Incidental Mutation 'R8735:Smpd4'
ID 663005
Institutional Source Beutler Lab
Gene Symbol Smpd4
Ensembl Gene ENSMUSG00000005899
Gene Name sphingomyelin phosphodiesterase 4
Synonyms 4122402O22Rik, neutral membrane (neutral sphingomyelinase-3)
MMRRC Submission 068583-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.098) question?
Stock # R8735 (G1)
Quality Score 225.009
Status Validated
Chromosome 16
Chromosomal Location 17437218-17462692 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 17453410 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Proline at position 309 (L309P)
Ref Sequence ENSEMBL: ENSMUSP00000006053 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006053] [ENSMUST00000090159] [ENSMUST00000163476] [ENSMUST00000165363] [ENSMUST00000231436] [ENSMUST00000231627] [ENSMUST00000231722] [ENSMUST00000231792] [ENSMUST00000232021] [ENSMUST00000232116] [ENSMUST00000232271]
AlphaFold Q6ZPR5
Predicted Effect possibly damaging
Transcript: ENSMUST00000006053
AA Change: L309P

PolyPhen 2 Score 0.920 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000006053
Gene: ENSMUSG00000005899
AA Change: L309P

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 probably benign
Transcript: ENSMUST00000090159
SMART Domains Protein: ENSMUSP00000087620
Gene: ENSMUSG00000005899

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 benign
Transcript: ENSMUST00000163476
SMART Domains Protein: ENSMUSP00000131867
Gene: ENSMUSG00000005899

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 benign
Transcript: ENSMUST00000165363
SMART Domains Protein: ENSMUSP00000130720
Gene: ENSMUSG00000005899

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 probably benign
Transcript: ENSMUST00000231436
Predicted Effect probably benign
Transcript: ENSMUST00000231627
Predicted Effect probably benign
Transcript: ENSMUST00000231722
Predicted Effect probably benign
Transcript: ENSMUST00000231792
Predicted Effect probably benign
Transcript: ENSMUST00000232021
Predicted Effect probably benign
Transcript: ENSMUST00000232116
Predicted Effect probably benign
Transcript: ENSMUST00000232271
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
Validation Efficiency 99% (76/77)
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: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
6430550D23Rik A G 2: 155,845,731 (GRCm39) F9S unknown Het
Abhd10 A G 16: 45,557,997 (GRCm39) F101L probably damaging Het
Acp2 A G 2: 91,034,651 (GRCm39) T93A probably benign Het
Adamts9 C T 6: 92,837,048 (GRCm39) probably benign Het
Aknad1 T A 3: 108,682,615 (GRCm39) probably benign Het
Ank3 A T 10: 69,822,785 (GRCm39) T485S probably benign Het
Caly G A 7: 139,652,503 (GRCm39) R82C probably damaging Het
Cfhr2 A G 1: 139,786,343 (GRCm39) L8P probably damaging Het
Cpeb2 T A 5: 43,438,775 (GRCm39) L869* probably null Het
Cxxc1 A G 18: 74,350,331 (GRCm39) K33E possibly damaging Het
Cyp17a1 T C 19: 46,659,533 (GRCm39) probably null Het
Cyp4a30b G A 4: 115,309,976 (GRCm39) W59* probably null Het
Dennd4b T C 3: 90,185,172 (GRCm39) V1204A probably damaging Het
Dpyd T A 3: 118,935,565 (GRCm39) D663E possibly damaging Het
Esrrg A T 1: 187,933,205 (GRCm39) probably benign Het
Exoc2 A C 13: 31,090,822 (GRCm39) L261V probably damaging Het
Exosc9 T C 3: 36,609,662 (GRCm39) L185S probably damaging Het
Gcnt3 T C 9: 69,941,728 (GRCm39) K280R probably benign Het
Ighv1-64 A T 12: 115,471,217 (GRCm39) M100K probably benign Het
Impdh2 G A 9: 108,441,978 (GRCm39) probably null Het
Itsn2 T A 12: 4,721,474 (GRCm39) I1068K probably damaging Het
Kif5c T C 2: 49,584,783 (GRCm39) C169R probably damaging Het
Kndc1 A G 7: 139,490,130 (GRCm39) S211G probably benign Het
Lama2 T A 10: 27,066,530 (GRCm39) E1117V probably damaging Het
Lgals4 C T 7: 28,540,921 (GRCm39) R282C probably damaging Het
Lsg1 T A 16: 30,399,865 (GRCm39) probably null Het
Mab21l4 C T 1: 93,082,208 (GRCm39) probably null Het
Msh3 A G 13: 92,411,374 (GRCm39) S608P possibly damaging Het
Mslnl T A 17: 25,964,062 (GRCm39) F464I probably benign Het
Mycbp2 T A 14: 103,460,586 (GRCm39) K1493N probably damaging Het
Myo15a A T 11: 60,401,679 (GRCm39) probably null Het
Myo1b A T 1: 51,794,896 (GRCm39) F1065I probably benign Het
Nf1 A G 11: 79,345,136 (GRCm39) probably benign Het
Nup153 C A 13: 46,881,027 (GRCm39) probably benign Het
Or4f4-ps1 T A 2: 111,330,497 (GRCm39) I300K probably damaging Het
Or5b97 A G 19: 12,878,274 (GRCm39) V290A possibly damaging Het
Osbpl7 A G 11: 96,943,194 (GRCm39) T149A probably benign Het
Parp1 A G 1: 180,396,690 (GRCm39) D31G probably benign Het
Pcdha6 T A 18: 37,101,203 (GRCm39) V132E possibly damaging Het
Pcdhb8 T A 18: 37,489,975 (GRCm39) L551Q possibly damaging Het
Pcsk9 T A 4: 106,311,808 (GRCm39) T190S probably damaging Het
Pdgfrb A T 18: 61,197,049 (GRCm39) T162S probably benign Het
Pi4ka C T 16: 17,136,234 (GRCm39) R908Q Het
Pnpla8 A G 12: 44,330,222 (GRCm39) E258G probably benign Het
Prrc2c A T 1: 162,537,127 (GRCm39) S643T unknown Het
Rnf20 T G 4: 49,655,964 (GRCm39) I970S possibly damaging Het
Robo2 A T 16: 73,755,247 (GRCm39) V758D probably damaging Het
Robo4 G A 9: 37,319,577 (GRCm39) S609N possibly damaging Het
Rrbp1 G A 2: 143,830,920 (GRCm39) Q416* probably null Het
Rsf1 GCG GCGACGGCGACG 7: 97,229,114 (GRCm39) probably benign Het
Ryr2 C A 13: 11,701,833 (GRCm39) E2941D probably damaging Het
Scd2 G T 19: 44,289,743 (GRCm39) C246F probably benign Het
Sh3rf1 G A 8: 61,825,687 (GRCm39) V561I probably benign Het
Slc4a4 T A 5: 89,280,301 (GRCm39) D366E probably damaging Het
Slfn14 T G 11: 83,174,715 (GRCm39) Q92P probably damaging Het
Slfn4 A T 11: 83,077,770 (GRCm39) Y186F probably damaging Het
Smyd3 G T 1: 178,920,482 (GRCm39) N217K probably benign Het
Spen T C 4: 141,197,129 (GRCm39) T3547A probably benign Het
Suclg1 A T 6: 73,253,729 (GRCm39) I126F unknown Het
Tenm4 C T 7: 96,555,148 (GRCm39) P2618S probably benign Het
Tmprss15 A T 16: 78,798,702 (GRCm39) I660N possibly damaging Het
Trf A T 9: 103,087,723 (GRCm39) V677D probably damaging Het
Trim36 T C 18: 46,302,452 (GRCm39) N532S probably benign Het
Trim37 T C 11: 87,037,885 (GRCm39) probably null Het
Ttn T C 2: 76,570,454 (GRCm39) N26813S probably benign Het
Vmn1r199 T A 13: 22,567,537 (GRCm39) V277D probably damaging Het
Wdfy3 T C 5: 102,077,951 (GRCm39) D873G probably benign Het
Wdr27 T C 17: 15,103,929 (GRCm39) T726A probably damaging Het
Wdr97 T C 15: 76,240,775 (GRCm39) Y488H Het
Wdtc1 A T 4: 133,031,511 (GRCm39) C236* probably null Het
Wnk4 A C 11: 101,167,092 (GRCm39) S1083R unknown Het
Wwc1 A T 11: 35,774,234 (GRCm39) I342N probably damaging Het
Zbtb40 A G 4: 136,725,957 (GRCm39) L534P probably damaging Het
Zfp62 T C 11: 49,108,227 (GRCm39) C773R probably damaging Het
Zfp709 T A 8: 72,643,027 (GRCm39) I152N probably benign Het
Zfp738 T C 13: 67,819,550 (GRCm39) Y147C probably damaging Het
Zscan18 A C 7: 12,503,625 (GRCm39) S645A probably benign Het
Zw10 A G 9: 48,988,861 (GRCm39) Y709C probably damaging Het
Other mutations in Smpd4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00944:Smpd4 APN 16 17,460,621 (GRCm39) missense probably benign 0.04
IGL01461:Smpd4 APN 16 17,439,370 (GRCm39) missense probably damaging 1.00
IGL02051:Smpd4 APN 16 17,444,382 (GRCm39) missense probably damaging 1.00
IGL02492:Smpd4 APN 16 17,457,215 (GRCm39) missense probably damaging 1.00
IGL03181:Smpd4 APN 16 17,443,671 (GRCm39) nonsense probably null
Victim UTSW 16 17,458,835 (GRCm39) missense probably damaging 1.00
weakling UTSW 16 17,456,350 (GRCm39) intron probably benign
G1citation:Smpd4 UTSW 16 17,458,097 (GRCm39) missense probably damaging 1.00
R0197:Smpd4 UTSW 16 17,459,461 (GRCm39) critical splice donor site probably null
R0549:Smpd4 UTSW 16 17,457,176 (GRCm39) missense probably benign 0.15
R0789:Smpd4 UTSW 16 17,443,690 (GRCm39) missense probably benign 0.14
R1077:Smpd4 UTSW 16 17,441,833 (GRCm39) missense probably damaging 1.00
R1120:Smpd4 UTSW 16 17,456,350 (GRCm39) intron probably benign
R1716:Smpd4 UTSW 16 17,460,365 (GRCm39) missense probably damaging 1.00
R1758:Smpd4 UTSW 16 17,458,744 (GRCm39) missense probably damaging 1.00
R1758:Smpd4 UTSW 16 17,443,872 (GRCm39) missense probably damaging 0.99
R1838:Smpd4 UTSW 16 17,460,166 (GRCm39) splice site probably null
R2115:Smpd4 UTSW 16 17,444,729 (GRCm39) missense probably benign 0.33
R2849:Smpd4 UTSW 16 17,460,076 (GRCm39) missense probably damaging 1.00
R4654:Smpd4 UTSW 16 17,459,992 (GRCm39) intron probably benign
R6157:Smpd4 UTSW 16 17,458,930 (GRCm39) splice site probably null
R6190:Smpd4 UTSW 16 17,449,877 (GRCm39) missense probably damaging 1.00
R6822:Smpd4 UTSW 16 17,458,097 (GRCm39) missense probably damaging 1.00
R7062:Smpd4 UTSW 16 17,458,835 (GRCm39) missense probably damaging 1.00
R7305:Smpd4 UTSW 16 17,459,647 (GRCm39) missense probably damaging 0.99
R7759:Smpd4 UTSW 16 17,456,497 (GRCm39) missense probably damaging 1.00
R7853:Smpd4 UTSW 16 17,460,605 (GRCm39) missense probably damaging 1.00
R8187:Smpd4 UTSW 16 17,446,999 (GRCm39) missense probably damaging 1.00
R8303:Smpd4 UTSW 16 17,457,195 (GRCm39) missense probably damaging 1.00
R8518:Smpd4 UTSW 16 17,458,884 (GRCm39) missense possibly damaging 0.89
R9075:Smpd4 UTSW 16 17,457,849 (GRCm39) missense unknown
R9439:Smpd4 UTSW 16 17,459,451 (GRCm39) missense probably benign
Z1176:Smpd4 UTSW 16 17,437,450 (GRCm39) intron probably benign
Z1177:Smpd4 UTSW 16 17,439,305 (GRCm39) critical splice acceptor site probably benign
Predicted Primers PCR Primer
(F):5'- TTGAGGATCCTCTGGCTCAG -3'
(R):5'- TCAGGCCTACCCTAACACATGG -3'

Sequencing Primer
(F):5'- TTACTGTGGGACCCAGGG -3'
(R):5'- AACACATGGGTTTCATTTTGCTCAGG -3'
Posted On 2021-03-08