Incidental Mutation 'R3683:Smpd1'
ID 269425
Institutional Source Beutler Lab
Gene Symbol Smpd1
Ensembl Gene ENSMUSG00000037049
Gene Name sphingomyelin phosphodiesterase 1, acid lysosomal
Synonyms ASM, A-SMase, Zn-SMase, aSMase, acid sphingomyelinase
MMRRC Submission 040681-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.305) question?
Stock # R3683 (G1)
Quality Score 225
Status Not validated
Chromosome 7
Chromosomal Location 105203567-105207596 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 105204609 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Serine at position 163 (C163S)
Ref Sequence ENSEMBL: ENSMUSP00000042187 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046983] [ENSMUST00000081165] [ENSMUST00000186814] [ENSMUST00000187057] [ENSMUST00000188001] [ENSMUST00000188368] [ENSMUST00000189072] [ENSMUST00000189378] [ENSMUST00000190369] [ENSMUST00000191601] [ENSMUST00000191011] [ENSMUST00000189265]
AlphaFold Q04519
Predicted Effect probably damaging
Transcript: ENSMUST00000046983
AA Change: C163S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000042187
Gene: ENSMUSG00000037049
AA Change: C163S

DomainStartEndE-ValueType
transmembrane domain 30 52 N/A INTRINSIC
SapB 85 163 1.05e-7 SMART
low complexity region 177 196 N/A INTRINSIC
Pfam:Metallophos 197 459 4.4e-21 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000081165
SMART Domains Protein: ENSMUSP00000079932
Gene: ENSMUSG00000037032

DomainStartEndE-ValueType
low complexity region 146 184 N/A INTRINSIC
WW 254 285 6.23e-5 SMART
low complexity region 287 299 N/A INTRINSIC
PTB 365 512 4.16e-38 SMART
PTB 538 667 1.76e-36 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000186814
Predicted Effect probably benign
Transcript: ENSMUST00000187057
SMART Domains Protein: ENSMUSP00000139899
Gene: ENSMUSG00000037032

DomainStartEndE-ValueType
WW 31 62 3.7e-7 SMART
low complexity region 64 76 N/A INTRINSIC
PTB 142 287 3.8e-41 SMART
PTB 313 442 9.5e-39 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000188001
Predicted Effect probably benign
Transcript: ENSMUST00000188368
SMART Domains Protein: ENSMUSP00000139788
Gene: ENSMUSG00000037032

DomainStartEndE-ValueType
WW 31 62 3.7e-7 SMART
low complexity region 64 76 N/A INTRINSIC
PTB 142 289 1.8e-40 SMART
PTB 315 444 9.5e-39 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000189072
SMART Domains Protein: ENSMUSP00000139575
Gene: ENSMUSG00000037032

DomainStartEndE-ValueType
Pfam:WW 1 24 8.1e-5 PFAM
low complexity region 28 40 N/A INTRINSIC
PTB 106 253 1.8e-40 SMART
PTB 279 408 9.5e-39 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000210934
Predicted Effect noncoding transcript
Transcript: ENSMUST00000191250
Predicted Effect probably benign
Transcript: ENSMUST00000211614
Predicted Effect noncoding transcript
Transcript: ENSMUST00000211307
Predicted Effect probably benign
Transcript: ENSMUST00000189378
SMART Domains Protein: ENSMUSP00000140979
Gene: ENSMUSG00000037032

DomainStartEndE-ValueType
low complexity region 146 184 N/A INTRINSIC
WW 254 285 6.23e-5 SMART
low complexity region 287 299 N/A INTRINSIC
PTB 365 510 6.86e-39 SMART
PTB 536 665 1.76e-36 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000190369
SMART Domains Protein: ENSMUSP00000140486
Gene: ENSMUSG00000037032

DomainStartEndE-ValueType
Pfam:WW 1 24 8.1e-5 PFAM
low complexity region 28 40 N/A INTRINSIC
PTB 106 253 1.8e-40 SMART
PTB 279 408 9.5e-39 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000191601
SMART Domains Protein: ENSMUSP00000140116
Gene: ENSMUSG00000037032

DomainStartEndE-ValueType
low complexity region 146 184 N/A INTRINSIC
WW 254 285 3.7e-7 SMART
low complexity region 287 299 N/A INTRINSIC
PTB 365 512 1.8e-40 SMART
PTB 538 667 9.5e-39 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000191011
SMART Domains Protein: ENSMUSP00000140973
Gene: ENSMUSG00000037032

DomainStartEndE-ValueType
low complexity region 146 184 N/A INTRINSIC
WW 254 285 6.23e-5 SMART
low complexity region 287 299 N/A INTRINSIC
PTB 365 510 6.86e-39 SMART
PTB 536 665 1.76e-36 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000189265
SMART Domains Protein: ENSMUSP00000140137
Gene: ENSMUSG00000037032

DomainStartEndE-ValueType
Pfam:PID 1 34 2.3e-6 PFAM
PTB 63 192 9.5e-39 SMART
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.5%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a lysosomal acid sphingomyelinase that converts sphingomyelin to ceramide. The encoded protein also has phospholipase C activity. Defects in this gene are a cause of Niemann-Pick disease type A (NPA) and Niemann-Pick disease type B (NPB). Multiple transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2010]
PHENOTYPE: Nullizygous mutations cause tremors, ataxia, altered lipid homeostasis, increased foam cell number, Purkinje cell loss and premature death, and may lead to hepatosplenomegaly, hunched posture, reduced weight, abnormal apoptosis, sperm defects, dyspnea, and high susceptibility to bacterial infection. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930595M18Rik T C X: 80,463,841 (GRCm39) D622G possibly damaging Het
Acad11 T C 9: 103,992,543 (GRCm39) I495T probably damaging Het
Acat1 C T 9: 53,498,765 (GRCm39) A307T probably damaging Het
Ahdc1 T C 4: 132,793,013 (GRCm39) L1418P possibly damaging Het
Bmp2 T A 2: 133,396,392 (GRCm39) V16D probably benign Het
Cables2 G A 2: 179,906,263 (GRCm39) R121* probably null Het
Calb2 A G 8: 110,883,620 (GRCm39) Y35H probably benign Het
Cdon A G 9: 35,400,328 (GRCm39) E1014G possibly damaging Het
Clcn7 T C 17: 25,369,567 (GRCm39) L301P possibly damaging Het
Corin T C 5: 72,488,198 (GRCm39) D610G probably damaging Het
Csrnp2 A T 15: 100,379,879 (GRCm39) S471T probably benign Het
Dnah7a C A 1: 53,483,675 (GRCm39) M3367I probably benign Het
Elp4 A T 2: 105,533,106 (GRCm39) M413K possibly damaging Het
Fat1 A G 8: 45,470,975 (GRCm39) D1593G probably benign Het
Fbxw24 G A 9: 109,437,110 (GRCm39) P259L possibly damaging Het
Ggta1 T A 2: 35,298,000 (GRCm39) T162S probably benign Het
Gldn G A 9: 54,245,624 (GRCm39) E392K possibly damaging Het
Klra9 T C 6: 130,168,260 (GRCm39) N2S probably benign Het
Lama1 A G 17: 68,075,328 (GRCm39) D1015G probably benign Het
Lct T C 1: 128,231,963 (GRCm39) M629V probably damaging Het
Myg1 G C 15: 102,246,171 (GRCm39) G349R probably damaging Het
Nrxn1 T C 17: 90,930,880 (GRCm39) D779G probably damaging Het
Or2d3c G A 7: 106,526,301 (GRCm39) R122* probably null Het
Or4a73 C A 2: 89,421,099 (GRCm39) R120L probably damaging Het
Or4c118 A T 2: 88,975,364 (GRCm39) M1K probably null Het
Or5d37 T A 2: 87,923,603 (GRCm39) I226F probably damaging Het
Osmr A C 15: 6,866,534 (GRCm39) V380G possibly damaging Het
Phf21b A G 15: 84,682,891 (GRCm39) I222T probably damaging Het
Ptprq G T 10: 107,544,489 (GRCm39) T347K probably benign Het
Sema6d G T 2: 124,496,146 (GRCm39) L63F possibly damaging Het
Serpinb9b C T 13: 33,213,581 (GRCm39) A46V probably damaging Het
Sf3b3 A G 8: 111,540,253 (GRCm39) probably null Het
Stat4 C T 1: 52,052,981 (GRCm39) T54I possibly damaging Het
Tacc2 A G 7: 130,226,800 (GRCm39) S1162G probably benign Het
Tbc1d20 C T 2: 152,153,737 (GRCm39) T354I probably benign Het
Tbc1d31 T C 15: 57,815,210 (GRCm39) probably null Het
Tmcc1 C CAT 6: 116,019,831 (GRCm39) probably null Het
Tmem181a T A 17: 6,346,061 (GRCm39) L185H probably damaging Het
Unc79 T A 12: 103,041,062 (GRCm39) N698K probably benign Het
Utrn A G 10: 12,542,579 (GRCm39) M1802T probably benign Het
Vmn1r8 A C 6: 57,013,260 (GRCm39) T104P probably damaging Het
Vmn2r13 C A 5: 109,304,721 (GRCm39) R570I probably damaging Het
Zfand6 G A 7: 84,283,570 (GRCm39) P11S probably damaging Het
Zfp1005 A G 2: 150,109,976 (GRCm39) K222R probably benign Het
Zmpste24 A G 4: 120,918,288 (GRCm39) F445L probably damaging Het
Other mutations in Smpd1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00493:Smpd1 APN 7 105,205,848 (GRCm39) missense probably damaging 0.99
IGL01147:Smpd1 APN 7 105,204,943 (GRCm39) missense probably damaging 1.00
IGL01526:Smpd1 APN 7 105,203,982 (GRCm39) missense probably benign 0.01
IGL01541:Smpd1 APN 7 105,205,033 (GRCm39) missense possibly damaging 0.48
IGL01619:Smpd1 APN 7 105,204,549 (GRCm39) missense possibly damaging 0.89
IGL01924:Smpd1 APN 7 105,204,655 (GRCm39) missense probably benign 0.01
IGL03004:Smpd1 APN 7 105,205,881 (GRCm39) missense possibly damaging 0.82
R0782:Smpd1 UTSW 7 105,204,550 (GRCm39) missense possibly damaging 0.80
R1445:Smpd1 UTSW 7 105,205,881 (GRCm39) missense possibly damaging 0.82
R1489:Smpd1 UTSW 7 105,205,761 (GRCm39) splice site probably null
R3685:Smpd1 UTSW 7 105,204,609 (GRCm39) missense probably damaging 1.00
R3977:Smpd1 UTSW 7 105,205,108 (GRCm39) missense probably benign 0.29
R4850:Smpd1 UTSW 7 105,205,192 (GRCm39) missense probably benign
R5084:Smpd1 UTSW 7 105,206,185 (GRCm39) missense probably damaging 1.00
R6316:Smpd1 UTSW 7 105,204,709 (GRCm39) missense probably benign 0.19
R6429:Smpd1 UTSW 7 105,206,135 (GRCm39) missense probably damaging 1.00
R6672:Smpd1 UTSW 7 105,204,480 (GRCm39) missense probably benign
R7156:Smpd1 UTSW 7 105,203,693 (GRCm39) unclassified probably benign
R7883:Smpd1 UTSW 7 105,206,192 (GRCm39) missense probably damaging 1.00
R8261:Smpd1 UTSW 7 105,204,520 (GRCm39) missense probably benign 0.01
R9287:Smpd1 UTSW 7 105,204,442 (GRCm39) missense probably benign 0.14
R9406:Smpd1 UTSW 7 105,203,750 (GRCm39) missense possibly damaging 0.62
R9461:Smpd1 UTSW 7 105,204,789 (GRCm39) missense probably damaging 1.00
R9496:Smpd1 UTSW 7 105,205,202 (GRCm39) critical splice donor site probably null
X0021:Smpd1 UTSW 7 105,206,852 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GCCAGGGTTCACTTGTTCTG -3'
(R):5'- TGGATCTGCACAGTAAGGGTCTG -3'

Sequencing Primer
(F):5'- ATTGGTTCCTTCCACCACAGAAG -3'
(R):5'- GGGTCTGTGCCCTCCAG -3'
Posted On 2015-02-19