Incidental Mutation 'IGL01461:Smpd4'
ID87977
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Smpd4
Ensembl Gene ENSMUSG00000005899
Gene Namesphingomyelin phosphodiesterase 4
Synonyms4122402O22Rik, neutral membrane (neutral sphingomyelinase-3)
Accession Numbers
Is this an essential gene? Probably non essential (E-score: 0.123) question?
Stock #IGL01461
Quality Score
Status
Chromosome16
Chromosomal Location17619354-17644828 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to C at 17621506 bp
ZygosityHeterozygous
Amino Acid Change Glutamine to Proline at position 7 (Q7P)
Ref Sequence ENSEMBL: ENSMUSP00000155897 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006053] [ENSMUST00000090159] [ENSMUST00000163476] [ENSMUST00000163592] [ENSMUST00000163997] [ENSMUST00000165092] [ENSMUST00000165363] [ENSMUST00000167217] [ENSMUST00000170117] [ENSMUST00000169662] [ENSMUST00000170273] [ENSMUST00000170366] [ENSMUST00000168101] [ENSMUST00000172182] [ENSMUST00000171435] [ENSMUST00000170996] [ENSMUST00000231257] [ENSMUST00000231436] [ENSMUST00000231792] [ENSMUST00000231887] [ENSMUST00000232043] [ENSMUST00000232116] [ENSMUST00000231627] [ENSMUST00000231722] [ENSMUST00000231311] [ENSMUST00000232021] [ENSMUST00000232442] [ENSMUST00000232271]
Predicted Effect probably damaging
Transcript: ENSMUST00000006053
AA Change: Q7P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000006053
Gene: ENSMUSG00000005899
AA Change: Q7P

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 768 N/A PFAM
transmembrane domain 769 791 N/A INTRINSIC
transmembrane domain 798 815 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000087486
Predicted Effect probably damaging
Transcript: ENSMUST00000090159
AA Change: Q7P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000087620
Gene: ENSMUSG00000005899
AA Change: Q7P

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 288 7.4e-177 PFAM
Pfam:mit_SMPDase 287 752 9.4e-259 PFAM
transmembrane domain 753 775 N/A INTRINSIC
transmembrane domain 782 799 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000163476
AA Change: Q7P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000131867
Gene: ENSMUSG00000005899
AA Change: Q7P

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 289 6.2e-177 PFAM
Pfam:mit_SMPDase 285 739 9.8e-266 PFAM
transmembrane domain 740 762 N/A INTRINSIC
transmembrane domain 769 786 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000163592
AA Change: Q7P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000126998
Gene: ENSMUSG00000005899
AA Change: Q7P

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 110 2.6e-66 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000163997
AA Change: Q7P

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000128595
Gene: ENSMUSG00000005899
AA Change: Q7P

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 43 2.1e-17 PFAM
Pfam:mit_SMPDase 42 68 2.5e-13 PFAM
Pfam:mit_SMPDase 65 518 4.9e-266 PFAM
transmembrane domain 519 541 N/A INTRINSIC
transmembrane domain 548 565 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000165092
AA Change: Q7P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
Predicted Effect probably damaging
Transcript: ENSMUST00000165363
AA Change: Q7P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000130720
Gene: ENSMUSG00000005899
AA Change: Q7P

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 289 6.2e-177 PFAM
Pfam:mit_SMPDase 285 738 4.1e-262 PFAM
transmembrane domain 739 761 N/A INTRINSIC
transmembrane domain 768 785 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000166091
Predicted Effect noncoding transcript
Transcript: ENSMUST00000166322
Predicted Effect probably benign
Transcript: ENSMUST00000167217
AA Change: Q7P

PolyPhen 2 Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000130570
Gene: ENSMUSG00000005899
AA Change: Q7P

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 92 3.4e-51 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000170117
AA Change: Q7P

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000132279
Gene: ENSMUSG00000005899
AA Change: Q7P

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 46 2.1e-19 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000169662
AA Change: Q7P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000125819
Gene: ENSMUSG00000005899
AA Change: Q7P

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 82 1.8e-46 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000170273
AA Change: Q7P

PolyPhen 2 Score 0.533 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000129957
Gene: ENSMUSG00000005899
AA Change: Q7P

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 43 2.6e-17 PFAM
Pfam:mit_SMPDase 41 215 4.1e-103 PFAM
Pfam:mit_SMPDase 214 666 1.3e-265 PFAM
transmembrane domain 667 689 N/A INTRINSIC
transmembrane domain 696 713 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000170366
AA Change: Q7P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000130990
Gene: ENSMUSG00000005899
AA Change: Q7P

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 288 7.1e-177 PFAM
Pfam:mit_SMPDase 286 643 1.8e-214 PFAM
Pfam:mit_SMPDase 642 696 8.6e-18 PFAM
transmembrane domain 697 719 N/A INTRINSIC
transmembrane domain 726 743 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000168101
AA Change: Q7P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000129995
Gene: ENSMUSG00000005899
AA Change: Q7P

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 125 6.8e-70 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000172182
AA Change: Q7P

PolyPhen 2 Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000126093
Gene: ENSMUSG00000005899
AA Change: Q7P

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 106 1.4e-51 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000171435
AA Change: Q7P

PolyPhen 2 Score 0.053 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000131560
Gene: ENSMUSG00000005899
AA Change: Q7P

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 129 4.4e-69 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000167362
Predicted Effect noncoding transcript
Transcript: ENSMUST00000170401
Predicted Effect probably benign
Transcript: ENSMUST00000170996
SMART Domains Protein: ENSMUSP00000129074
Gene: ENSMUSG00000005899

DomainStartEndE-ValueType
Pfam:mit_SMPDase 26 444 4.4e-234 PFAM
transmembrane domain 445 467 N/A INTRINSIC
transmembrane domain 474 491 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000231257
AA Change: Q7P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
Predicted Effect probably damaging
Transcript: ENSMUST00000231436
AA Change: Q7P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
Predicted Effect probably benign
Transcript: ENSMUST00000231792
AA Change: Q7P

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)
Predicted Effect probably damaging
Transcript: ENSMUST00000231887
AA Change: Q7P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
Predicted Effect probably damaging
Transcript: ENSMUST00000232043
AA Change: Q7P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
Predicted Effect probably benign
Transcript: ENSMUST00000232116
AA Change: Q7P

PolyPhen 2 Score 0.036 (Sensitivity: 0.94; Specificity: 0.82)
Predicted Effect unknown
Transcript: ENSMUST00000231627
AA Change: Q7P
Predicted Effect possibly damaging
Transcript: ENSMUST00000231722
AA Change: Q7P

PolyPhen 2 Score 0.663 (Sensitivity: 0.86; Specificity: 0.91)
Predicted Effect probably benign
Transcript: ENSMUST00000231311
AA Change: Q7P

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)
Predicted Effect possibly damaging
Transcript: ENSMUST00000232021
AA Change: Q7P

PolyPhen 2 Score 0.663 (Sensitivity: 0.86; Specificity: 0.91)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000231949
Predicted Effect noncoding transcript
Transcript: ENSMUST00000231736
Predicted Effect probably damaging
Transcript: ENSMUST00000232442
AA Change: Q7P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232417
Predicted Effect probably benign
Transcript: ENSMUST00000232271
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232578
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232185
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232468
Coding Region Coverage
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Sphingomyelinases (EC 3.1.4.12), such as SMPD4, catalyze the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide (Krut et al., 2006 [PubMed 16517606]).[supplied by OMIM, Mar 2008]
Allele List at MGI
Other mutations in this stock
Total: 28 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2210408I21Rik T C 13: 77,281,095 F767S probably benign Het
2810474O19Rik T C 6: 149,331,515 probably benign Het
Abca13 A G 11: 9,403,834 T3719A probably damaging Het
Apob A T 12: 8,001,884 M1137L probably benign Het
Brd9 C T 13: 73,951,598 Q445* probably null Het
Cdh23 T C 10: 60,409,147 T990A possibly damaging Het
Cenpf A G 1: 189,657,096 L1513S probably damaging Het
Col27a1 A G 4: 63,224,243 K56R probably damaging Het
Cryaa A G 17: 31,681,026 Y118C probably damaging Het
Dtl T C 1: 191,546,617 T378A possibly damaging Het
E330020D12Rik A G 1: 153,408,359 noncoding transcript Het
F7 A G 8: 13,032,245 D145G possibly damaging Het
Flvcr2 A G 12: 85,803,131 probably benign Het
Hltf A T 3: 20,099,939 K680* probably null Het
Ing1 T G 8: 11,561,453 F22V probably benign Het
Ipo5 A G 14: 120,928,533 D330G probably damaging Het
Itgax G T 7: 128,135,018 D321Y probably damaging Het
Kdelc1 T C 1: 44,110,934 Q365R probably damaging Het
Kel A C 6: 41,701,911 probably null Het
March10 T C 11: 105,389,605 K618R probably damaging Het
Mast4 T A 13: 102,754,068 M925L probably damaging Het
Miga1 C T 3: 152,335,297 E78K probably damaging Het
Olfr1204 G T 2: 88,852,325 C125F probably damaging Het
Olfr58 T A 9: 19,783,949 probably null Het
Pkdrej T C 15: 85,820,374 I454V possibly damaging Het
Prpf6 C A 2: 181,631,511 T283N probably benign Het
R3hdm1 A G 1: 128,178,906 H197R probably damaging Het
Vmn2r84 A T 10: 130,391,225 I248K possibly damaging Het
Other mutations in Smpd4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00944:Smpd4 APN 16 17642757 missense probably benign 0.04
IGL02051:Smpd4 APN 16 17626518 missense probably damaging 1.00
IGL02492:Smpd4 APN 16 17639351 missense probably damaging 1.00
IGL03181:Smpd4 APN 16 17625807 nonsense probably null
Victim UTSW 16 17640971 missense probably damaging 1.00
weakling UTSW 16 17638486 intron probably benign
R0197:Smpd4 UTSW 16 17641597 critical splice donor site probably null
R0549:Smpd4 UTSW 16 17639312 missense probably benign 0.15
R0789:Smpd4 UTSW 16 17625826 missense probably benign 0.14
R1077:Smpd4 UTSW 16 17623969 missense probably damaging 1.00
R1120:Smpd4 UTSW 16 17638486 intron probably benign
R1716:Smpd4 UTSW 16 17642501 missense probably damaging 1.00
R1758:Smpd4 UTSW 16 17626008 missense probably damaging 0.99
R1758:Smpd4 UTSW 16 17640880 missense probably damaging 1.00
R1838:Smpd4 UTSW 16 17642302 splice site probably null
R2115:Smpd4 UTSW 16 17626865 missense probably benign 0.33
R2849:Smpd4 UTSW 16 17642212 missense probably damaging 1.00
R4654:Smpd4 UTSW 16 17642128 intron probably benign
R6157:Smpd4 UTSW 16 17641066 splice site probably null
R6190:Smpd4 UTSW 16 17632013 missense probably damaging 1.00
R6822:Smpd4 UTSW 16 17640233 missense probably damaging 1.00
R7062:Smpd4 UTSW 16 17640971 missense probably damaging 1.00
R7305:Smpd4 UTSW 16 17641783 missense probably damaging 0.99
R7759:Smpd4 UTSW 16 17638633 missense probably damaging 1.00
R7853:Smpd4 UTSW 16 17642741 missense probably damaging 1.00
R8187:Smpd4 UTSW 16 17629135 missense probably damaging 1.00
R8303:Smpd4 UTSW 16 17639331 missense probably damaging 1.00
R8518:Smpd4 UTSW 16 17641020 missense possibly damaging 0.89
Z1176:Smpd4 UTSW 16 17619586 intron probably benign
Z1177:Smpd4 UTSW 16 17621441 critical splice acceptor site probably benign
Posted On2013-11-18