Incidental Mutation 'IGL03380:Smpd3'
ID 420660
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Smpd3
Ensembl Gene ENSMUSG00000031906
Gene Name sphingomyelin phosphodiesterase 3, neutral
Synonyms 4631433G07Rik, neutral sphingomyelinase II, nSMase2, fro, Nsm2
Accession Numbers
Essential gene? Probably essential (E-score: 0.904) question?
Stock # IGL03380
Quality Score
Status
Chromosome 8
Chromosomal Location 106979180-107064597 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 106986291 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Isoleucine at position 504 (V504I)
Ref Sequence ENSEMBL: ENSMUSP00000148282 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000067512] [ENSMUST00000212896]
AlphaFold Q9JJY3
Predicted Effect probably benign
Transcript: ENSMUST00000067512
AA Change: V504I

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000069255
Gene: ENSMUSG00000031906
AA Change: V504I

DomainStartEndE-ValueType
transmembrane domain 15 37 N/A INTRINSIC
transmembrane domain 57 79 N/A INTRINSIC
low complexity region 178 189 N/A INTRINSIC
Pfam:Exo_endo_phos 321 639 1.2e-15 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000180410
Predicted Effect probably benign
Transcript: ENSMUST00000212896
AA Change: V504I

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
Coding Region Coverage
Validation Efficiency
MGI Phenotype PHENOTYPE: Homozygous null mice exhibit dwarfism, delayed sexual and gonad maturation, delayed ossification of the long bones, and reduced serum levels of thyroxine, triiodothyronine, cortisol, and insulin-like growth factor. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 38 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 A G 11: 9,248,574 (GRCm39) N2774D probably benign Het
Aldh1a2 T G 9: 71,162,399 (GRCm39) Y149* probably null Het
Ank2 C A 3: 126,749,519 (GRCm39) E503D probably damaging Het
Arhgap23 A G 11: 97,343,344 (GRCm39) D542G probably damaging Het
Atp8a1 T C 5: 67,889,529 (GRCm39) E582G probably benign Het
C4b A T 17: 34,959,260 (GRCm39) V438D probably benign Het
Caps2 A G 10: 112,036,601 (GRCm39) E345G probably benign Het
Cdk19 C T 10: 40,352,908 (GRCm39) P308L probably benign Het
Drc3 A G 11: 60,268,731 (GRCm39) E307G probably benign Het
Dst G A 1: 34,296,881 (GRCm39) A1041T probably damaging Het
Elp2 T C 18: 24,755,537 (GRCm39) V428A probably benign Het
Eml5 G T 12: 98,840,906 (GRCm39) probably benign Het
Fam120b G A 17: 15,623,396 (GRCm39) probably benign Het
Fpr-rs6 G A 17: 20,403,245 (GRCm39) L39F possibly damaging Het
Fsd1 T C 17: 56,302,456 (GRCm39) I300T probably benign Het
Hsd17b6 T C 10: 127,830,207 (GRCm39) probably null Het
Hspa1a T C 17: 35,189,253 (GRCm39) K550R probably benign Het
Krba1 A G 6: 48,380,387 (GRCm39) H37R possibly damaging Het
Lama2 T C 10: 26,926,261 (GRCm39) D2117G probably damaging Het
Map4k2 T C 19: 6,394,620 (GRCm39) F332S possibly damaging Het
Mindy1 T C 3: 95,198,329 (GRCm39) probably benign Het
Nhsl1 T G 10: 18,399,627 (GRCm39) Y284* probably null Het
Or5b109 T A 19: 13,212,365 (GRCm39) F250L probably benign Het
Pkhd1 T A 1: 20,270,894 (GRCm39) T3220S probably damaging Het
Pramel7 A T 2: 87,321,716 (GRCm39) D106E probably benign Het
Psme3 T C 11: 101,210,852 (GRCm39) probably null Het
Rsph1 T C 17: 31,496,210 (GRCm39) E7G unknown Het
Slc13a2 T C 11: 78,289,908 (GRCm39) T469A probably benign Het
Slc30a9 C T 5: 67,473,054 (GRCm39) T46I probably benign Het
Slc37a4 T G 9: 44,311,320 (GRCm39) S204A probably benign Het
Slc8b1 T C 5: 120,657,800 (GRCm39) F88L probably damaging Het
Tbx4 A G 11: 85,805,465 (GRCm39) N418S probably benign Het
Tmem132c A G 5: 127,613,506 (GRCm39) T470A probably benign Het
Tmem207 A T 16: 26,345,407 (GRCm39) C20S probably damaging Het
Usp43 G A 11: 67,766,142 (GRCm39) A761V possibly damaging Het
Vmn1r191 C T 13: 22,363,055 (GRCm39) S233N probably damaging Het
Vmn2r58 T A 7: 41,513,874 (GRCm39) E256D probably benign Het
Zc3hav1 T C 6: 38,313,493 (GRCm39) Y184C probably damaging Het
Other mutations in Smpd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
BB010:Smpd3 UTSW 8 106,982,254 (GRCm39) missense probably benign
BB020:Smpd3 UTSW 8 106,982,254 (GRCm39) missense probably benign
G1citation:Smpd3 UTSW 8 106,992,596 (GRCm39) start gained probably benign
R0240:Smpd3 UTSW 8 106,991,788 (GRCm39) missense probably damaging 0.96
R0240:Smpd3 UTSW 8 106,991,788 (GRCm39) missense probably damaging 0.96
R0456:Smpd3 UTSW 8 106,986,288 (GRCm39) missense probably benign
R0759:Smpd3 UTSW 8 106,991,860 (GRCm39) missense probably benign 0.34
R0799:Smpd3 UTSW 8 106,991,421 (GRCm39) missense possibly damaging 0.92
R1544:Smpd3 UTSW 8 106,992,199 (GRCm39) missense possibly damaging 0.70
R1756:Smpd3 UTSW 8 106,991,603 (GRCm39) missense probably benign
R2937:Smpd3 UTSW 8 106,991,452 (GRCm39) missense probably damaging 1.00
R2939:Smpd3 UTSW 8 106,984,039 (GRCm39) missense probably benign 0.00
R4614:Smpd3 UTSW 8 106,986,371 (GRCm39) missense probably damaging 1.00
R5829:Smpd3 UTSW 8 106,991,512 (GRCm39) missense probably benign 0.15
R6822:Smpd3 UTSW 8 106,992,596 (GRCm39) start gained probably benign
R6891:Smpd3 UTSW 8 106,991,300 (GRCm39) missense probably damaging 1.00
R6962:Smpd3 UTSW 8 106,991,851 (GRCm39) missense probably benign 0.34
R6965:Smpd3 UTSW 8 106,986,513 (GRCm39) missense probably damaging 1.00
R7344:Smpd3 UTSW 8 106,991,825 (GRCm39) missense probably damaging 1.00
R7394:Smpd3 UTSW 8 106,991,642 (GRCm39) missense probably damaging 0.99
R7823:Smpd3 UTSW 8 106,982,254 (GRCm39) missense probably benign
R7825:Smpd3 UTSW 8 106,982,254 (GRCm39) missense probably benign
R7933:Smpd3 UTSW 8 106,982,254 (GRCm39) missense probably benign
R7974:Smpd3 UTSW 8 106,982,254 (GRCm39) missense probably benign
R7975:Smpd3 UTSW 8 106,982,254 (GRCm39) missense probably benign
R7976:Smpd3 UTSW 8 106,982,254 (GRCm39) missense probably benign
R7977:Smpd3 UTSW 8 106,986,526 (GRCm39) missense probably benign 0.11
R7987:Smpd3 UTSW 8 106,986,526 (GRCm39) missense probably benign 0.11
R8260:Smpd3 UTSW 8 106,984,047 (GRCm39) missense probably benign 0.13
R8264:Smpd3 UTSW 8 106,991,290 (GRCm39) missense probably damaging 1.00
R8292:Smpd3 UTSW 8 106,991,422 (GRCm39) missense probably benign 0.08
R8432:Smpd3 UTSW 8 106,984,309 (GRCm39) critical splice acceptor site probably null
R8494:Smpd3 UTSW 8 106,981,982 (GRCm39) missense probably damaging 0.99
R8779:Smpd3 UTSW 8 106,992,121 (GRCm39) missense probably benign 0.37
R8787:Smpd3 UTSW 8 106,982,377 (GRCm39) missense probably damaging 1.00
R9005:Smpd3 UTSW 8 106,984,058 (GRCm39) missense probably benign 0.02
R9008:Smpd3 UTSW 8 106,984,058 (GRCm39) missense probably benign 0.02
R9355:Smpd3 UTSW 8 106,991,825 (GRCm39) missense probably damaging 1.00
R9516:Smpd3 UTSW 8 106,992,119 (GRCm39) missense probably benign 0.03
R9698:Smpd3 UTSW 8 106,992,296 (GRCm39) missense possibly damaging 0.54
R9703:Smpd3 UTSW 8 106,991,713 (GRCm39) missense probably damaging 0.99
Z1177:Smpd3 UTSW 8 106,991,474 (GRCm39) missense probably damaging 1.00
Posted On 2016-08-02