Incidental Mutation 'R8787:Smpd3'
| ID |
670708 |
| 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 |
068633-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.922)
|
| Stock # |
R8787 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
106979180-107064597 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 106982377 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Cysteine
at position 576
(R576C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000069255
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000067512]
[ENSMUST00000071592]
[ENSMUST00000212896]
|
| AlphaFold |
Q9JJY3 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000067512
AA Change: R576C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000069255
Gene: ENSMUSG00000031906
AA Change: R576C
| 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 damaging
Transcript: ENSMUST00000212896
AA Change: R576C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.1%
|
| Validation Efficiency |
98% (62/63) |
| 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: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca13 |
C |
T |
11: 9,225,053 (GRCm39) |
H511Y |
possibly damaging |
Het |
| Acp5 |
G |
A |
9: 22,038,489 (GRCm39) |
R271* |
probably null |
Het |
| Adamts20 |
A |
T |
15: 94,184,294 (GRCm39) |
V1503E |
possibly damaging |
Het |
| Adra2b |
A |
T |
2: 127,206,417 (GRCm39) |
E311D |
probably benign |
Het |
| Aldh18a1 |
T |
C |
19: 40,546,230 (GRCm39) |
I556V |
possibly damaging |
Het |
| Alox12 |
C |
A |
11: 70,144,146 (GRCm39) |
A116S |
probably benign |
Het |
| Alox5 |
G |
T |
6: 116,390,102 (GRCm39) |
A552E |
probably damaging |
Het |
| Angpt1 |
G |
T |
15: 42,375,780 (GRCm39) |
L159I |
probably damaging |
Het |
| Atp2b4 |
CTT |
CTTTTT |
1: 133,629,485 (GRCm39) |
|
probably benign |
Het |
| Bub1b |
T |
A |
2: 118,462,305 (GRCm39) |
L726I |
probably damaging |
Het |
| Ccdc78 |
A |
T |
17: 26,006,807 (GRCm39) |
T165S |
probably benign |
Het |
| Ccdc88b |
T |
C |
19: 6,824,791 (GRCm39) |
D1323G |
probably damaging |
Het |
| Chek1 |
A |
T |
9: 36,625,033 (GRCm39) |
C349* |
probably null |
Het |
| Clec1a |
A |
T |
6: 129,428,617 (GRCm39) |
L21Q |
possibly damaging |
Het |
| Col1a1 |
T |
C |
11: 94,833,634 (GRCm39) |
V445A |
possibly damaging |
Het |
| Efcab7 |
A |
G |
4: 99,757,791 (GRCm39) |
T313A |
probably null |
Het |
| Fads1 |
T |
A |
19: 10,170,325 (GRCm39) |
Y288* |
probably null |
Het |
| Fgb |
T |
A |
3: 82,953,969 (GRCm39) |
T90S |
probably benign |
Het |
| Glg1 |
C |
A |
8: 111,888,114 (GRCm39) |
V1026L |
probably damaging |
Het |
| Hadh |
T |
A |
3: 131,027,825 (GRCm39) |
Y313F |
probably damaging |
Het |
| Htr4 |
A |
G |
18: 62,570,853 (GRCm39) |
I303V |
possibly damaging |
Het |
| Kcnn3 |
A |
G |
3: 89,552,757 (GRCm39) |
D487G |
possibly damaging |
Het |
| L1td1 |
G |
A |
4: 98,625,814 (GRCm39) |
V604I |
probably benign |
Het |
| Lao1 |
A |
G |
4: 118,825,565 (GRCm39) |
T462A |
probably damaging |
Het |
| Lefty1 |
C |
A |
1: 180,764,118 (GRCm39) |
A86E |
probably damaging |
Het |
| Lmx1b |
T |
C |
2: 33,529,522 (GRCm39) |
Y79C |
|
Het |
| Lrp2 |
A |
G |
2: 69,382,745 (GRCm39) |
C47R |
probably damaging |
Het |
| Mrc2 |
A |
T |
11: 105,238,465 (GRCm39) |
N1204I |
probably benign |
Het |
| Ncf1 |
A |
C |
5: 134,254,145 (GRCm39) |
Y209* |
probably null |
Het |
| Or14j7 |
T |
A |
17: 38,235,075 (GRCm39) |
M206K |
probably benign |
Het |
| Or2ad1 |
A |
T |
13: 21,326,453 (GRCm39) |
M258K |
possibly damaging |
Het |
| Or8k33 |
G |
A |
2: 86,384,297 (GRCm39) |
T57M |
probably damaging |
Het |
| Oxtr |
T |
G |
6: 112,466,871 (GRCm39) |
|
probably benign |
Het |
| Pcdhac1 |
T |
C |
18: 37,224,942 (GRCm39) |
V585A |
probably damaging |
Het |
| Pdcd11 |
T |
G |
19: 47,097,019 (GRCm39) |
L755R |
probably damaging |
Het |
| Pkhd1 |
A |
G |
1: 20,358,461 (GRCm39) |
V2705A |
probably damaging |
Het |
| Plch2 |
C |
A |
4: 155,070,875 (GRCm39) |
G1168V |
probably benign |
Het |
| Prpf39 |
T |
C |
12: 65,089,555 (GRCm39) |
Y98H |
possibly damaging |
Het |
| R3hdm2 |
T |
G |
10: 127,293,521 (GRCm39) |
S142A |
probably damaging |
Het |
| Rassf10 |
T |
A |
7: 112,554,738 (GRCm39) |
D446E |
probably benign |
Het |
| Rgs13 |
T |
C |
1: 144,016,482 (GRCm39) |
Y87C |
probably damaging |
Het |
| Serpinb9h |
G |
A |
13: 33,588,204 (GRCm39) |
R263H |
probably benign |
Het |
| Spata31e1 |
T |
C |
13: 49,938,704 (GRCm39) |
Y1002C |
probably damaging |
Het |
| Srsf11 |
A |
T |
3: 157,718,037 (GRCm39) |
D382E |
unknown |
Het |
| Stpg1 |
T |
A |
4: 135,261,108 (GRCm39) |
M306K |
probably benign |
Het |
| Svil |
C |
T |
18: 5,059,332 (GRCm39) |
Q696* |
probably null |
Het |
| Syna |
C |
T |
5: 134,588,723 (GRCm39) |
M75I |
probably benign |
Het |
| Synj2 |
T |
C |
17: 6,036,514 (GRCm39) |
F161S |
possibly damaging |
Het |
| Tek |
T |
C |
4: 94,738,037 (GRCm39) |
Y696H |
probably damaging |
Het |
| Tgfbr1 |
A |
T |
4: 47,405,555 (GRCm39) |
D386V |
possibly damaging |
Het |
| Tgm4 |
G |
T |
9: 122,890,910 (GRCm39) |
G503V |
probably damaging |
Het |
| Tnni3k |
T |
C |
3: 154,645,691 (GRCm39) |
E461G |
probably damaging |
Het |
| Tom1l1 |
A |
T |
11: 90,561,931 (GRCm39) |
H232Q |
probably benign |
Het |
| Ubqln5 |
T |
C |
7: 103,778,329 (GRCm39) |
N165S |
probably benign |
Het |
| Vmn1r24 |
G |
A |
6: 57,932,958 (GRCm39) |
L187F |
probably benign |
Het |
| Vmn2r82 |
C |
T |
10: 79,213,894 (GRCm39) |
T160I |
probably damaging |
Het |
| Vmn2r96 |
G |
T |
17: 18,818,250 (GRCm39) |
G801V |
probably damaging |
Het |
| Vps39 |
A |
G |
2: 120,172,506 (GRCm39) |
S176P |
probably damaging |
Het |
| Vsig10 |
C |
A |
5: 117,472,981 (GRCm39) |
H191Q |
probably benign |
Het |
| Wtap |
G |
A |
17: 13,186,488 (GRCm39) |
S353L |
possibly damaging |
Het |
| Zmym4 |
T |
G |
4: 126,816,953 (GRCm39) |
R248S |
probably benign |
Het |
| Zscan10 |
A |
G |
17: 23,829,011 (GRCm39) |
S518G |
probably benign |
Het |
| Zscan29 |
A |
T |
2: 120,996,876 (GRCm39) |
Y282N |
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 |
|
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'- TACTATACATGGCTGCGGGC -3'
(R):5'- AAACTGGCTAGCCTGAGGTG -3'
Sequencing Primer
(F):5'- GGCCCAGCCTCACACTC -3'
(R):5'- AGATGGATAGTGGAAGGCCTCTTC -3'
|
| Posted On |
2021-04-30 |
Incidental Mutation