Incidental Mutation 'R7933:Smpd3'
| ID |
643710 |
| 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 |
045979-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.904)
|
| Stock # |
R7933 (G1)
|
| Quality Score |
999 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
106979180-107064597 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to C
at 106982254 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Glycine
at position 617
(C617G)
|
| 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: C617G
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000069255
Gene: ENSMUSG00000031906
AA Change: C617G
| 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 benign
Transcript: ENSMUST00000212896
AA Change: C617G
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.9%
- 20x: 99.7%
|
| Validation Efficiency |
98% (42/43) |
| 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: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4933414I15Rik |
A |
G |
11: 50,833,227 (GRCm39) |
V125A |
unknown |
Het |
| Adam34 |
T |
A |
8: 44,103,911 (GRCm39) |
H578L |
probably damaging |
Het |
| Agap2 |
C |
A |
10: 126,922,789 (GRCm39) |
|
probably benign |
Het |
| Ago4 |
A |
T |
4: 126,400,811 (GRCm39) |
M678K |
probably benign |
Het |
| Ankrd27 |
A |
G |
7: 35,301,074 (GRCm39) |
|
probably benign |
Het |
| Atosb |
A |
T |
4: 43,035,919 (GRCm39) |
C271S |
probably benign |
Het |
| Atrn |
T |
C |
2: 130,836,986 (GRCm39) |
L1150P |
probably damaging |
Het |
| Bbs1 |
T |
A |
19: 4,941,678 (GRCm39) |
|
probably benign |
Het |
| Camta1 |
C |
T |
4: 151,168,214 (GRCm39) |
E279K |
probably damaging |
Het |
| Ccdc88c |
T |
C |
12: 100,911,749 (GRCm39) |
D695G |
possibly damaging |
Het |
| Col11a2 |
A |
T |
17: 34,275,029 (GRCm39) |
K400* |
probably null |
Het |
| Cpsf4 |
T |
A |
5: 145,104,168 (GRCm39) |
M1K |
probably null |
Het |
| Dnah12 |
A |
T |
14: 26,488,072 (GRCm39) |
Q992L |
probably benign |
Het |
| Dnajc7 |
T |
C |
11: 100,487,038 (GRCm39) |
Y145C |
probably damaging |
Het |
| Eml5 |
A |
T |
12: 98,810,279 (GRCm39) |
D892E |
possibly damaging |
Het |
| Fam193a |
A |
G |
5: 34,623,539 (GRCm39) |
K23E |
possibly damaging |
Het |
| Filip1 |
T |
G |
9: 79,727,329 (GRCm39) |
K430T |
possibly damaging |
Het |
| Gm5089 |
T |
C |
14: 122,673,403 (GRCm39) |
D106G |
unknown |
Het |
| Hip1 |
A |
T |
5: 135,489,310 (GRCm39) |
N45K |
probably damaging |
Het |
| Hivep2 |
T |
C |
10: 14,003,581 (GRCm39) |
S60P |
probably damaging |
Het |
| Ighv1-53 |
A |
T |
12: 115,122,029 (GRCm39) |
C115* |
probably null |
Het |
| Macf1 |
T |
C |
4: 123,303,444 (GRCm39) |
T353A |
probably benign |
Het |
| Mast3 |
A |
T |
8: 71,239,279 (GRCm39) |
V433E |
probably damaging |
Het |
| Mast4 |
A |
T |
13: 102,909,071 (GRCm39) |
M660K |
probably damaging |
Het |
| Nr2e1 |
T |
C |
10: 42,439,379 (GRCm39) |
Y380C |
probably damaging |
Het |
| Or10g9b |
T |
C |
9: 39,918,431 (GRCm39) |
|
probably benign |
Het |
| Or5b111 |
T |
A |
19: 13,291,569 (GRCm39) |
M27L |
probably benign |
Het |
| Otog |
A |
G |
7: 45,959,571 (GRCm39) |
D720G |
probably damaging |
Het |
| Slc6a1 |
T |
A |
6: 114,288,859 (GRCm39) |
W473R |
probably damaging |
Het |
| Spata31d1e |
A |
G |
13: 59,891,565 (GRCm39) |
L85P |
probably damaging |
Het |
| Sprr3 |
T |
C |
3: 92,364,515 (GRCm39) |
I110V |
possibly damaging |
Het |
| Ston1 |
A |
G |
17: 88,943,572 (GRCm39) |
E326G |
probably benign |
Het |
| Tapbpl |
T |
G |
6: 125,207,233 (GRCm39) |
Q152P |
probably damaging |
Het |
| Tectb |
C |
T |
19: 55,183,105 (GRCm39) |
L319F |
possibly damaging |
Het |
| Tpp2 |
G |
A |
1: 44,000,121 (GRCm39) |
G413D |
probably damaging |
Het |
| Tpsg1 |
A |
G |
17: 25,592,178 (GRCm39) |
H84R |
probably damaging |
Het |
| Usp24 |
A |
G |
4: 106,285,686 (GRCm39) |
N2437S |
probably benign |
Het |
| Usp32 |
T |
C |
11: 84,897,885 (GRCm39) |
Q1152R |
probably damaging |
Het |
| Vmn2r6 |
T |
C |
3: 64,467,224 (GRCm39) |
T92A |
probably benign |
Het |
| Xpo7 |
A |
G |
14: 70,944,788 (GRCm39) |
V35A |
probably benign |
Het |
| Zan |
T |
A |
5: 137,461,841 (GRCm39) |
T1113S |
unknown |
Het |
| Zfp169 |
A |
G |
13: 48,643,957 (GRCm39) |
V390A |
unknown |
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 |
|
|
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'- AGCTCCAAAGAGAAGTGCTC -3'
(R):5'- GGCACAGAACTTTAGCTTGTTTCC -3'
Sequencing Primer
(F):5'- CTCTGTGAAGGGGAGTGCC -3'
(R):5'- AGAACTTTAGCTTGTTTCCCTTCTG -3'
|
| Posted On |
2020-08-07 |
Incidental Mutation