Incidental Mutation 'R9703:Smpd3'
| ID |
729666 |
| 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 |
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.922)
|
| Stock # |
R9703 (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 A
at 106991713 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Leucine
at position 280
(H280L)
|
| 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: H280L
PolyPhen 2
Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000069255
Gene: ENSMUSG00000031906
AA Change: H280L
| 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: H280L
PolyPhen 2
Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.3%
- 20x: 98.2%
|
| 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: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam20 |
T |
A |
8: 41,248,971 (GRCm39) |
N360K |
probably damaging |
Het |
| Aoc1l2 |
A |
G |
6: 48,909,629 (GRCm39) |
T625A |
probably benign |
Het |
| Apob |
T |
A |
12: 8,030,507 (GRCm39) |
L82Q |
probably damaging |
Het |
| Arhgap30 |
T |
G |
1: 171,235,339 (GRCm39) |
L571R |
probably damaging |
Het |
| Atg9a |
C |
T |
1: 75,162,431 (GRCm39) |
C493Y |
probably damaging |
Het |
| Brip1 |
T |
C |
11: 85,952,830 (GRCm39) |
T984A |
possibly damaging |
Het |
| Btbd9 |
A |
G |
17: 30,749,200 (GRCm39) |
V38A |
possibly damaging |
Het |
| Crocc2 |
C |
A |
1: 93,130,444 (GRCm39) |
D908E |
probably benign |
Het |
| Crybg3 |
C |
G |
16: 59,375,939 (GRCm39) |
A58P |
probably damaging |
Het |
| Cts7 |
T |
C |
13: 61,504,350 (GRCm39) |
N71S |
probably damaging |
Het |
| Ddx46 |
A |
G |
13: 55,824,635 (GRCm39) |
Y962C |
probably damaging |
Het |
| Dock10 |
G |
A |
1: 80,517,540 (GRCm39) |
R1373C |
probably damaging |
Het |
| Dock9 |
A |
T |
14: 121,781,989 (GRCm39) |
*2043R |
probably null |
Het |
| Efs |
A |
T |
14: 55,156,871 (GRCm39) |
V388E |
possibly damaging |
Het |
| Esyt1 |
C |
T |
10: 128,354,796 (GRCm39) |
|
probably null |
Het |
| Extl3 |
G |
T |
14: 65,292,103 (GRCm39) |
R907S |
probably damaging |
Het |
| Fcgbp |
G |
A |
7: 27,806,400 (GRCm39) |
V2123M |
probably damaging |
Het |
| Gas2l3 |
C |
T |
10: 89,249,943 (GRCm39) |
A392T |
probably benign |
Het |
| Golm1 |
A |
T |
13: 59,797,433 (GRCm39) |
D137E |
probably benign |
Het |
| Grxcr2 |
T |
C |
18: 42,124,988 (GRCm39) |
D140G |
possibly damaging |
Het |
| H2ac19 |
G |
A |
3: 96,147,557 (GRCm39) |
R4C |
probably benign |
Het |
| Hrh1 |
G |
A |
6: 114,457,979 (GRCm39) |
C420Y |
probably benign |
Het |
| Ints13 |
A |
T |
6: 146,459,063 (GRCm39) |
L316Q |
probably damaging |
Het |
| Iws1 |
T |
A |
18: 32,212,738 (GRCm39) |
D55E |
probably damaging |
Het |
| Kcnrg |
CACAACAA |
CACAA |
14: 61,845,009 (GRCm39) |
|
probably benign |
Het |
| Klrc2 |
G |
C |
6: 129,633,407 (GRCm39) |
S215* |
probably null |
Het |
| Muc5b |
A |
G |
7: 141,425,535 (GRCm39) |
T4727A |
possibly damaging |
Het |
| Nsd3 |
T |
C |
8: 26,131,228 (GRCm39) |
S198P |
probably benign |
Het |
| Or2n1b |
A |
T |
17: 38,459,856 (GRCm39) |
I126F |
possibly damaging |
Het |
| Or6c214 |
A |
T |
10: 129,591,286 (GRCm39) |
I11N |
possibly damaging |
Het |
| Ovch2 |
T |
A |
7: 107,383,777 (GRCm39) |
I523F |
probably damaging |
Het |
| Pals1 |
T |
A |
12: 78,843,850 (GRCm39) |
I18K |
probably benign |
Het |
| Pcdhb1 |
T |
A |
18: 37,399,019 (GRCm39) |
D323E |
probably damaging |
Het |
| Pfkl |
T |
A |
10: 77,826,142 (GRCm39) |
|
probably null |
Het |
| Pigc |
T |
A |
1: 161,798,176 (GRCm39) |
F53I |
probably benign |
Het |
| Pramel29 |
T |
A |
4: 143,939,510 (GRCm39) |
D9V |
probably damaging |
Het |
| Prph2 |
G |
A |
17: 47,234,447 (GRCm39) |
A339T |
unknown |
Het |
| Prrc2a |
T |
C |
17: 35,378,320 (GRCm39) |
K452E |
unknown |
Het |
| Rab36 |
T |
C |
10: 74,886,474 (GRCm39) |
W151R |
possibly damaging |
Het |
| Sdk1 |
A |
G |
5: 142,100,283 (GRCm39) |
T1438A |
possibly damaging |
Het |
| Slc25a17 |
A |
T |
15: 81,224,193 (GRCm39) |
I55K |
probably damaging |
Het |
| Smg1 |
A |
T |
7: 117,739,744 (GRCm39) |
I3401N |
possibly damaging |
Het |
| Srsf10 |
A |
G |
4: 135,591,153 (GRCm39) |
H202R |
probably benign |
Het |
| Swap70 |
C |
T |
7: 109,872,512 (GRCm39) |
R376C |
probably damaging |
Het |
| Syde1 |
G |
T |
10: 78,421,557 (GRCm39) |
L665M |
probably damaging |
Het |
| Tha1 |
A |
G |
11: 117,761,863 (GRCm39) |
V126A |
probably damaging |
Het |
| Tln2 |
T |
C |
9: 67,293,938 (GRCm39) |
H230R |
probably damaging |
Het |
| Tnc |
G |
A |
4: 63,889,412 (GRCm39) |
A1698V |
probably benign |
Het |
| Twist2 |
C |
A |
1: 91,729,744 (GRCm39) |
S132R |
probably damaging |
Het |
| Ubr1 |
C |
T |
2: 120,732,092 (GRCm39) |
C1170Y |
probably damaging |
Het |
| Vwa1 |
G |
A |
4: 155,857,336 (GRCm39) |
P154L |
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 |
|
|
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 |
|
Z1177:Smpd3
|
UTSW |
8 |
106,991,474 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- CAAAGGCTTCATCAGGGTGG -3'
(R):5'- CCTCTGTGGAATACAAGGGG -3'
Sequencing Primer
(F):5'- TTCATCAGGGTGGCGCCTC -3'
(R):5'- CTCTGTGGAATACAAGGGGGATGG -3'
|
| Posted On |
2022-10-06 |
Incidental Mutation