Incidental Mutation 'R0799:Smpd3'
| ID |
76535 |
| 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 |
038979-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.904)
|
| Stock # |
R0799 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
106979180-107064597 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 106991421 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Glutamine
at position 377
(H377Q)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000148282
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000067512]
[ENSMUST00000212896]
|
| AlphaFold |
Q9JJY3 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000067512
AA Change: H377Q
PolyPhen 2
Score 0.918 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000069255
Gene: ENSMUSG00000031906
AA Change: H377Q
| 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 |
noncoding transcript
Transcript: ENSMUST00000180410
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000212896
AA Change: H377Q
PolyPhen 2
Score 0.918 (Sensitivity: 0.81; Specificity: 0.94)
|
| Meta Mutation Damage Score |
0.0910 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.8%
- 10x: 97.4%
- 20x: 94.9%
|
| Validation Efficiency |
100% (60/60) |
| 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: 59 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4921539E11Rik |
G |
A |
4: 103,100,101 (GRCm39) |
T33I |
possibly damaging |
Het |
| 4930555F03Rik |
A |
G |
8: 49,948,474 (GRCm39) |
|
noncoding transcript |
Het |
| Abcf3 |
T |
C |
16: 20,378,084 (GRCm39) |
L538P |
probably damaging |
Het |
| Adamts6 |
T |
C |
13: 104,450,779 (GRCm39) |
S321P |
probably damaging |
Het |
| Adgra2 |
G |
A |
8: 27,602,523 (GRCm39) |
R362H |
probably damaging |
Het |
| AI597479 |
T |
G |
1: 43,150,330 (GRCm39) |
S147A |
probably benign |
Het |
| Ajm1 |
A |
G |
2: 25,468,574 (GRCm39) |
S446P |
possibly damaging |
Het |
| Ampd3 |
T |
C |
7: 110,399,904 (GRCm39) |
F340L |
probably damaging |
Het |
| Atad3a |
A |
G |
4: 155,831,927 (GRCm39) |
V449A |
probably damaging |
Het |
| Bmal2 |
T |
C |
6: 146,724,751 (GRCm39) |
|
probably benign |
Het |
| Bpifa6 |
A |
T |
2: 153,834,192 (GRCm39) |
D328V |
probably benign |
Het |
| Brca2 |
T |
C |
5: 150,483,658 (GRCm39) |
S2903P |
probably damaging |
Het |
| Cct3 |
A |
T |
3: 88,206,652 (GRCm39) |
|
probably null |
Het |
| Cdk4 |
A |
G |
10: 126,900,863 (GRCm39) |
T172A |
probably damaging |
Het |
| Chd5 |
A |
G |
4: 152,468,616 (GRCm39) |
D1760G |
probably damaging |
Het |
| Chd7 |
A |
G |
4: 8,801,310 (GRCm39) |
|
probably benign |
Het |
| Crybb2 |
T |
C |
5: 113,210,037 (GRCm39) |
I109V |
probably benign |
Het |
| Csmd3 |
A |
G |
15: 48,048,780 (GRCm39) |
|
probably benign |
Het |
| Dach1 |
G |
T |
14: 98,406,051 (GRCm39) |
T232K |
possibly damaging |
Het |
| Dnlz |
A |
G |
2: 26,241,485 (GRCm39) |
V81A |
possibly damaging |
Het |
| Epb41l4b |
A |
G |
4: 57,086,003 (GRCm39) |
S191P |
probably damaging |
Het |
| Eps15l1 |
C |
T |
8: 73,099,929 (GRCm39) |
D821N |
probably damaging |
Het |
| Fam186a |
G |
A |
15: 99,839,893 (GRCm39) |
P2117L |
probably damaging |
Het |
| Fam83d |
T |
A |
2: 158,621,808 (GRCm39) |
F173Y |
probably damaging |
Het |
| Gm9116 |
A |
T |
3: 93,817,772 (GRCm39) |
R214S |
probably benign |
Het |
| Gtpbp1 |
A |
G |
15: 79,600,401 (GRCm39) |
I445V |
probably damaging |
Het |
| H2-M2 |
G |
A |
17: 37,793,640 (GRCm39) |
T122I |
probably damaging |
Het |
| Hgd |
C |
T |
16: 37,448,971 (GRCm39) |
|
probably benign |
Het |
| Hip1r |
A |
G |
5: 124,135,004 (GRCm39) |
Y380C |
probably benign |
Het |
| Hspa8 |
G |
A |
9: 40,715,137 (GRCm39) |
G389R |
probably damaging |
Het |
| Htt |
C |
A |
5: 34,975,097 (GRCm39) |
D622E |
probably benign |
Het |
| Iqca1 |
C |
A |
1: 90,070,453 (GRCm39) |
G133V |
probably null |
Het |
| Kdm4a |
A |
G |
4: 118,004,189 (GRCm39) |
|
probably null |
Het |
| Map3k9 |
G |
A |
12: 81,769,043 (GRCm39) |
P1025S |
probably benign |
Het |
| Or8b47 |
G |
A |
9: 38,435,437 (GRCm39) |
M136I |
probably benign |
Het |
| Pabpc1l |
C |
A |
2: 163,873,134 (GRCm39) |
H135N |
probably benign |
Het |
| Pacsin2 |
A |
T |
15: 83,263,998 (GRCm39) |
S346R |
probably benign |
Het |
| Pcdhb20 |
A |
G |
18: 37,638,938 (GRCm39) |
Y488C |
probably damaging |
Het |
| Pkdcc |
G |
A |
17: 83,531,347 (GRCm39) |
C452Y |
probably damaging |
Het |
| Poglut1 |
T |
C |
16: 38,355,083 (GRCm39) |
|
probably null |
Het |
| Prss59 |
A |
G |
6: 40,905,533 (GRCm39) |
M41T |
probably damaging |
Het |
| Pxk |
T |
C |
14: 8,148,123 (GRCm38) |
F409L |
probably benign |
Het |
| Pygm |
G |
A |
19: 6,436,048 (GRCm39) |
|
probably benign |
Het |
| Rabep2 |
T |
C |
7: 126,037,896 (GRCm39) |
S223P |
probably damaging |
Het |
| Rpp40 |
C |
T |
13: 36,086,034 (GRCm39) |
R109H |
probably benign |
Het |
| Sbf2 |
T |
C |
7: 109,940,562 (GRCm39) |
Y1266C |
possibly damaging |
Het |
| Slc5a4a |
T |
C |
10: 76,012,368 (GRCm39) |
V346A |
probably benign |
Het |
| Sppl2a |
C |
A |
2: 126,762,227 (GRCm39) |
|
probably benign |
Het |
| Tas2r134 |
T |
C |
2: 51,518,385 (GRCm39) |
I288T |
probably benign |
Het |
| Trim35 |
T |
A |
14: 66,546,650 (GRCm39) |
H472Q |
probably damaging |
Het |
| Trpm5 |
C |
A |
7: 142,632,088 (GRCm39) |
R907L |
probably damaging |
Het |
| Ube2e2 |
G |
T |
14: 18,630,393 (GRCm38) |
S56* |
probably null |
Het |
| Vmn2r88 |
A |
C |
14: 51,651,959 (GRCm39) |
R432S |
possibly damaging |
Het |
| Wdr24 |
A |
G |
17: 26,045,102 (GRCm39) |
Y279C |
probably damaging |
Het |
| Wdr90 |
A |
G |
17: 26,079,104 (GRCm39) |
V246A |
probably benign |
Het |
| Xrn2 |
T |
A |
2: 146,871,818 (GRCm39) |
N385K |
probably benign |
Het |
| Zfp28 |
T |
A |
7: 6,387,182 (GRCm39) |
S73T |
possibly damaging |
Het |
| Zfp345 |
T |
C |
2: 150,314,271 (GRCm39) |
E422G |
probably benign |
Het |
| Zhx2 |
A |
G |
15: 57,684,709 (GRCm39) |
E26G |
probably benign |
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 |
|
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 |
|
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'- AAGCTGCACCCATTGGGGTAAC -3'
(R):5'- TCGGCCACAAGAAGCTGATGAC -3'
Sequencing Primer
(F):5'- GTAACAGTGATAGGCCACGTCC -3'
(R):5'- AGAAGCTGATGACCCTGCTG -3'
|
| Posted On |
2013-10-16 |
Incidental Mutation