Incidental Mutation 'R7825:Smpd3'
ID |
602137 |
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 |
045879-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.904)
|
Stock # |
R7825 (G1)
|
Quality Score |
225.009 |
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: 99.8%
- 20x: 99.3%
|
Validation Efficiency |
98% (55/56) |
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: 55 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700013G24Rik |
C |
T |
4: 137,182,654 (GRCm39) |
R270C |
probably damaging |
Het |
Adprs |
C |
A |
4: 126,215,489 (GRCm39) |
|
probably benign |
Het |
Akp3 |
TCACCACCACCACCACCACCACCACCACCAC |
TCACCACCACCACCACCACCACCACCAC |
1: 87,055,489 (GRCm39) |
|
probably benign |
Het |
Ambra1 |
A |
G |
2: 91,598,106 (GRCm39) |
H89R |
probably damaging |
Het |
Atp1a1 |
T |
C |
3: 101,493,485 (GRCm39) |
N540D |
probably benign |
Het |
Cd38 |
A |
T |
5: 44,058,797 (GRCm39) |
H137L |
probably damaging |
Het |
Clasp1 |
T |
C |
1: 118,473,123 (GRCm39) |
V3A |
probably benign |
Het |
Cmya5 |
G |
T |
13: 93,234,136 (GRCm39) |
H317Q |
possibly damaging |
Het |
Cpeb2 |
A |
T |
5: 43,394,882 (GRCm39) |
D95V |
probably damaging |
Het |
Cyp2f2 |
G |
A |
7: 26,828,678 (GRCm39) |
V183I |
probably benign |
Het |
Dcst1 |
A |
G |
3: 89,260,128 (GRCm39) |
L572P |
possibly damaging |
Het |
Eif3e |
A |
C |
15: 43,129,667 (GRCm39) |
|
probably null |
Het |
Ephb4 |
T |
C |
5: 137,370,699 (GRCm39) |
S911P |
probably damaging |
Het |
Fam186b |
T |
C |
15: 99,181,728 (GRCm39) |
T157A |
not run |
Het |
Gnmt |
T |
C |
17: 47,040,019 (GRCm39) |
D20G |
probably damaging |
Het |
Gpatch8 |
A |
C |
11: 102,372,268 (GRCm39) |
D423E |
unknown |
Het |
Gtf3c2 |
T |
C |
5: 31,315,715 (GRCm39) |
H790R |
probably damaging |
Het |
Hepacam |
T |
C |
9: 37,296,064 (GRCm39) |
I405T |
probably benign |
Het |
Hspg2 |
T |
A |
4: 137,286,160 (GRCm39) |
V3574E |
probably damaging |
Het |
Ifi202b |
A |
C |
1: 173,802,616 (GRCm39) |
F73V |
probably damaging |
Het |
Kcnb1 |
A |
T |
2: 166,947,892 (GRCm39) |
S319T |
probably damaging |
Het |
Krt16 |
T |
A |
11: 100,139,460 (GRCm39) |
D86V |
unknown |
Het |
Krt76 |
T |
A |
15: 101,795,938 (GRCm39) |
T411S |
possibly damaging |
Het |
Myh8 |
A |
T |
11: 67,194,538 (GRCm39) |
D1583V |
possibly damaging |
Het |
Nav1 |
A |
T |
1: 135,377,782 (GRCm39) |
V1689D |
probably damaging |
Het |
Ncor2 |
T |
C |
5: 125,114,141 (GRCm39) |
T611A |
possibly damaging |
Het |
Nipbl |
T |
A |
15: 8,320,971 (GRCm39) |
Y2712F |
probably damaging |
Het |
Ntng2 |
T |
A |
2: 29,094,090 (GRCm39) |
H427L |
probably benign |
Het |
Pcdhga4 |
T |
A |
18: 37,820,374 (GRCm39) |
L641Q |
probably damaging |
Het |
Phc1 |
T |
C |
6: 122,299,340 (GRCm39) |
K623R |
probably benign |
Het |
Polr1b |
C |
A |
2: 128,967,464 (GRCm39) |
F952L |
probably damaging |
Het |
Prcc |
T |
A |
3: 87,777,052 (GRCm39) |
E307D |
possibly damaging |
Het |
Prss27 |
T |
C |
17: 24,261,932 (GRCm39) |
F80S |
probably damaging |
Het |
Rsf1 |
G |
GACGGCGGCC |
7: 97,229,116 (GRCm39) |
|
probably benign |
Het |
Serpina11 |
T |
C |
12: 103,950,836 (GRCm39) |
Q295R |
probably benign |
Het |
Sgk2 |
G |
T |
2: 162,848,801 (GRCm39) |
V284L |
possibly damaging |
Het |
Slc15a2 |
C |
T |
16: 36,573,396 (GRCm39) |
V603I |
possibly damaging |
Het |
Stat1 |
A |
G |
1: 52,190,467 (GRCm39) |
H574R |
probably damaging |
Het |
Ston1 |
T |
C |
17: 88,943,881 (GRCm39) |
V429A |
possibly damaging |
Het |
Tep1 |
T |
C |
14: 51,081,344 (GRCm39) |
|
probably null |
Het |
Tesk1 |
A |
C |
4: 43,447,143 (GRCm39) |
R510S |
probably damaging |
Het |
Themis |
A |
G |
10: 28,658,470 (GRCm39) |
E499G |
probably benign |
Het |
Thra |
G |
A |
11: 98,653,774 (GRCm39) |
V202I |
probably benign |
Het |
Tiam1 |
A |
T |
16: 89,694,977 (GRCm39) |
M160K |
probably benign |
Het |
Tmc1 |
T |
C |
19: 20,782,009 (GRCm39) |
I570V |
possibly damaging |
Het |
Treml1 |
C |
A |
17: 48,673,784 (GRCm39) |
P270Q |
probably damaging |
Het |
Ttc39d |
A |
G |
17: 80,523,575 (GRCm39) |
N78S |
probably damaging |
Het |
Ttll3 |
CAAAGTAA |
CAAAGTAAAGTAA |
6: 113,376,118 (GRCm39) |
|
probably null |
Het |
Ttll3 |
AAGTA |
AAGTAGAGTA |
6: 113,376,120 (GRCm39) |
|
probably null |
Het |
Ube3b |
T |
A |
5: 114,539,373 (GRCm39) |
L388Q |
probably damaging |
Het |
Ugt2b35 |
T |
A |
5: 87,149,218 (GRCm39) |
C156* |
probably null |
Het |
Vmn1r35 |
A |
T |
6: 66,656,443 (GRCm39) |
C76S |
probably damaging |
Het |
Wwc2 |
A |
G |
8: 48,443,197 (GRCm39) |
L12P |
probably damaging |
Het |
Zfat |
T |
C |
15: 68,051,769 (GRCm39) |
E668G |
probably benign |
Het |
Zfp40 |
T |
C |
17: 23,395,301 (GRCm39) |
T429A |
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 |
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 |
|
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'- TAGCTCCAAAGAGAAGTGCTC -3'
(R):5'- TGGCACAGAACTTTAGCTTGTTTC -3'
Sequencing Primer
(F):5'- CTCTGTGAAGGGGAGTGCC -3'
(R):5'- AGAACTTTAGCTTGTTTCCCTTCTG -3'
|
Posted On |
2019-12-03 |