Incidental Mutation 'R2939:Smpd3'
ID |
264578 |
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 |
040516-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.904)
|
Stock # |
R2939 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
8 |
Chromosomal Location |
106979180-107064597 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 106984039 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Alanine
at position 560
(V560A)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000148282
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000067512]
[ENSMUST00000071592]
[ENSMUST00000212896]
|
AlphaFold |
Q9JJY3 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000067512
AA Change: V560A
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
SMART Domains |
Protein: ENSMUSP00000069255 Gene: ENSMUSG00000031906 AA Change: V560A
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 |
noncoding transcript
Transcript: ENSMUST00000180410
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000212896
AA Change: V560A
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
Meta Mutation Damage Score |
0.1033 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.6%
|
Validation Efficiency |
98% (62/63) |
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 |
Actl11 |
T |
C |
9: 107,808,409 (GRCm39) |
Y911H |
possibly damaging |
Het |
Arhgef26 |
A |
C |
3: 62,288,331 (GRCm39) |
K467T |
possibly damaging |
Het |
Armcx6 |
A |
T |
X: 133,650,625 (GRCm39) |
W69R |
probably damaging |
Het |
Asl |
T |
C |
5: 130,042,245 (GRCm39) |
Y277C |
probably damaging |
Het |
Atm |
T |
C |
9: 53,406,011 (GRCm39) |
Y1219C |
probably damaging |
Het |
Azin2 |
C |
T |
4: 128,828,397 (GRCm39) |
C270Y |
probably benign |
Het |
Brsk1 |
A |
T |
7: 4,711,139 (GRCm39) |
I545F |
possibly damaging |
Het |
Carm1 |
C |
A |
9: 21,490,692 (GRCm39) |
|
probably null |
Het |
Cfap410 |
A |
G |
10: 77,817,507 (GRCm39) |
N78S |
probably benign |
Het |
Cfap69 |
G |
A |
5: 5,694,432 (GRCm39) |
A143V |
probably damaging |
Het |
Cldn14 |
T |
C |
16: 93,716,192 (GRCm39) |
K218R |
probably damaging |
Het |
Col5a3 |
T |
C |
9: 20,706,954 (GRCm39) |
K714R |
unknown |
Het |
Crybg2 |
A |
G |
4: 133,809,745 (GRCm39) |
H1517R |
possibly damaging |
Het |
Dagla |
A |
C |
19: 10,233,728 (GRCm39) |
F382C |
probably damaging |
Het |
Dixdc1 |
G |
A |
9: 50,622,259 (GRCm39) |
A25V |
probably damaging |
Het |
Dock6 |
A |
G |
9: 21,750,496 (GRCm39) |
F473L |
possibly damaging |
Het |
Eif5 |
T |
C |
12: 111,506,713 (GRCm39) |
C102R |
probably damaging |
Het |
Faiml |
A |
G |
9: 99,114,527 (GRCm39) |
C121R |
probably damaging |
Het |
Fhdc1 |
A |
G |
3: 84,364,577 (GRCm39) |
V223A |
possibly damaging |
Het |
Garin4 |
T |
C |
1: 190,896,103 (GRCm39) |
D180G |
possibly damaging |
Het |
Gpatch8 |
A |
G |
11: 102,399,010 (GRCm39) |
V74A |
unknown |
Het |
Haghl |
A |
G |
17: 26,004,060 (GRCm39) |
V8A |
possibly damaging |
Het |
Ksr1 |
A |
G |
11: 78,936,007 (GRCm39) |
|
probably null |
Het |
Lama5 |
A |
C |
2: 179,840,747 (GRCm39) |
Y584D |
probably damaging |
Het |
Lgi4 |
C |
T |
7: 30,767,253 (GRCm39) |
R427* |
probably null |
Het |
Lrriq1 |
T |
A |
10: 102,980,750 (GRCm39) |
S1462C |
probably damaging |
Het |
Map3k4 |
C |
T |
17: 12,480,157 (GRCm39) |
E682K |
probably damaging |
Het |
Myo9b |
G |
A |
8: 71,786,981 (GRCm39) |
R721Q |
probably benign |
Het |
Nherf1 |
C |
T |
11: 115,071,270 (GRCm39) |
R335C |
probably damaging |
Het |
Nmnat2 |
C |
A |
1: 152,950,474 (GRCm39) |
S53Y |
probably damaging |
Het |
Or8b12i |
C |
A |
9: 20,082,061 (GRCm39) |
G269W |
probably benign |
Het |
Or8g34 |
G |
A |
9: 39,373,226 (GRCm39) |
M166I |
probably benign |
Het |
Pcsk7 |
C |
T |
9: 45,827,322 (GRCm39) |
A363V |
probably damaging |
Het |
Pdrg1 |
C |
T |
2: 152,854,355 (GRCm39) |
G62R |
probably damaging |
Het |
Pdzd7 |
A |
G |
19: 45,033,862 (GRCm39) |
I74T |
possibly damaging |
Het |
Plcb4 |
T |
C |
2: 135,781,123 (GRCm39) |
|
probably benign |
Het |
Pramel28 |
A |
G |
4: 143,693,247 (GRCm39) |
V77A |
probably benign |
Het |
Rnf25 |
A |
G |
1: 74,635,047 (GRCm39) |
V135A |
possibly damaging |
Het |
Rph3a |
A |
G |
5: 121,118,212 (GRCm39) |
|
probably benign |
Het |
Rsf1 |
CG |
CGACGGCGGTG |
7: 97,229,115 (GRCm39) |
|
probably benign |
Het |
Senp6 |
G |
A |
9: 80,051,124 (GRCm39) |
A1134T |
probably benign |
Het |
Slc1a6 |
G |
T |
10: 78,650,448 (GRCm39) |
*562L |
probably null |
Het |
Slc26a6 |
G |
A |
9: 108,734,236 (GRCm39) |
V206I |
probably benign |
Het |
Slc45a3 |
A |
G |
1: 131,905,637 (GRCm39) |
E206G |
probably damaging |
Het |
Smc1a |
T |
A |
X: 150,816,695 (GRCm39) |
Y516N |
probably damaging |
Het |
Spata31g1 |
A |
G |
4: 42,972,946 (GRCm39) |
K760E |
probably benign |
Het |
Ssc4d |
T |
C |
5: 135,994,578 (GRCm39) |
T51A |
possibly damaging |
Het |
Suco |
A |
G |
1: 161,676,220 (GRCm39) |
I386T |
probably damaging |
Het |
Tecta |
A |
T |
9: 42,289,290 (GRCm39) |
M425K |
possibly damaging |
Het |
Tmprss11e |
G |
A |
5: 86,869,266 (GRCm39) |
R96W |
probably damaging |
Het |
Trim63 |
T |
C |
4: 134,050,308 (GRCm39) |
|
probably benign |
Het |
Trpv1 |
A |
G |
11: 73,145,675 (GRCm39) |
K403R |
probably damaging |
Het |
Ttc39d |
A |
G |
17: 80,524,982 (GRCm39) |
Y547C |
probably damaging |
Het |
Unc79 |
C |
T |
12: 102,957,684 (GRCm39) |
T33I |
probably damaging |
Het |
Usp47 |
G |
A |
7: 111,681,743 (GRCm39) |
S518N |
probably damaging |
Het |
Vmn2r22 |
T |
A |
6: 123,614,594 (GRCm39) |
D332V |
probably damaging |
Het |
Vmn2r55 |
A |
G |
7: 12,385,832 (GRCm39) |
L716P |
probably damaging |
Het |
Zfp558 |
T |
C |
9: 18,367,924 (GRCm39) |
N288S |
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 |
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 |
|
Predicted Primers |
PCR Primer
(F):5'- GCTTGAGTGAATTGGCCTTCC -3'
(R):5'- TTACTCGCTACAAAGACCCCTG -3'
Sequencing Primer
(F):5'- AGTGAATTGGCCTTCCTGGAACC -3'
(R):5'- CCTTGGGCCATTGGTAAGCAG -3'
|
Posted On |
2015-02-05 |