Incidental Mutation 'R6645:Sptssa'
ID 526084
Institutional Source Beutler Lab
Gene Symbol Sptssa
Ensembl Gene ENSMUSG00000044408
Gene Name serine palmitoyltransferase, small subunit A
Synonyms 1110002B05Rik
MMRRC Submission 044766-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6645 (G1)
Quality Score 225.009
Status Not validated
Chromosome 12
Chromosomal Location 54692177-54703358 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 54693275 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 53 (Y53C)
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: Y53C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000053671
Gene: ENSMUSG00000044408
AA Change: Y53C

DomainStartEndE-ValueType
Pfam:DUF3317 10 63 9.9e-21 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000197752
Predicted Effect probably benign
Transcript: ENSMUST00000218147
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220090
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.0%
  • 20x: 93.9%
Validation Efficiency
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: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Anp32e T A 3: 95,844,414 (GRCm39) F95I probably damaging Het
Arap1 A G 7: 101,057,318 (GRCm39) K628R possibly damaging Het
Arid4b A T 13: 14,294,737 (GRCm39) E6D probably damaging Het
Atxn10 G T 15: 85,260,904 (GRCm39) probably null Het
Ccdc170 A G 10: 4,510,974 (GRCm39) I678V possibly damaging Het
Ccdc18 T A 5: 108,286,796 (GRCm39) V110D probably benign Het
Cep85l C T 10: 53,177,768 (GRCm39) E322K probably benign Het
Cilp A T 9: 65,186,587 (GRCm39) Y894F possibly damaging Het
Ddx4 A G 13: 112,777,708 (GRCm39) S62P possibly damaging Het
Dph7 T C 2: 24,855,663 (GRCm39) V154A probably benign Het
Ephb6 T C 6: 41,594,206 (GRCm39) S579P probably benign Het
Fam53a G T 5: 33,758,128 (GRCm39) Q332K probably benign Het
Fancm A G 12: 65,152,874 (GRCm39) D1110G probably damaging Het
Fh1 A T 1: 175,442,442 (GRCm39) V136E possibly damaging Het
Greb1 G T 12: 16,748,580 (GRCm39) H1132Q probably benign Het
Jph1 A G 1: 17,161,985 (GRCm39) S226P probably damaging Het
Kbtbd8 C T 6: 95,103,730 (GRCm39) R460* probably null Het
Lama5 T A 2: 179,821,463 (GRCm39) N3059Y probably damaging Het
Lipc G A 9: 70,711,030 (GRCm39) T289I probably damaging Het
Lrrc2 T C 9: 110,799,175 (GRCm39) W241R probably damaging Het
Mfn2 T A 4: 147,979,069 (GRCm39) I88F probably damaging Het
Mms19 G C 19: 41,943,630 (GRCm39) N366K probably benign Het
Myo15a A G 11: 60,368,118 (GRCm39) T293A probably benign Het
Ndfip2 T A 14: 105,529,707 (GRCm39) Y179N probably damaging Het
Notch4 A G 17: 34,806,790 (GRCm39) D1909G probably benign Het
Obscn C T 11: 58,976,088 (GRCm39) S2013N probably damaging Het
Oca2 G T 7: 55,964,522 (GRCm39) A357S probably benign Het
Or8b43 T C 9: 38,360,219 (GRCm39) L17S probably damaging Het
Or8g35 T A 9: 39,381,562 (GRCm39) L153F probably benign Het
Pde7b C A 10: 20,486,312 (GRCm39) probably null Het
Ppef2 T C 5: 92,378,320 (GRCm39) N625S probably benign Het
Prom1 A T 5: 44,204,856 (GRCm39) L192Q probably damaging Het
Satb2 T C 1: 56,836,166 (GRCm39) I542V possibly damaging Het
Sgpp2 C T 1: 78,336,799 (GRCm39) T59M probably damaging Het
Skint6 T C 4: 112,749,235 (GRCm39) T782A possibly damaging Het
Slc13a4 G T 6: 35,245,774 (GRCm39) Q624K probably benign Het
Slc9a3 T A 13: 74,312,291 (GRCm39) H629Q probably damaging Het
Slitrk3 G T 3: 72,957,194 (GRCm39) A526E probably benign Het
Spata31e2 T A 1: 26,722,198 (GRCm39) D994V probably benign Het
Srsf10 T C 4: 135,590,874 (GRCm39) S159P possibly damaging Het
Tbce T C 13: 14,179,814 (GRCm39) T341A probably benign Het
Tdrd6 A G 17: 43,935,423 (GRCm39) L1875P probably benign Het
Tkt G A 14: 30,292,168 (GRCm39) G425R probably damaging Het
Tmprss7 T C 16: 45,511,326 (GRCm39) I17M possibly damaging Het
Ttc21b T C 2: 66,066,721 (GRCm39) S311G probably benign Het
Ubr5 A G 15: 38,029,750 (GRCm39) Y492H probably damaging Het
Ush2a T C 1: 188,255,528 (GRCm39) I1535T probably damaging Het
Vmn2r17 A T 5: 109,576,247 (GRCm39) N373Y probably damaging Het
Vmn2r6 A T 3: 64,464,297 (GRCm39) V179E probably damaging Het
Vps13b A G 15: 35,910,451 (GRCm39) E3405G probably benign Het
Wac A T 18: 7,973,523 (GRCm39) Q212H probably damaging Het
Washc4 C T 10: 83,408,059 (GRCm39) R555* probably null Het
Zmat4 G A 8: 24,287,417 (GRCm39) probably null 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
R3726:Sptssa UTSW 12 54,703,180 (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'- TTATAAGGTTGGTCACGTGGAC -3'
(R):5'- GTTGTCATGGTGAGTACCCC -3'

Sequencing Primer
(F):5'- GTGGACATCCGTAGCACATCTTAC -3'
(R):5'- CTTAACCATCACGCAGATTC -3'
Posted On 2018-06-22