Incidental Mutation 'R8264:Smpd3'
ID |
639731 |
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 |
067689-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.904)
|
Stock # |
R8264 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
8 |
Chromosomal Location |
106979180-107064597 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 106991290 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Tyrosine to Cysteine
at position 421
(Y421C)
|
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: Y421C
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000069255 Gene: ENSMUSG00000031906 AA Change: Y421C
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: Y421C
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.8%
|
Validation Efficiency |
98% (51/52) |
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: 50 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1110002E22Rik |
T |
A |
3: 137,773,543 (GRCm39) |
C911S |
probably damaging |
Het |
Abcc4 |
T |
A |
14: 118,832,254 (GRCm39) |
N792I |
possibly damaging |
Het |
Acacb |
A |
T |
5: 114,345,427 (GRCm39) |
H960L |
probably benign |
Het |
Aox1 |
A |
G |
1: 58,092,873 (GRCm39) |
T162A |
possibly damaging |
Het |
Cacna1g |
T |
C |
11: 94,364,392 (GRCm39) |
S18G |
probably benign |
Het |
Chfr |
T |
A |
5: 110,300,300 (GRCm39) |
I348N |
possibly damaging |
Het |
Cntln |
G |
A |
4: 85,016,648 (GRCm39) |
R12Q |
probably damaging |
Het |
Cyp2c40 |
A |
G |
19: 39,795,971 (GRCm39) |
S136P |
possibly damaging |
Het |
Dnah14 |
T |
A |
1: 181,572,357 (GRCm39) |
M2896K |
probably damaging |
Het |
Elp6 |
A |
G |
9: 110,148,755 (GRCm39) |
T215A |
probably damaging |
Het |
Esyt2 |
A |
C |
12: 116,329,540 (GRCm39) |
Q699H |
probably benign |
Het |
Fbxo25 |
A |
G |
8: 13,979,393 (GRCm39) |
T204A |
possibly damaging |
Het |
Fhdc1 |
A |
G |
3: 84,362,339 (GRCm39) |
S294P |
probably damaging |
Het |
G530012D18Rik |
C |
G |
1: 85,504,935 (GRCm39) |
D113E |
unknown |
Het |
Galnt10 |
A |
G |
11: 57,673,032 (GRCm39) |
I463V |
probably benign |
Het |
Glce |
A |
G |
9: 61,967,712 (GRCm39) |
F480L |
probably benign |
Het |
H2-Aa |
A |
G |
17: 34,506,709 (GRCm39) |
V11A |
probably benign |
Het |
Hsd17b4 |
A |
G |
18: 50,279,593 (GRCm39) |
T191A |
possibly damaging |
Het |
Itpr3 |
G |
T |
17: 27,323,086 (GRCm39) |
|
silent |
Het |
Izumo4 |
G |
T |
10: 80,538,572 (GRCm39) |
G8V |
|
Het |
Klk1b5 |
T |
A |
7: 43,869,454 (GRCm39) |
L178H |
probably damaging |
Het |
Lama2 |
T |
C |
10: 27,343,218 (GRCm39) |
N85D |
probably benign |
Het |
Liph |
A |
C |
16: 21,802,721 (GRCm39) |
I116R |
possibly damaging |
Het |
Lpar5 |
T |
A |
6: 125,058,465 (GRCm39) |
V62D |
probably damaging |
Het |
Map3k19 |
T |
A |
1: 127,751,528 (GRCm39) |
I303F |
|
Het |
Mymk |
A |
G |
2: 26,957,868 (GRCm39) |
|
probably benign |
Het |
Myo10 |
G |
A |
15: 25,800,195 (GRCm39) |
V1424M |
probably damaging |
Het |
Myof |
T |
G |
19: 37,909,881 (GRCm39) |
Q1528P |
probably damaging |
Het |
Ncapd3 |
T |
C |
9: 27,006,038 (GRCm39) |
|
probably benign |
Het |
Nup214 |
T |
A |
2: 31,884,738 (GRCm39) |
Y500N |
possibly damaging |
Het |
Or5al6 |
T |
C |
2: 85,976,538 (GRCm39) |
D180G |
probably damaging |
Het |
Pappa2 |
T |
C |
1: 158,682,543 (GRCm39) |
Y835C |
probably damaging |
Het |
Pcdh18 |
T |
C |
3: 49,711,030 (GRCm39) |
E95G |
probably damaging |
Het |
Phf3 |
A |
T |
1: 30,870,138 (GRCm39) |
N303K |
possibly damaging |
Het |
Pnn |
C |
T |
12: 59,119,363 (GRCm39) |
H649Y |
unknown |
Het |
Rab11fip1 |
G |
A |
8: 27,642,508 (GRCm39) |
Q764* |
probably null |
Het |
Ralgapa2 |
A |
T |
2: 146,175,370 (GRCm39) |
M1762K |
possibly damaging |
Het |
Rif1 |
G |
A |
2: 51,980,290 (GRCm39) |
A496T |
noncoding transcript |
Het |
Rnase13 |
A |
T |
14: 52,159,914 (GRCm39) |
V75D |
probably damaging |
Het |
Sema3c |
G |
A |
5: 17,881,537 (GRCm39) |
|
probably benign |
Het |
Sema4c |
C |
G |
1: 36,591,966 (GRCm39) |
G266R |
probably damaging |
Het |
Slfn5 |
A |
T |
11: 82,847,376 (GRCm39) |
D87V |
probably damaging |
Het |
Snrnp40 |
T |
C |
4: 130,271,867 (GRCm39) |
V188A |
probably benign |
Het |
Srms |
A |
G |
2: 180,854,343 (GRCm39) |
Y75H |
probably benign |
Het |
Tent2 |
C |
T |
13: 93,312,077 (GRCm39) |
G208S |
probably damaging |
Het |
Tex15 |
T |
C |
8: 34,072,390 (GRCm39) |
S2646P |
probably benign |
Het |
Togaram1 |
A |
G |
12: 65,042,330 (GRCm39) |
I1130V |
probably benign |
Het |
Ttf1 |
A |
G |
2: 28,954,689 (GRCm39) |
K18E |
possibly damaging |
Het |
Unc5b |
G |
T |
10: 60,604,113 (GRCm39) |
T827K |
probably benign |
Het |
Zfhx2 |
T |
A |
14: 55,302,969 (GRCm39) |
T1672S |
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 |
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 |
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'- CTGAGTTCAGTTCCATGAAAGGC -3'
(R):5'- TGCAGGAGGTGTTTGACAAGC -3'
Sequencing Primer
(F):5'- CAGTTCCATGAAAGGCTTTGTC -3'
(R):5'- TTTGACAAGCGTGCGGC -3'
|
Posted On |
2020-07-28 |