Incidental Mutation 'R0197:Smpd4'
ID 23515
Institutional Source Beutler Lab
Gene Symbol Smpd4
Ensembl Gene ENSMUSG00000005899
Gene Name sphingomyelin phosphodiesterase 4
Synonyms 4122402O22Rik, neutral membrane (neutral sphingomyelinase-3)
MMRRC Submission 038456-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.098) question?
Stock # R0197 (G1)
Quality Score 225
Status Validated
Chromosome 16
Chromosomal Location 17437218-17462692 bp(+) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) T to A at 17459461 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000156215 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006053] [ENSMUST00000056962] [ENSMUST00000090159] [ENSMUST00000163476] [ENSMUST00000163997] [ENSMUST00000165363] [ENSMUST00000170117] [ENSMUST00000170273] [ENSMUST00000170366] [ENSMUST00000170996] [ENSMUST00000182117] [ENSMUST00000182368] [ENSMUST00000232271] [ENSMUST00000231627] [ENSMUST00000232021] [ENSMUST00000231436] [ENSMUST00000232116] [ENSMUST00000231792] [ENSMUST00000231722]
AlphaFold Q6ZPR5
Predicted Effect probably null
Transcript: ENSMUST00000006053
SMART Domains Protein: ENSMUSP00000006053
Gene: ENSMUSG00000005899

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: ENSMUST00000056962
SMART Domains Protein: ENSMUSP00000049541
Gene: ENSMUSG00000041617

DomainStartEndE-ValueType
low complexity region 12 34 N/A INTRINSIC
Pfam:CCDC92 50 105 4.1e-24 PFAM
low complexity region 154 164 N/A INTRINSIC
Pfam:CCDC74_C 209 326 1.4e-49 PFAM
Predicted Effect probably null
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 null
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 null
Transcript: ENSMUST00000163997
SMART Domains Protein: ENSMUSP00000128595
Gene: ENSMUSG00000005899

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 noncoding transcript
Transcript: ENSMUST00000164292
Predicted Effect probably null
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 noncoding transcript
Transcript: ENSMUST00000166091
Predicted Effect
SMART Domains Protein: ENSMUSP00000132279
Gene: ENSMUSG00000005899

DomainStartEndE-ValueType
Pfam:mit_SMPDase 8 46 2.1e-19 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000170273
SMART Domains Protein: ENSMUSP00000129957
Gene: ENSMUSG00000005899

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 null
Transcript: ENSMUST00000170366
SMART Domains Protein: ENSMUSP00000130990
Gene: ENSMUSG00000005899

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 null
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 noncoding transcript
Transcript: ENSMUST00000170401
Predicted Effect noncoding transcript
Transcript: ENSMUST00000167362
Predicted Effect noncoding transcript
Transcript: ENSMUST00000167592
Predicted Effect noncoding transcript
Transcript: ENSMUST00000182822
Predicted Effect probably benign
Transcript: ENSMUST00000182117
SMART Domains Protein: ENSMUSP00000138657
Gene: ENSMUSG00000041617

DomainStartEndE-ValueType
low complexity region 1 21 N/A INTRINSIC
Pfam:CCDC92 36 97 2e-26 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000182368
SMART Domains Protein: ENSMUSP00000138262
Gene: ENSMUSG00000041617

DomainStartEndE-ValueType
low complexity region 12 34 N/A INTRINSIC
Pfam:CCDC92 49 110 2.9e-26 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000183101
Predicted Effect probably benign
Transcript: ENSMUST00000182976
Predicted Effect probably null
Transcript: ENSMUST00000232271
Predicted Effect noncoding transcript
Transcript: ENSMUST00000231378
Predicted Effect probably benign
Transcript: ENSMUST00000231627
Predicted Effect probably null
Transcript: ENSMUST00000232021
Predicted Effect probably null
Transcript: ENSMUST00000231436
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232185
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232468
Predicted Effect probably benign
Transcript: ENSMUST00000232116
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232270
Predicted Effect probably null
Transcript: ENSMUST00000231792
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232417
Predicted Effect probably benign
Transcript: ENSMUST00000231722
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 98.6%
  • 3x: 97.3%
  • 10x: 92.5%
  • 20x: 75.9%
Validation Efficiency 97% (121/125)
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: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik T C 3: 137,775,632 (GRCm39) L1607P probably damaging Het
1700016H13Rik T C 5: 103,796,687 (GRCm39) *118W probably null Het
Abcc2 A T 19: 43,815,053 (GRCm39) R1147* probably null Het
Acsbg3 A T 17: 57,190,835 (GRCm39) N468Y probably benign Het
Agap2 A G 10: 126,927,571 (GRCm39) T1131A possibly damaging Het
Aldh9a1 A G 1: 167,189,416 (GRCm39) D388G probably damaging Het
Ap3d1 G T 10: 80,565,876 (GRCm39) A97E probably damaging Het
Arhgef10 T A 8: 15,012,636 (GRCm39) V320E probably damaging Het
Baiap2l1 C A 5: 144,202,820 (GRCm39) V498L probably damaging Het
Bltp2 A C 11: 78,160,530 (GRCm39) probably benign Het
Cdh2 T C 18: 16,762,633 (GRCm39) N437S probably benign Het
Cert1 T A 13: 96,685,795 (GRCm39) Y63N probably benign Het
Cfap119 T C 7: 127,184,034 (GRCm39) E261G probably damaging Het
Cfap20dc C T 14: 8,518,695 (GRCm38) G254R probably damaging Het
Chd1 C A 17: 15,945,693 (GRCm39) N72K probably benign Het
Cstf2t A T 19: 31,062,026 (GRCm39) M521L probably benign Het
Dlx5 T C 6: 6,881,619 (GRCm39) K90E possibly damaging Het
Dmp1 A G 5: 104,355,496 (GRCm39) E32G possibly damaging Het
Espnl T G 1: 91,272,211 (GRCm39) Y524D probably damaging Het
Fam20c T C 5: 138,741,479 (GRCm39) L30P probably damaging Het
Fat1 G T 8: 45,479,590 (GRCm39) A2879S probably benign Het
Gabrg1 A T 5: 70,931,732 (GRCm39) V337D probably damaging Het
Gart C A 16: 91,420,291 (GRCm39) D851Y possibly damaging Het
Gcc1 T C 6: 28,420,615 (GRCm39) H234R probably damaging Het
Gemin6 T A 17: 80,535,524 (GRCm39) H161Q probably damaging Het
Glt6d1 A G 2: 25,684,082 (GRCm39) I308T probably benign Het
Gm10320 T C 13: 98,628,491 (GRCm39) T7A probably benign Het
Gm10912 T C 2: 103,896,875 (GRCm39) S5P probably benign Het
Gmpr2 T A 14: 55,910,192 (GRCm39) D7E possibly damaging Het
Hc A G 2: 34,874,762 (GRCm39) Y1620H probably damaging Het
Hoxa3 T C 6: 52,147,123 (GRCm39) probably benign Het
Ift140 A G 17: 25,309,907 (GRCm39) T1105A probably benign Het
Kdr G T 5: 76,129,082 (GRCm39) T188N possibly damaging Het
Lepr A T 4: 101,609,349 (GRCm39) D312V possibly damaging Het
Mcm3 A G 1: 20,880,329 (GRCm39) V501A probably damaging Het
Mcur1 T C 13: 43,699,216 (GRCm39) Y267C probably damaging Het
Med13 T A 11: 86,197,864 (GRCm39) T736S probably benign Het
Med13l T C 5: 118,809,067 (GRCm39) probably benign Het
Mroh2a G C 1: 88,173,764 (GRCm39) A871P probably damaging Het
Ndrg2 T A 14: 52,144,460 (GRCm39) probably benign Het
Oas3 G A 5: 120,894,210 (GRCm39) R39C probably damaging Het
Onecut2 T A 18: 64,474,543 (GRCm39) S365T possibly damaging Het
Or13c25 G A 4: 52,910,849 (GRCm39) T315M probably benign Het
Or4c10 A G 2: 89,760,545 (GRCm39) T131A probably benign Het
Or4k48 C T 2: 111,476,136 (GRCm39) V69I probably benign Het
Or51e1 T A 7: 102,359,202 (GRCm39) H245Q probably damaging Het
Pds5b C A 5: 150,677,896 (GRCm39) Q505K probably benign Het
Pramel22 C T 4: 143,383,010 (GRCm39) E70K possibly damaging Het
Rfx2 T C 17: 57,110,722 (GRCm39) Y88C probably damaging Het
Rpl6 T C 5: 121,346,541 (GRCm39) V214A probably benign Het
Samd3 T A 10: 26,147,752 (GRCm39) C476S possibly damaging Het
Sfi1 TCGC TC 11: 3,096,254 (GRCm39) probably null Het
Shank1 C T 7: 44,001,718 (GRCm39) R1146W unknown Het
Smcr8 T C 11: 60,668,941 (GRCm39) Y30H probably damaging Het
Strip1 C A 3: 107,521,929 (GRCm39) D750Y probably damaging Het
Svep1 T C 4: 58,070,851 (GRCm39) K2312E possibly damaging Het
Taf1c A T 8: 120,326,722 (GRCm39) I438N probably damaging Het
Tnfaip1 A T 11: 78,420,840 (GRCm39) probably benign Het
Unc45b T A 11: 82,831,031 (GRCm39) L797Q possibly damaging Het
Usp24 T A 4: 106,264,330 (GRCm39) W1754R probably damaging Het
Utp20 G A 10: 88,613,378 (GRCm39) P1301L probably benign Het
Vmn2r115 T A 17: 23,578,755 (GRCm39) S743T probably damaging Het
Vps41 T G 13: 19,038,833 (GRCm39) probably null Het
Vps72 G T 3: 95,029,894 (GRCm39) L304F probably damaging Het
Wiz A T 17: 32,575,415 (GRCm39) I907N probably damaging Het
Zfp521 T C 18: 13,978,119 (GRCm39) T765A probably benign Het
Zfp616 A T 11: 73,976,500 (GRCm39) H923L probably damaging Het
Zp2 A T 7: 119,742,799 (GRCm39) probably benign 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
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
R8735:Smpd4 UTSW 16 17,453,410 (GRCm39) missense possibly damaging 0.92
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'- TTGCTCAGCTCATCACACAGGC -3'
(R):5'- TGAGAAACGACAGCTCATGCGAC -3'

Sequencing Primer
(F):5'- AGACTGCCAAGTCCATCTCTG -3'
(R):5'- CAATGCAATCTGGGAGCTGC -3'
Posted On 2013-04-16