Incidental Mutation 'R7344:Smpd3'
ID |
570095 |
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 |
045434-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.904)
|
Stock # |
R7344 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
8 |
Chromosomal Location |
106979180-107064597 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 106991825 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Methionine
at position 243
(V243M)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000069255
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000067512]
[ENSMUST00000212896]
|
AlphaFold |
Q9JJY3 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000067512
AA Change: V243M
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000069255 Gene: ENSMUSG00000031906 AA Change: V243M
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 damaging
Transcript: ENSMUST00000212896
AA Change: V243M
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.2%
|
Validation Efficiency |
100% (58/58) |
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: 58 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4930438A08Rik |
A |
C |
11: 58,182,273 (GRCm39) |
Y216S |
|
Het |
Anpep |
G |
T |
7: 79,488,398 (GRCm39) |
S477R |
possibly damaging |
Het |
Atp7b |
T |
C |
8: 22,487,515 (GRCm39) |
D1293G |
probably damaging |
Het |
Caprin2 |
A |
G |
6: 148,774,565 (GRCm39) |
V249A |
probably benign |
Het |
Cep41 |
C |
T |
6: 30,693,655 (GRCm39) |
R5K |
probably benign |
Het |
Cyp2c23 |
A |
T |
19: 44,010,176 (GRCm39) |
|
probably null |
Het |
Dazap2 |
T |
A |
15: 100,514,824 (GRCm39) |
V15E |
possibly damaging |
Het |
Ecpas |
A |
T |
4: 58,824,770 (GRCm39) |
D1070E |
probably benign |
Het |
Epha8 |
T |
A |
4: 136,661,849 (GRCm39) |
H582L |
probably benign |
Het |
Fam193a |
A |
G |
5: 34,643,074 (GRCm39) |
T1513A |
possibly damaging |
Het |
Fancd2 |
T |
C |
6: 113,545,670 (GRCm39) |
V901A |
probably benign |
Het |
Fbl |
T |
A |
7: 27,878,360 (GRCm39) |
V284E |
probably damaging |
Het |
Fbln2 |
A |
G |
6: 91,246,955 (GRCm39) |
E1065G |
probably damaging |
Het |
Fbxw16 |
A |
G |
9: 109,278,103 (GRCm39) |
V25A |
probably benign |
Het |
Fcgbpl1 |
C |
T |
7: 27,852,185 (GRCm39) |
T1236I |
possibly damaging |
Het |
Fcgbpl1 |
T |
C |
7: 27,839,704 (GRCm39) |
S506P |
possibly damaging |
Het |
Gm11562 |
T |
G |
11: 99,511,195 (GRCm39) |
T2P |
unknown |
Het |
Gm17728 |
G |
T |
17: 9,640,955 (GRCm39) |
G22W |
probably damaging |
Het |
Gm30083 |
A |
G |
14: 33,721,537 (GRCm39) |
Y190H |
probably benign |
Het |
Gm6793 |
T |
A |
8: 112,741,561 (GRCm39) |
D27V |
probably damaging |
Het |
Gm7324 |
A |
G |
14: 43,952,134 (GRCm39) |
D259G |
probably benign |
Het |
Gtf2a1l |
G |
A |
17: 89,001,531 (GRCm39) |
G129D |
probably damaging |
Het |
Ildr2 |
T |
A |
1: 166,122,166 (GRCm39) |
V203E |
probably damaging |
Het |
Ipo4 |
C |
T |
14: 55,872,988 (GRCm39) |
R23Q |
probably benign |
Het |
Irx5 |
A |
G |
8: 93,086,183 (GRCm39) |
T89A |
probably benign |
Het |
Itga7 |
A |
G |
10: 128,776,798 (GRCm39) |
N221S |
possibly damaging |
Het |
Lpcat2 |
T |
C |
8: 93,602,195 (GRCm39) |
W259R |
probably damaging |
Het |
Lrrc8e |
C |
T |
8: 4,284,815 (GRCm39) |
R347C |
probably damaging |
Het |
Lyst |
T |
A |
13: 13,881,140 (GRCm39) |
D2790E |
probably benign |
Het |
Magi2 |
G |
A |
5: 20,755,238 (GRCm39) |
R604Q |
probably benign |
Het |
Mertk |
C |
A |
2: 128,613,417 (GRCm39) |
H478N |
probably benign |
Het |
Mical3 |
T |
A |
6: 121,013,505 (GRCm39) |
K293* |
probably null |
Het |
Nod2 |
T |
C |
8: 89,387,210 (GRCm39) |
L168P |
probably damaging |
Het |
Npnt |
T |
C |
3: 132,614,100 (GRCm39) |
|
probably null |
Het |
Or1x6 |
T |
G |
11: 50,939,122 (GRCm39) |
F63V |
probably damaging |
Het |
Or5af1 |
A |
T |
11: 58,722,308 (GRCm39) |
E109D |
probably damaging |
Het |
Or8b37 |
T |
C |
9: 37,959,253 (GRCm39) |
M245T |
probably benign |
Het |
Or9g4 |
A |
T |
2: 85,505,275 (GRCm39) |
Y73* |
probably null |
Het |
Plcd4 |
A |
T |
1: 74,593,811 (GRCm39) |
D312V |
probably damaging |
Het |
Prss58 |
A |
G |
6: 40,872,399 (GRCm39) |
I208T |
probably damaging |
Het |
Pus7l |
A |
G |
15: 94,438,498 (GRCm39) |
S116P |
probably benign |
Het |
Rcc1l |
A |
T |
5: 134,205,276 (GRCm39) |
I93N |
probably benign |
Het |
Rftn2 |
A |
C |
1: 55,265,311 (GRCm39) |
Y36* |
probably null |
Het |
Rp1l1 |
G |
A |
14: 64,267,069 (GRCm39) |
R885Q |
probably benign |
Het |
Rpgrip1 |
A |
T |
14: 52,378,116 (GRCm39) |
D488V |
probably damaging |
Het |
Sacs |
A |
G |
14: 61,444,893 (GRCm39) |
Y2313C |
possibly damaging |
Het |
Scrib |
T |
C |
15: 75,921,107 (GRCm39) |
Y1332C |
probably damaging |
Het |
Serpinb10 |
T |
C |
1: 107,468,672 (GRCm39) |
V105A |
probably damaging |
Het |
Slc35d1 |
A |
T |
4: 103,070,243 (GRCm39) |
|
probably null |
Het |
Slfn3 |
T |
C |
11: 83,103,648 (GRCm39) |
V173A |
probably benign |
Het |
Stard9 |
A |
T |
2: 120,535,167 (GRCm39) |
D3808V |
possibly damaging |
Het |
Supt16 |
A |
T |
14: 52,411,028 (GRCm39) |
V692D |
probably damaging |
Het |
Tapt1 |
A |
T |
5: 44,345,999 (GRCm39) |
V317E |
probably damaging |
Het |
Vmn2r101 |
T |
C |
17: 19,832,059 (GRCm39) |
I685T |
probably benign |
Het |
Vmn2r92 |
A |
G |
17: 18,387,513 (GRCm39) |
I173V |
probably benign |
Het |
Vps54 |
T |
C |
11: 21,224,999 (GRCm39) |
I165T |
probably damaging |
Het |
Zswim4 |
G |
A |
8: 84,950,327 (GRCm39) |
R628* |
probably null |
Het |
Zzz3 |
T |
C |
3: 152,157,736 (GRCm39) |
S770P |
probably 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 |
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'- ACAGAGGTCTTATACAGCAGCTTG -3'
(R):5'- ATCAGTGCAGCCAGCTTCAG -3'
Sequencing Primer
(F):5'- AGCTTGCTGTTAGCCCCTGG -3'
(R):5'- TTCAGCAGCCTGGTGTCG -3'
|
Posted On |
2019-09-13 |