ENSMUSG00000044408
Gene Name serine palmitoyltransferase, small subunit A
Synonyms 1110002B05Rik
MMRRC Submission 040500-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2913 (G1)
Quality Score 41
Status Validated
Chromosome 12
Chromosomal Location 54692177-54703358 bp(-) (GRCm39)
Type of Mutation start codon destroyed
DNA Base Change (assembly) A to T at 54703267 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 1 (M1K)
Ref Sequence ENSEMBL: ENSMUSP00000053671 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056228] [ENSMUST00000218147]
AlphaFold Q8R207
Predicted Effect probably null
Transcript: ENSMUST00000056228
AA Change: M1K

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000053671
Gene: ENSMUSG00000044408
AA Change: M1K

DomainStartEndE-ValueType
Pfam:DUF3317 10 63 9.9e-21 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000218147
AA Change: M1K

PolyPhen 2 Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220090
Predicted Effect noncoding transcript
Transcript: ENSMUST00000223505
Meta Mutation Damage Score 0.1839 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.5%
  • 20x: 95.7%
Validation Efficiency 100% (58/58)
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: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acap2 T C 16: 30,934,887 (GRCm39) Q357R probably damaging Het
Adap1 C T 5: 139,260,576 (GRCm39) probably null Het
Adgrf3 A G 5: 30,401,992 (GRCm39) S679P probably damaging Het
Aldh3b1 T C 19: 3,971,275 (GRCm39) probably benign Het
Arih2 A G 9: 108,521,275 (GRCm39) S68P probably damaging Het
Cdcp3 T C 7: 130,783,753 (GRCm39) S49P possibly damaging Het
Col1a2 C T 6: 4,519,923 (GRCm39) probably benign Het
Cplane1 T C 15: 8,300,169 (GRCm39) S3159P unknown Het
Crocc C T 4: 140,747,661 (GRCm39) R1496H probably damaging Het
Cryl1 T C 14: 57,513,375 (GRCm39) E282G probably benign Het
Cyp11b1 T C 15: 74,708,270 (GRCm39) T402A probably damaging Het
Etfa C A 9: 55,389,613 (GRCm39) A254S probably damaging Het
Fcgbpl1 A T 7: 27,863,732 (GRCm39) L2501F probably damaging Het
Fdxacb1 C T 9: 50,679,699 (GRCm39) A39V probably benign Het
Fras1 G A 5: 96,881,774 (GRCm39) R2502K probably benign Het
Gpr157 G A 4: 150,183,222 (GRCm39) V131I probably benign Het
Hbb-bh1 C T 7: 103,492,254 (GRCm39) E22K possibly damaging Het
Hmcn2 A G 2: 31,350,222 (GRCm39) T5040A possibly damaging Het
Hprt1 T C X: 52,109,016 (GRCm39) Y174H probably damaging Het
Igsf10 T A 3: 59,239,157 (GRCm39) L341F possibly damaging Het
Ints1 A G 5: 139,743,668 (GRCm39) S1592P possibly damaging Het
Itgam T C 7: 127,711,578 (GRCm39) I641T probably damaging Het
Macf1 T A 4: 123,369,704 (GRCm39) I121F probably damaging Het
Mapk3 T A 7: 126,359,978 (GRCm39) C19* probably null Het
Mapk4 C T 18: 74,068,236 (GRCm39) A232T probably benign Het
Med26 T G 8: 73,249,956 (GRCm39) K381T possibly damaging Het
Mki67 T C 7: 135,302,415 (GRCm39) E873G possibly damaging Het
Mrgpra9 T C 7: 46,884,828 (GRCm39) I280V probably benign Het
Mroh9 T C 1: 162,871,572 (GRCm39) Y637C probably damaging Het
Nktr T C 9: 121,578,670 (GRCm39) probably benign Het
Or4c11 A T 2: 88,695,458 (GRCm39) N170Y probably benign Het
Or5j3 A G 2: 86,128,733 (GRCm39) D191G probably damaging Het
Pam A C 1: 97,850,854 (GRCm39) L168R probably damaging Het
Pikfyve G A 1: 65,292,676 (GRCm39) V1376M probably damaging Het
Pomt2 A T 12: 87,175,743 (GRCm39) N400K probably damaging Het
Pramel13 T C 4: 144,119,304 (GRCm39) E421G probably damaging Het
Rbm45 C T 2: 76,205,798 (GRCm39) P217S probably benign Het
Rc3h2 A G 2: 37,268,971 (GRCm39) S832P possibly damaging Het
Ric3 A G 7: 108,653,660 (GRCm39) F144L possibly damaging Het
Rrh G T 3: 129,609,258 (GRCm39) A83E probably damaging Het
Rspo2 T A 15: 42,941,510 (GRCm39) T138S probably benign Het
Skint5 A G 4: 113,381,289 (GRCm39) probably benign Het
Snx29 C T 16: 11,265,317 (GRCm39) R516W probably damaging Het
Spata31d1d T C 13: 59,874,769 (GRCm39) E922G possibly damaging Het
Spc25 T C 2: 69,030,331 (GRCm39) H104R probably benign Het
Srrm2 G T 17: 24,034,658 (GRCm39) probably benign Het
Tcof1 T C 18: 60,949,156 (GRCm39) D1253G possibly damaging Het
Tmem181c-ps A G 17: 6,888,608 (GRCm39) noncoding transcript Het
Tmprss15 T C 16: 78,759,078 (GRCm39) N880S probably benign Het
Trio T A 15: 27,854,998 (GRCm39) Q728L probably damaging Het
Txk T C 5: 72,881,794 (GRCm39) N154S probably damaging Het
Vwf T A 6: 125,662,809 (GRCm39) V2731E probably benign Het
Yes1 T C 5: 32,797,926 (GRCm39) S82P probably benign Het
Zgrf1 T C 3: 127,392,356 (GRCm39) V1292A possibly damaging Het
Other mutations in Sptssa
AlleleSourceChrCoordTypePredicted EffectPPH Score
R3725:Sptssa UTSW 12 54,703,180 (GRCm39) missense probably damaging 1.00
R3726: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'- ATTGCGTACAAGACCCGGATC -3'
(R):5'- CTTGGCCAATAAGCGCAAG -3'

Sequencing Primer
(F):5'- GATCTCCGCGGTTCCAC -3'
(R):5'- GCAAGCCAGGAGGAGCC -3'
Posted On 2015-09-02