Incidental Mutation 'R8494:Smpd3'
ID |
658186 |
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 |
067936-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.904)
|
Stock # |
R8494 (G1)
|
Quality Score |
225.009 |
Status
|
Not validated
|
Chromosome |
8 |
Chromosomal Location |
106979180-107064597 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 106981982 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Glutamic Acid to Glycine
at position 626
(E626G)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000148282
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000067512]
[ENSMUST00000071592]
[ENSMUST00000212896]
|
AlphaFold |
Q9JJY3 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000067512
AA Change: E626G
PolyPhen 2
Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
|
SMART Domains |
Protein: ENSMUSP00000069255 Gene: ENSMUSG00000031906 AA Change: E626G
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: ENSMUST00000071592
|
SMART Domains |
Protein: ENSMUSP00000071521 Gene: ENSMUSG00000060098
Domain | Start | End | E-Value | Type |
Pfam:PrmA
|
53 |
148 |
1.6e-7 |
PFAM |
internal_repeat_1
|
382 |
652 |
1.71e-8 |
PROSPERO |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000212896
AA Change: E626G
PolyPhen 2
Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.2%
|
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: 44 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca12 |
T |
A |
1: 71,327,821 (GRCm39) |
M1420L |
probably benign |
Het |
Adamts14 |
T |
A |
10: 61,038,708 (GRCm39) |
H934L |
probably benign |
Het |
Adamtsl1 |
T |
C |
4: 86,240,221 (GRCm39) |
C661R |
probably damaging |
Het |
Akap5 |
A |
G |
12: 76,376,455 (GRCm39) |
D629G |
probably benign |
Het |
Anapc16 |
A |
T |
10: 59,832,340 (GRCm39) |
|
probably benign |
Het |
Ankar |
T |
C |
1: 72,697,953 (GRCm39) |
I758V |
probably benign |
Het |
Apc2 |
G |
T |
10: 80,150,313 (GRCm39) |
R1760L |
probably damaging |
Het |
C1qb |
T |
C |
4: 136,608,115 (GRCm39) |
T83A |
probably benign |
Het |
Canx |
T |
A |
11: 50,202,609 (GRCm39) |
|
probably null |
Het |
Cblb |
T |
A |
16: 52,025,003 (GRCm39) |
I966K |
probably damaging |
Het |
Crocc2 |
A |
T |
1: 93,144,788 (GRCm39) |
Q1444L |
probably damaging |
Het |
Dennd4c |
C |
T |
4: 86,759,312 (GRCm39) |
P1781S |
probably damaging |
Het |
Diaph3 |
T |
C |
14: 87,274,958 (GRCm39) |
Y166C |
probably benign |
Het |
Dnah5 |
A |
C |
15: 28,345,977 (GRCm39) |
N2439T |
probably benign |
Het |
Dsg3 |
T |
A |
18: 20,673,271 (GRCm39) |
Y981N |
probably benign |
Het |
Esrp2 |
C |
T |
8: 106,861,350 (GRCm39) |
V150M |
probably damaging |
Het |
Fbxo15 |
T |
G |
18: 84,982,252 (GRCm39) |
F235V |
probably damaging |
Het |
Ffar2 |
A |
T |
7: 30,519,164 (GRCm39) |
Y125* |
probably null |
Het |
Gm1110 |
T |
A |
9: 26,792,154 (GRCm39) |
D622V |
probably benign |
Het |
Gpcpd1 |
A |
G |
2: 132,386,355 (GRCm39) |
V341A |
probably damaging |
Het |
Gpx3 |
G |
A |
11: 54,793,846 (GRCm39) |
V19I |
probably benign |
Het |
Hadha |
T |
C |
5: 30,347,810 (GRCm39) |
I160M |
probably damaging |
Het |
Igkv3-4 |
G |
T |
6: 70,649,147 (GRCm39) |
V49F |
probably damaging |
Het |
Kcng1 |
A |
G |
2: 168,105,018 (GRCm39) |
V276A |
probably damaging |
Het |
Kif7 |
A |
T |
7: 79,360,145 (GRCm39) |
V364D |
probably benign |
Het |
Kirrel3 |
A |
G |
9: 34,902,341 (GRCm39) |
I182V |
probably benign |
Het |
Lfng |
G |
A |
5: 140,598,981 (GRCm39) |
E297K |
probably damaging |
Het |
Mcm9 |
G |
A |
10: 53,501,856 (GRCm39) |
T243M |
possibly damaging |
Het |
Micall1 |
T |
C |
15: 79,005,080 (GRCm39) |
L184P |
probably damaging |
Het |
Mief1 |
T |
A |
15: 80,133,593 (GRCm39) |
C217S |
probably benign |
Het |
Mier2 |
T |
C |
10: 79,377,546 (GRCm39) |
D469G |
probably damaging |
Het |
Mst1r |
T |
G |
9: 107,791,718 (GRCm39) |
W799G |
possibly damaging |
Het |
Mybpc1 |
C |
T |
10: 88,362,291 (GRCm39) |
V950I |
probably benign |
Het |
Neurl4 |
A |
G |
11: 69,801,871 (GRCm39) |
D1296G |
probably benign |
Het |
Or4b12 |
A |
T |
2: 90,095,880 (GRCm39) |
M298K |
probably null |
Het |
Parg |
T |
A |
14: 31,930,978 (GRCm39) |
H199Q |
probably benign |
Het |
Pcnx3 |
C |
A |
19: 5,725,404 (GRCm39) |
D1170Y |
probably damaging |
Het |
Phactr1 |
T |
A |
13: 43,250,144 (GRCm39) |
V487E |
probably damaging |
Het |
Selp |
T |
G |
1: 163,957,835 (GRCm39) |
|
probably null |
Het |
Syn3 |
A |
G |
10: 86,190,265 (GRCm39) |
L188P |
probably damaging |
Het |
Tle1 |
T |
C |
4: 72,043,241 (GRCm39) |
I543V |
possibly damaging |
Het |
Trp53rkb |
A |
G |
2: 166,637,779 (GRCm39) |
*245W |
probably null |
Het |
Ttc28 |
A |
G |
5: 111,383,506 (GRCm39) |
R1336G |
probably damaging |
Het |
Vps13b |
T |
A |
15: 35,422,594 (GRCm39) |
W185R |
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 |
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 |
|
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'- ATTGATGGGCTCGTCCTTC -3'
(R):5'- CCACAGCCTGAAATCCTCTG -3'
Sequencing Primer
(F):5'- CACTGGGTGCTCAATGGAG -3'
(R):5'- TGAACAACCCTAGCCCACTTGG -3'
|
Posted On |
2021-01-18 |