Incidental Mutation 'R5829:Smpd3'
ID |
450324 |
Institutional Source |
Beutler Lab
|
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)
|
Stock # |
R5829 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
8 |
Chromosomal Location |
106979180-107064597 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 106991512 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Alanine
at position 347
(V347A)
|
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: V347A
PolyPhen 2
Score 0.152 (Sensitivity: 0.92; Specificity: 0.87)
|
SMART Domains |
Protein: ENSMUSP00000069255 Gene: ENSMUSG00000031906 AA Change: V347A
Domain | Start | End | E-Value | Type |
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: V347A
PolyPhen 2
Score 0.152 (Sensitivity: 0.92; Specificity: 0.87)
|
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 98.4%
- 20x: 95.6%
|
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
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca8b |
C |
A |
11: 109,868,639 (GRCm39) |
G175V |
probably damaging |
Het |
Atp6v1e2 |
T |
C |
17: 87,252,144 (GRCm39) |
R85G |
probably benign |
Het |
Bmpr1b |
T |
C |
3: 141,550,918 (GRCm39) |
H391R |
probably benign |
Het |
Camsap3 |
A |
G |
8: 3,647,899 (GRCm39) |
H69R |
probably damaging |
Het |
Cimip2a |
G |
A |
2: 25,108,869 (GRCm39) |
|
probably null |
Het |
Col12a1 |
C |
T |
9: 79,540,955 (GRCm39) |
G2391R |
probably damaging |
Het |
Dab2ip |
ATCCT |
ATCCTCCT |
2: 35,597,787 (GRCm39) |
|
probably benign |
Het |
Epha4 |
G |
A |
1: 77,421,631 (GRCm39) |
L284F |
probably benign |
Het |
Fat4 |
T |
C |
3: 39,061,454 (GRCm39) |
S4346P |
probably damaging |
Het |
Fbxo22 |
T |
A |
9: 55,125,596 (GRCm39) |
|
probably null |
Het |
Gcc1 |
C |
A |
6: 28,419,690 (GRCm39) |
|
probably benign |
Het |
Gdf10 |
T |
C |
14: 33,654,674 (GRCm39) |
S394P |
probably damaging |
Het |
Gdf9 |
C |
T |
11: 53,324,516 (GRCm39) |
T95M |
probably benign |
Het |
Gpr179 |
G |
A |
11: 97,226,524 (GRCm39) |
S1877L |
probably benign |
Het |
Gtf2i |
A |
G |
5: 134,292,547 (GRCm39) |
V380A |
probably damaging |
Het |
Il17c |
G |
A |
8: 123,148,970 (GRCm39) |
R38Q |
probably damaging |
Het |
Il17rd |
G |
A |
14: 26,814,042 (GRCm39) |
|
probably null |
Het |
Iqch |
C |
T |
9: 63,332,639 (GRCm39) |
|
probably null |
Het |
Lrrc37 |
C |
T |
11: 103,432,712 (GRCm39) |
E1310K |
possibly damaging |
Het |
Mpp4 |
A |
T |
1: 59,168,101 (GRCm39) |
S456R |
probably damaging |
Het |
Nek10 |
T |
C |
14: 14,865,404 (GRCm38) |
Y601H |
probably damaging |
Het |
Nrxn2 |
C |
T |
19: 6,540,879 (GRCm39) |
P936L |
probably benign |
Het |
Or8b44 |
T |
A |
9: 38,410,545 (GRCm39) |
Y193* |
probably null |
Het |
Pcdhb9 |
T |
C |
18: 37,534,942 (GRCm39) |
V312A |
probably damaging |
Het |
Pex5l |
T |
C |
3: 33,060,139 (GRCm39) |
T211A |
probably benign |
Het |
Pik3c2a |
T |
C |
7: 115,972,049 (GRCm39) |
T794A |
probably benign |
Het |
Pla2g6 |
A |
G |
15: 79,171,893 (GRCm39) |
F710L |
possibly damaging |
Het |
Repin1 |
A |
T |
6: 48,571,766 (GRCm39) |
|
probably benign |
Het |
Rev3l |
A |
T |
10: 39,682,902 (GRCm39) |
E340V |
probably damaging |
Het |
Ryr3 |
A |
G |
2: 112,690,076 (GRCm39) |
S1158P |
probably damaging |
Het |
S100a16 |
A |
T |
3: 90,449,454 (GRCm39) |
Q43L |
possibly damaging |
Het |
Scg2 |
A |
G |
1: 79,414,637 (GRCm39) |
S29P |
probably damaging |
Het |
Sfrp5 |
T |
C |
19: 42,190,095 (GRCm39) |
Y119C |
probably damaging |
Het |
Sh3tc2 |
A |
G |
18: 62,123,986 (GRCm39) |
T916A |
probably benign |
Het |
Tmem212 |
C |
A |
3: 27,939,081 (GRCm39) |
C135F |
possibly damaging |
Het |
Unc13c |
T |
A |
9: 73,600,650 (GRCm39) |
N1365Y |
probably benign |
Het |
Usp13 |
G |
T |
3: 32,940,672 (GRCm39) |
G395C |
possibly damaging |
Het |
Vmn2r68 |
T |
C |
7: 84,886,812 (GRCm39) |
N34S |
probably benign |
Het |
|
Other mutations in Smpd3 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL03380:Smpd3
|
APN |
8 |
106,986,291 (GRCm39) |
missense |
probably benign |
0.01 |
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 |
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 |
|
Predicted Primers |
PCR Primer
(F):5'- TGATAGGCCACGTCCATGAC -3'
(R):5'- CAATCAGCGAGATGGGGATTCTG -3'
Sequencing Primer
(F):5'- ACGTCCATGACAGGGTAGC -3'
(R):5'- ATTCTGGGAGCCTGGGCAG -3'
|
Posted On |
2016-12-20 |