Incidental Mutation 'R8292:Smpd3'
| ID |
638747 |
| 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 |
067782-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.904)
|
| Stock # |
R8292 (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 C
at 106991422 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Arginine
at position 377
(H377R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000069255
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000067512]
[ENSMUST00000212896]
|
| AlphaFold |
Q9JJY3 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000067512
AA Change: H377R
PolyPhen 2
Score 0.083 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000069255
Gene: ENSMUSG00000031906
AA Change: H377R
| 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: ENSMUST00000212896
AA Change: H377R
PolyPhen 2
Score 0.083 (Sensitivity: 0.93; Specificity: 0.85)
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 99.1%
|
| 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: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acacb |
A |
T |
5: 114,338,555 (GRCm39) |
|
probably null |
Het |
| Akirin2 |
T |
C |
4: 34,566,007 (GRCm39) |
|
probably null |
Het |
| Akr1c14 |
A |
G |
13: 4,130,995 (GRCm39) |
D229G |
possibly damaging |
Het |
| Arfgef1 |
T |
C |
1: 10,227,194 (GRCm39) |
I1382V |
probably benign |
Het |
| Bcas3 |
C |
A |
11: 85,348,729 (GRCm39) |
A207D |
probably damaging |
Het |
| Bcl2l10 |
T |
C |
9: 75,255,160 (GRCm39) |
|
probably benign |
Het |
| Cdc42 |
T |
C |
4: 137,063,384 (GRCm39) |
T3A |
probably benign |
Het |
| Celsr1 |
C |
A |
15: 85,791,819 (GRCm39) |
W2594L |
possibly damaging |
Het |
| Chrna6 |
A |
T |
8: 27,896,754 (GRCm39) |
H374Q |
probably benign |
Het |
| Cibar1 |
T |
G |
4: 12,153,963 (GRCm39) |
T330P |
possibly damaging |
Het |
| Clcnka |
G |
A |
4: 141,125,272 (GRCm39) |
R30* |
probably null |
Het |
| Clptm1l |
A |
T |
13: 73,765,854 (GRCm39) |
H464L |
probably damaging |
Het |
| Col6a4 |
A |
T |
9: 105,954,076 (GRCm39) |
M421K |
probably benign |
Het |
| Crybg2 |
T |
C |
4: 133,802,842 (GRCm39) |
S873P |
probably damaging |
Het |
| Dixdc1 |
A |
G |
9: 50,621,989 (GRCm39) |
V114A |
probably benign |
Het |
| Etv6 |
T |
C |
6: 134,225,509 (GRCm39) |
C247R |
probably benign |
Het |
| Farp2 |
T |
C |
1: 93,456,350 (GRCm39) |
L11S |
probably damaging |
Het |
| Gbp2 |
G |
A |
3: 142,329,584 (GRCm39) |
V44M |
probably damaging |
Het |
| Get4 |
A |
G |
5: 139,248,686 (GRCm39) |
D99G |
probably null |
Het |
| Glcci1 |
G |
A |
6: 8,558,549 (GRCm39) |
R212H |
probably damaging |
Het |
| Gm14295 |
T |
A |
2: 176,501,351 (GRCm39) |
F280L |
probably damaging |
Het |
| Gm5407 |
T |
A |
16: 49,117,550 (GRCm39) |
N70Y |
noncoding transcript |
Het |
| Hace1 |
C |
G |
10: 45,587,557 (GRCm39) |
Y885* |
probably null |
Het |
| Hectd4 |
G |
A |
5: 121,455,288 (GRCm39) |
R644Q |
possibly damaging |
Het |
| Impg2 |
A |
T |
16: 56,080,989 (GRCm39) |
E931V |
probably damaging |
Het |
| Kif5c |
A |
T |
2: 49,625,497 (GRCm39) |
Y589F |
probably benign |
Het |
| Krr1 |
T |
A |
10: 111,813,021 (GRCm39) |
V132E |
possibly damaging |
Het |
| Luzp1 |
T |
G |
4: 136,269,764 (GRCm39) |
D662E |
probably benign |
Het |
| Mc4r |
A |
T |
18: 66,993,082 (GRCm39) |
Y10* |
probably null |
Het |
| Mfng |
T |
C |
15: 78,657,370 (GRCm39) |
I35V |
probably benign |
Het |
| Mprip |
T |
A |
11: 59,650,340 (GRCm39) |
I1348K |
probably benign |
Het |
| Mrgprb3 |
G |
T |
7: 48,293,255 (GRCm39) |
Q99K |
probably benign |
Het |
| Mrgprb4 |
A |
T |
7: 47,848,554 (GRCm39) |
S125T |
probably damaging |
Het |
| Mrgprg |
A |
T |
7: 143,318,656 (GRCm39) |
M152K |
probably benign |
Het |
| Muc5ac |
A |
C |
7: 141,363,000 (GRCm39) |
I2104L |
unknown |
Het |
| Myom2 |
A |
G |
8: 15,182,888 (GRCm39) |
I1442V |
probably benign |
Het |
| Nell1 |
T |
C |
7: 49,907,995 (GRCm39) |
C385R |
probably damaging |
Het |
| Nid2 |
T |
G |
14: 19,818,346 (GRCm39) |
V280G |
probably damaging |
Het |
| Npr2 |
T |
A |
4: 43,643,086 (GRCm39) |
M490K |
possibly damaging |
Het |
| Prr12 |
A |
G |
7: 44,684,112 (GRCm39) |
F1643L |
probably damaging |
Het |
| Psg16 |
G |
A |
7: 16,827,701 (GRCm39) |
G128D |
probably damaging |
Het |
| Racgap1 |
A |
T |
15: 99,520,127 (GRCm39) |
L595* |
probably null |
Het |
| Rbbp8 |
T |
C |
18: 11,838,769 (GRCm39) |
V150A |
probably benign |
Het |
| Rbbp9 |
T |
C |
2: 144,390,017 (GRCm39) |
T49A |
probably benign |
Het |
| Rbm20 |
C |
A |
19: 53,839,930 (GRCm39) |
T973K |
possibly damaging |
Het |
| Robo1 |
A |
T |
16: 72,769,420 (GRCm39) |
I582F |
possibly damaging |
Het |
| Rps6ka5 |
A |
T |
12: 100,644,791 (GRCm39) |
V53D |
possibly damaging |
Het |
| Slc35f6 |
G |
T |
5: 30,813,375 (GRCm39) |
V156L |
probably benign |
Het |
| Son |
G |
A |
16: 91,453,545 (GRCm39) |
S764N |
possibly damaging |
Het |
| Srgn |
A |
T |
10: 62,343,447 (GRCm39) |
V16D |
possibly damaging |
Het |
| Tex14 |
G |
A |
11: 87,388,664 (GRCm39) |
R297Q |
probably damaging |
Het |
| Tiam2 |
T |
C |
17: 3,557,142 (GRCm39) |
V1194A |
probably benign |
Het |
| Tlr6 |
A |
C |
5: 65,111,134 (GRCm39) |
L591R |
probably damaging |
Het |
| Tmem143 |
A |
G |
7: 45,558,964 (GRCm39) |
K302R |
probably damaging |
Het |
| Ttc28 |
A |
G |
5: 111,371,123 (GRCm39) |
Y555C |
probably damaging |
Het |
| Usp32 |
T |
A |
11: 84,968,227 (GRCm39) |
K145N |
probably damaging |
Het |
| Zbtb40 |
T |
C |
4: 136,726,878 (GRCm39) |
Y486C |
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 |
|
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'- ACAGTAGTGTGTAGCCCTCAG -3'
(R):5'- CAAGCTGCTGTATAAGACCTCTG -3'
Sequencing Primer
(F):5'- GTTGCCTACCTTGAGAAACAGAGC -3'
(R):5'- CCTCTGTGGTGAAGAAGGC -3'
|
| Posted On |
2020-07-28 |
Incidental Mutation