Incidental Mutation 'IGL01541:Smpd1'
ID 90155
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 # IGL01541
Quality Score
Status
Chromosome 7
Chromosomal Location 105203567-105207596 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 105205033 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Serine at position 304 (F304S)
Ref Sequence ENSEMBL: ENSMUSP00000042187 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046983] [ENSMUST00000081165] [ENSMUST00000186814] [ENSMUST00000187057] [ENSMUST00000188001] [ENSMUST00000188368] [ENSMUST00000191601] [ENSMUST00000189072] [ENSMUST00000191011] [ENSMUST00000189378] [ENSMUST00000190369] [ENSMUST00000189265]
AlphaFold Q04519
Predicted Effect possibly damaging
Transcript: ENSMUST00000046983
AA Change: F304S

PolyPhen 2 Score 0.478 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000042187
Gene: ENSMUSG00000037049
AA Change: F304S

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: ENSMUST00000191250
Predicted Effect noncoding transcript
Transcript: ENSMUST00000210934
Predicted Effect noncoding transcript
Transcript: ENSMUST00000211307
Predicted Effect probably benign
Transcript: ENSMUST00000211614
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
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: 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
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: 39 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb5 G A 12: 118,875,169 (GRCm39) H668Y probably benign Het
Adamts10 A G 17: 33,762,205 (GRCm39) S505G probably benign Het
Ahnak C T 19: 8,985,243 (GRCm39) H2176Y possibly damaging Het
Ash1l G T 3: 88,973,572 (GRCm39) D2544Y probably damaging Het
Ccdc88a T A 11: 29,350,283 (GRCm39) F88L probably benign Het
Cdc42bpa A T 1: 179,978,723 (GRCm39) probably null Het
Celsr3 T C 9: 108,708,907 (GRCm39) V1251A probably damaging Het
CN725425 T A 15: 91,129,955 (GRCm39) F273I possibly damaging Het
Eif2b1 A G 5: 124,714,965 (GRCm39) C104R probably damaging Het
Ercc3 A T 18: 32,381,372 (GRCm39) D396V possibly damaging Het
Fga A T 3: 82,940,014 (GRCm39) D556V probably damaging Het
Frg1 C T 8: 41,863,362 (GRCm39) probably benign Het
Fto T C 8: 92,136,376 (GRCm39) Y217H probably damaging Het
Garin4 A T 1: 190,896,606 (GRCm39) Y12* probably null Het
Grin3a A T 4: 49,792,533 (GRCm39) V400E probably damaging Het
Gtse1 T A 15: 85,759,855 (GRCm39) L682* probably null Het
Igkv6-32 A G 6: 70,051,290 (GRCm39) I22T probably benign Het
Lama1 G A 17: 68,092,065 (GRCm39) R1646H probably benign Het
Lamp1 T C 8: 13,215,905 (GRCm39) C35R probably damaging Het
Lzts3 A T 2: 130,478,126 (GRCm39) L324Q probably damaging Het
Muc6 T A 7: 141,236,069 (GRCm39) R453* probably null Het
Naa35 T A 13: 59,748,777 (GRCm39) H132Q probably damaging Het
Pgm5 C A 19: 24,793,777 (GRCm39) G296W probably damaging Het
Pkd1 T A 17: 24,805,272 (GRCm39) C3275S probably damaging Het
Podxl2 A G 6: 88,826,331 (GRCm39) L325P probably benign Het
Prom2 A G 2: 127,371,050 (GRCm39) probably null Het
Rab12 T C 17: 66,804,404 (GRCm39) S185G probably damaging Het
Rnf43 T G 11: 87,621,046 (GRCm39) M313R probably null Het
Rusc2 T C 4: 43,415,840 (GRCm39) V382A probably benign Het
Sbno1 A T 5: 124,516,618 (GRCm39) probably benign Het
Smg6 T C 11: 74,816,770 (GRCm39) I10T probably benign Het
Spta1 G A 1: 174,044,725 (GRCm39) V1454I probably benign Het
Tdrd7 A T 4: 46,018,551 (GRCm39) I722F possibly damaging Het
Topors T C 4: 40,262,364 (GRCm39) T307A possibly damaging Het
Ttn C T 2: 76,807,502 (GRCm39) R77Q probably damaging Het
Vmn1r210 C T 13: 23,011,778 (GRCm39) M169I probably benign Het
Zc3h4 A G 7: 16,168,257 (GRCm39) S789G unknown Het
Zfp629 G T 7: 127,211,917 (GRCm39) probably benign Het
Zfp977 C A 7: 42,230,156 (GRCm39) R123I probably benign 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
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