Incidental Mutation 'IGL01526:Smpd1'
ID 89557
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Smpd1
Ensembl Gene ENSMUSG00000037049
Gene Name sphingomyelin phosphodiesterase 1, acid lysosomal
Synonyms ASM, A-SMase, Zn-SMase, aSMase, acid sphingomyelinase
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.305) question?
Stock # IGL01526
Quality Score
Status
Chromosome 7
Chromosomal Location 105203567-105207596 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 105203982 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tryptophan to Glycine at position 82 (W82G)
Ref Sequence ENSEMBL: ENSMUSP00000042187 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046983] [ENSMUST00000081165] [ENSMUST00000186814] [ENSMUST00000187057] [ENSMUST00000188001] [ENSMUST00000188368] [ENSMUST00000189265] [ENSMUST00000189378] [ENSMUST00000190369] [ENSMUST00000191601] [ENSMUST00000189072] [ENSMUST00000191011]
AlphaFold Q04519
Predicted Effect probably benign
Transcript: ENSMUST00000046983
AA Change: W82G

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000042187
Gene: ENSMUSG00000037049
AA Change: W82G

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 noncoding transcript
Transcript: ENSMUST00000211307
Predicted Effect noncoding transcript
Transcript: ENSMUST00000191250
Predicted Effect noncoding transcript
Transcript: ENSMUST00000210934
Predicted Effect probably benign
Transcript: ENSMUST00000211614
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
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: 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 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
Coding Region Coverage
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: 32 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1500002C15Rik G T 4: 155,818,628 (GRCm39) probably benign Het
4933430I17Rik G T 4: 62,450,858 (GRCm39) R107L possibly damaging Het
Acvr1 A T 2: 58,348,997 (GRCm39) D388E probably benign Het
Art3 T C 5: 92,562,199 (GRCm39) S354P probably damaging Het
Bpnt1 C A 1: 185,077,591 (GRCm39) S102* probably null Het
Ces1a G T 8: 93,771,726 (GRCm39) P24T probably damaging Het
Cfap65 A T 1: 74,950,237 (GRCm39) S1171T probably damaging Het
Cracd T A 5: 77,005,478 (GRCm39) M613K unknown Het
Csn2 T C 5: 87,842,838 (GRCm39) H47R possibly damaging Het
Gm14496 T A 2: 181,637,458 (GRCm39) D177E probably benign Het
Hmbs A G 9: 44,250,845 (GRCm39) V126A possibly damaging Het
Ica1l A G 1: 60,054,916 (GRCm39) M105T probably damaging Het
Morc2a G A 11: 3,600,428 (GRCm39) E17K probably benign Het
Mroh8 T C 2: 157,080,232 (GRCm39) probably benign Het
Mroh9 G T 1: 162,883,172 (GRCm39) L436I probably damaging Het
Nup54 T C 5: 92,565,334 (GRCm39) D461G probably benign Het
Or10ag2 A T 2: 87,249,319 (GRCm39) D309V probably damaging Het
Or2t45 A G 11: 58,669,123 (GRCm39) T57A probably benign Het
Pcid2 G A 8: 13,135,319 (GRCm39) probably benign Het
Ppp1r3b G T 8: 35,851,872 (GRCm39) R237L probably benign Het
Prdm11 A G 2: 92,843,102 (GRCm39) V119A probably damaging Het
S100a7l2 T A 3: 90,995,612 (GRCm39) probably benign Het
Serpina5 T A 12: 104,068,149 (GRCm39) V70E probably damaging Het
Skap2 C T 6: 51,884,894 (GRCm39) D249N probably benign Het
Slc22a29 A T 19: 8,184,542 (GRCm39) probably benign Het
Slc4a1ap C A 5: 31,685,571 (GRCm39) T283K possibly damaging Het
Slc6a21 T G 7: 44,937,220 (GRCm39) I575S probably damaging Het
Snx14 T A 9: 88,263,553 (GRCm39) M897L probably damaging Het
Tjp1 A G 7: 64,972,406 (GRCm39) V586A probably damaging Het
Tmc8 T C 11: 117,682,910 (GRCm39) probably benign Het
Trim34a A G 7: 103,909,706 (GRCm39) Y298C probably damaging Het
Ube3c T C 5: 29,872,960 (GRCm39) V1000A 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
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
R3683:Smpd1 UTSW 7 105,204,609 (GRCm39) missense probably damaging 1.00
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
Posted On 2013-12-03