Incidental Mutation 'R7987:Smpd3'
| ID |
651540 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smpd3
|
| Ensembl Gene |
ENSMUSG00000031906 |
| Gene Name |
sphingomyelin phosphodiesterase 3, neutral |
| Synonyms |
4631433G07Rik, neutral sphingomyelinase II, nSMase2, fro, Nsm2 |
| MMRRC Submission |
046028-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.904)
|
| Stock # |
R7987 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
106979180-107064597 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 106986526 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 455
(I455V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000069255
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000067512]
[ENSMUST00000212896]
|
| AlphaFold |
Q9JJY3 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000067512
AA Change: I455V
PolyPhen 2
Score 0.112 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000069255
Gene: ENSMUSG00000031906
AA Change: I455V
| 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 |
probably benign
Transcript: ENSMUST00000212896
AA Change: I455V
PolyPhen 2
Score 0.112 (Sensitivity: 0.93; Specificity: 0.86)
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.9%
|
| Validation Efficiency |
96% (50/52) |
| 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: 55 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 9430097D07Rik |
G |
T |
2: 32,464,317 (GRCm39) |
Q161K |
unknown |
Het |
| Acsl5 |
T |
C |
19: 55,266,405 (GRCm39) |
|
probably null |
Het |
| Adgre1 |
T |
A |
17: 57,754,987 (GRCm39) |
I695N |
possibly damaging |
Het |
| Ank2 |
T |
C |
3: 126,739,356 (GRCm39) |
D2176G |
unknown |
Het |
| Atp6v0a2 |
G |
A |
5: 124,797,050 (GRCm39) |
G810D |
probably damaging |
Het |
| Bod1l |
A |
C |
5: 41,952,413 (GRCm39) |
N2868K |
probably damaging |
Het |
| Brd7 |
T |
C |
8: 89,060,769 (GRCm39) |
T526A |
probably benign |
Het |
| C9 |
T |
A |
15: 6,496,943 (GRCm39) |
Y213* |
probably null |
Het |
| Cacna1i |
G |
A |
15: 80,204,553 (GRCm39) |
|
probably null |
Het |
| Card6 |
T |
A |
15: 5,130,007 (GRCm39) |
N463I |
probably damaging |
Het |
| Ccdc81 |
T |
C |
7: 89,525,319 (GRCm39) |
Y485C |
probably damaging |
Het |
| Celsr1 |
A |
G |
15: 85,917,194 (GRCm39) |
F260L |
probably damaging |
Het |
| Dnah8 |
A |
G |
17: 30,963,498 (GRCm39) |
D2304G |
probably damaging |
Het |
| Dnase1 |
A |
G |
16: 3,855,834 (GRCm39) |
D55G |
probably damaging |
Het |
| Ecsit |
C |
A |
9: 21,984,780 (GRCm39) |
R296L |
probably damaging |
Het |
| Entpd8 |
A |
G |
2: 24,974,778 (GRCm39) |
D403G |
probably damaging |
Het |
| Epha2 |
C |
A |
4: 141,035,791 (GRCm39) |
Q76K |
probably damaging |
Het |
| Exoc1 |
T |
A |
5: 76,691,432 (GRCm39) |
V252E |
probably damaging |
Het |
| Fmnl3 |
T |
A |
15: 99,225,979 (GRCm39) |
H225L |
possibly damaging |
Het |
| Gm4565 |
A |
C |
7: 22,282,812 (GRCm39) |
M2R |
probably benign |
Het |
| Gpr146 |
G |
T |
5: 139,378,440 (GRCm39) |
A81S |
possibly damaging |
Het |
| Heg1 |
C |
A |
16: 33,541,100 (GRCm39) |
S419* |
probably null |
Het |
| Hps5 |
A |
C |
7: 46,418,475 (GRCm39) |
I865S |
probably benign |
Het |
| Hsp90ab1 |
A |
C |
17: 45,882,532 (GRCm39) |
I54S |
probably damaging |
Het |
| Hyal4 |
T |
G |
6: 24,763,865 (GRCm39) |
M342R |
probably damaging |
Het |
| Itgal |
A |
G |
7: 126,927,470 (GRCm39) |
T987A |
possibly damaging |
Het |
| Kat6b |
A |
G |
14: 21,719,931 (GRCm39) |
T1428A |
probably benign |
Het |
| Ldlrad4 |
G |
T |
18: 68,368,740 (GRCm39) |
A66S |
possibly damaging |
Het |
| Lmtk2 |
A |
G |
5: 144,111,959 (GRCm39) |
D893G |
probably benign |
Het |
| Mst1r |
A |
T |
9: 107,789,997 (GRCm39) |
|
probably null |
Het |
| Mtus2 |
G |
T |
5: 148,168,836 (GRCm39) |
|
probably null |
Het |
| Myo3b |
A |
G |
2: 70,161,277 (GRCm39) |
T1174A |
probably benign |
Het |
| Nsun5 |
G |
A |
5: 135,404,534 (GRCm39) |
R424H |
probably damaging |
Het |
| Oacyl |
A |
G |
18: 65,831,462 (GRCm39) |
E33G |
probably benign |
Het |
| Or6c66 |
T |
C |
10: 129,461,838 (GRCm39) |
I31V |
probably benign |
Het |
| Or7d10 |
T |
C |
9: 19,831,610 (GRCm39) |
F35S |
possibly damaging |
Het |
| Palm |
C |
T |
10: 79,629,539 (GRCm39) |
|
probably benign |
Het |
| Papln |
A |
G |
12: 83,822,156 (GRCm39) |
E337G |
probably damaging |
Het |
| Pira2 |
A |
T |
7: 3,844,696 (GRCm39) |
F445Y |
probably benign |
Het |
| Setd1b |
A |
G |
5: 123,285,743 (GRCm39) |
D263G |
unknown |
Het |
| Slc10a7 |
T |
A |
8: 79,423,843 (GRCm39) |
F202I |
probably benign |
Het |
| Snip1 |
G |
T |
4: 124,960,732 (GRCm39) |
G63W |
probably damaging |
Het |
| Sorl1 |
T |
A |
9: 41,888,857 (GRCm39) |
Y1981F |
probably damaging |
Het |
| Tagln2 |
A |
G |
1: 172,332,820 (GRCm39) |
T36A |
probably benign |
Het |
| Tnxb |
T |
C |
17: 34,929,194 (GRCm39) |
S2746P |
possibly damaging |
Het |
| Tob2 |
G |
A |
15: 81,735,681 (GRCm39) |
P96L |
probably damaging |
Het |
| Triobp |
T |
A |
15: 78,885,744 (GRCm39) |
Y1816N |
probably damaging |
Het |
| Trpc3 |
A |
G |
3: 36,698,318 (GRCm39) |
I647T |
probably benign |
Het |
| Ttn |
A |
G |
2: 76,721,905 (GRCm39) |
S6600P |
unknown |
Het |
| Vmn1r200 |
A |
T |
13: 22,580,025 (GRCm39) |
Y276F |
possibly damaging |
Het |
| Vmn1r230 |
T |
C |
17: 21,067,159 (GRCm39) |
I116T |
probably benign |
Het |
| Vmn1r26 |
A |
T |
6: 57,985,264 (GRCm39) |
Y308* |
probably null |
Het |
| Vmn2r16 |
C |
T |
5: 109,488,015 (GRCm39) |
T296I |
probably damaging |
Het |
| Vmn2r50 |
T |
C |
7: 9,772,016 (GRCm39) |
T562A |
probably benign |
Het |
| Wdfy2 |
A |
G |
14: 63,189,380 (GRCm39) |
D283G |
possibly damaging |
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 |
|
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 |
|
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'- AAATCAGCCAGCCAGTCCTG -3'
(R):5'- CAGACTCTTCTAGAAGCAGAGCC -3'
Sequencing Primer
(F):5'- TGAAGCAGGTCCAGCTGCTC -3'
(R):5'- TGTCTCCACCTGGGCACTAG -3'
|
| Posted On |
2020-09-15 |
Incidental Mutation