Incidental Mutation 'R1216:Smpdl3a'
ID 99653
Institutional Source Beutler Lab
Gene Symbol Smpdl3a
Ensembl Gene ENSMUSG00000019872
Gene Name sphingomyelin phosphodiesterase, acid-like 3A
Synonyms ASM3A, 0610010C24Rik, ASML3A
MMRRC Submission 039285-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1216 (G1)
Quality Score 225
Status Validated
Chromosome 10
Chromosomal Location 57670640-57687926 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 57678575 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Serine at position 126 (I126S)
Ref Sequence ENSEMBL: ENSMUSP00000020022 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020022] [ENSMUST00000151623]
AlphaFold P70158
Predicted Effect probably null
Transcript: ENSMUST00000020022
AA Change: I126S

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000020022
Gene: ENSMUSG00000019872
AA Change: I126S

DomainStartEndE-ValueType
signal peptide 1 22 N/A INTRINSIC
Pfam:Metallophos 35 294 1.7e-16 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125076
Predicted Effect probably null
Transcript: ENSMUST00000151623
AA Change: I96S

PolyPhen 2 Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)
Meta Mutation Damage Score 0.8036 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 96.1%
  • 20x: 92.3%
Validation Efficiency 98% (45/46)
Allele List at MGI
Other mutations in this stock
Total: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A830018L16Rik A T 1: 11,868,716 (GRCm39) D332V probably damaging Het
Akr1c12 T C 13: 4,326,322 (GRCm39) Y53C probably benign Het
Arhgap23 T C 11: 97,383,498 (GRCm39) probably benign Het
AU040320 T C 4: 126,710,276 (GRCm39) probably benign Het
B4galnt2 A G 11: 95,782,767 (GRCm39) L15P probably benign Het
Cadps2 A G 6: 23,583,472 (GRCm39) probably benign Het
Cul9 C G 17: 46,833,101 (GRCm39) A1326P probably damaging Het
Dppa4 T C 16: 48,113,343 (GRCm39) F244S possibly damaging Het
Exoc1 A G 5: 76,702,035 (GRCm39) K445R probably benign Het
Fam47e A G 5: 92,710,343 (GRCm39) E114G probably damaging Het
Fgf12 A T 16: 27,981,202 (GRCm39) N171K possibly damaging Het
Fyb2 G A 4: 104,852,903 (GRCm39) V528M possibly damaging Het
Ghr A G 15: 3,349,337 (GRCm39) S614P probably damaging Het
Gm10985 A C 3: 53,752,674 (GRCm39) Y19S probably damaging Het
Gpr152 T A 19: 4,193,554 (GRCm39) V365D possibly damaging Het
Guca1a A G 17: 47,706,637 (GRCm39) probably benign Het
Hivep1 G A 13: 42,310,997 (GRCm39) G1079D probably benign Het
Hnrnpm T C 17: 33,868,687 (GRCm39) D580G probably damaging Het
Ints6 A T 14: 62,945,147 (GRCm39) D394E probably damaging Het
Kat6b T A 14: 21,672,108 (GRCm39) Y339* probably null Het
Kcnj11 C A 7: 45,749,285 (GRCm39) V13L probably benign Het
Lama3 C T 18: 12,554,191 (GRCm39) probably benign Het
Mtrex A G 13: 113,050,876 (GRCm39) probably benign Het
Myo18a A G 11: 77,709,473 (GRCm39) T161A probably benign Het
Ncapg G T 5: 45,857,261 (GRCm39) S991I possibly damaging Het
Nrde2 G A 12: 100,116,069 (GRCm39) probably benign Het
Or4c127 T A 2: 89,832,822 (GRCm39) I24N probably benign Het
Or5d18 T C 2: 87,864,602 (GRCm39) R294G probably damaging Het
Pcdhb7 A T 18: 37,476,927 (GRCm39) T688S probably damaging Het
Pla2g6 T C 15: 79,190,635 (GRCm39) D309G probably benign Het
Plod1 A T 4: 148,005,584 (GRCm39) V404D probably damaging Het
Ppp2r2a G T 14: 67,266,447 (GRCm39) Y71* probably null Het
Prcp A G 7: 92,566,954 (GRCm39) N222S probably benign Het
Rad21 T C 15: 51,833,532 (GRCm39) T316A possibly damaging Het
Ranbp2 T C 10: 58,319,034 (GRCm39) probably benign Het
Rapgef4 C A 2: 72,038,492 (GRCm39) P548T possibly damaging Het
Ric1 G T 19: 29,555,135 (GRCm39) M416I probably benign Het
Slc9a8 T C 2: 167,266,041 (GRCm39) F6S probably benign Het
Sphkap A T 1: 83,268,698 (GRCm39) L98Q probably damaging Het
Spink4 T G 4: 40,924,974 (GRCm39) probably benign Het
Taar5 A T 10: 23,847,605 (GRCm39) L334F probably damaging Het
Tecta A T 9: 42,289,203 (GRCm39) I454K probably benign Het
Ttc7 C T 17: 87,654,006 (GRCm39) T561M possibly damaging Het
Vmn2r9 G T 5: 108,995,440 (GRCm39) H403N probably damaging Het
Zdbf2 G A 1: 63,342,161 (GRCm39) C180Y possibly damaging Het
Other mutations in Smpdl3a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00561:Smpdl3a APN 10 57,684,042 (GRCm39) missense probably benign 0.01
IGL01530:Smpdl3a APN 10 57,683,989 (GRCm39) missense probably damaging 1.00
IGL01936:Smpdl3a APN 10 57,678,530 (GRCm39) missense probably damaging 1.00
IGL02342:Smpdl3a APN 10 57,685,276 (GRCm39) splice site probably benign
IGL02372:Smpdl3a APN 10 57,683,611 (GRCm39) missense probably benign 0.05
IGL02827:Smpdl3a APN 10 57,678,592 (GRCm39) missense probably damaging 1.00
R0462:Smpdl3a UTSW 10 57,670,827 (GRCm39) missense probably benign 0.07
R0658:Smpdl3a UTSW 10 57,687,336 (GRCm39) missense probably damaging 0.99
R1502:Smpdl3a UTSW 10 57,685,187 (GRCm39) missense probably damaging 1.00
R1559:Smpdl3a UTSW 10 57,683,588 (GRCm39) missense probably damaging 0.99
R1807:Smpdl3a UTSW 10 57,677,118 (GRCm39) missense probably damaging 0.99
R2872:Smpdl3a UTSW 10 57,678,626 (GRCm39) missense possibly damaging 0.51
R2872:Smpdl3a UTSW 10 57,678,626 (GRCm39) missense possibly damaging 0.51
R2877:Smpdl3a UTSW 10 57,685,181 (GRCm39) missense probably damaging 1.00
R4799:Smpdl3a UTSW 10 57,684,111 (GRCm39) missense probably damaging 1.00
R4814:Smpdl3a UTSW 10 57,687,337 (GRCm39) missense probably damaging 1.00
R4916:Smpdl3a UTSW 10 57,677,127 (GRCm39) missense probably damaging 1.00
R5137:Smpdl3a UTSW 10 57,677,163 (GRCm39) missense possibly damaging 0.93
R5778:Smpdl3a UTSW 10 57,677,097 (GRCm39) missense probably damaging 0.98
R5781:Smpdl3a UTSW 10 57,684,034 (GRCm39) missense possibly damaging 0.78
R5917:Smpdl3a UTSW 10 57,681,654 (GRCm39) splice site probably null
R6044:Smpdl3a UTSW 10 57,687,358 (GRCm39) missense possibly damaging 0.82
R6773:Smpdl3a UTSW 10 57,678,533 (GRCm39) missense probably damaging 0.99
R6863:Smpdl3a UTSW 10 57,684,107 (GRCm39) nonsense probably null
R7480:Smpdl3a UTSW 10 57,678,574 (GRCm39) missense possibly damaging 0.87
R7731:Smpdl3a UTSW 10 57,678,650 (GRCm39) missense probably damaging 1.00
R7923:Smpdl3a UTSW 10 57,677,141 (GRCm39) missense probably damaging 1.00
R8120:Smpdl3a UTSW 10 57,683,547 (GRCm39) missense probably damaging 1.00
R8344:Smpdl3a UTSW 10 57,677,073 (GRCm39) missense possibly damaging 0.81
R8377:Smpdl3a UTSW 10 57,677,032 (GRCm39) missense possibly damaging 0.88
R8712:Smpdl3a UTSW 10 57,687,526 (GRCm39) missense probably benign 0.44
R8876:Smpdl3a UTSW 10 57,685,166 (GRCm39) missense probably damaging 1.00
R9003:Smpdl3a UTSW 10 57,683,977 (GRCm39) missense probably damaging 1.00
R9145:Smpdl3a UTSW 10 57,677,028 (GRCm39) missense possibly damaging 0.76
R9266:Smpdl3a UTSW 10 57,678,596 (GRCm39) missense possibly damaging 0.51
Z1176:Smpdl3a UTSW 10 57,681,714 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GCTGATCCTGTGGAATAGGCAGTG -3'
(R):5'- CAGGAATGCTTCCTTATACGCCACC -3'

Sequencing Primer
(F):5'- gctcaaaccatcccttgcttc -3'
(R):5'- CCACTGTCATAACTCTGACACTG -3'
Posted On 2014-01-15