Incidental Mutation 'R5388:Smpd2'
ID |
425422 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Smpd2
|
Ensembl Gene |
ENSMUSG00000019822 |
Gene Name |
sphingomyelin phosphodiesterase 2, neutral |
Synonyms |
nSMase |
MMRRC Submission |
042960-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R5388 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
10 |
Chromosomal Location |
41363168-41366410 bp(-) (GRCm39) |
Type of Mutation |
splice site (22 bp from exon) |
DNA Base Change (assembly) |
A to G
at 41363967 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
|
Ref Sequence |
ENSEMBL: ENSMUSP00000019965
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000019965]
[ENSMUST00000019965]
[ENSMUST00000019965]
[ENSMUST00000019967]
[ENSMUST00000099934]
[ENSMUST00000105507]
[ENSMUST00000119962]
[ENSMUST00000155411]
[ENSMUST00000155411]
[ENSMUST00000126436]
|
AlphaFold |
O70572 |
Predicted Effect |
probably null
Transcript: ENSMUST00000019965
|
SMART Domains |
Protein: ENSMUSP00000019965 Gene: ENSMUSG00000019822
Domain | Start | End | E-Value | Type |
Pfam:Exo_endo_phos
|
11 |
272 |
3.9e-24 |
PFAM |
transmembrane domain
|
322 |
344 |
N/A |
INTRINSIC |
transmembrane domain
|
353 |
375 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably null
Transcript: ENSMUST00000019965
|
SMART Domains |
Protein: ENSMUSP00000019965 Gene: ENSMUSG00000019822
Domain | Start | End | E-Value | Type |
Pfam:Exo_endo_phos
|
11 |
272 |
3.9e-24 |
PFAM |
transmembrane domain
|
322 |
344 |
N/A |
INTRINSIC |
transmembrane domain
|
353 |
375 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably null
Transcript: ENSMUST00000019965
|
SMART Domains |
Protein: ENSMUSP00000019965 Gene: ENSMUSG00000019822
Domain | Start | End | E-Value | Type |
Pfam:Exo_endo_phos
|
11 |
272 |
3.9e-24 |
PFAM |
transmembrane domain
|
322 |
344 |
N/A |
INTRINSIC |
transmembrane domain
|
353 |
375 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000019967
|
SMART Domains |
Protein: ENSMUSP00000019967 Gene: ENSMUSG00000019823
Domain | Start | End | E-Value | Type |
Pfam:FAD_binding_3
|
84 |
140 |
5.5e-8 |
PFAM |
Pfam:FAD_binding_2
|
86 |
125 |
6.1e-6 |
PFAM |
low complexity region
|
160 |
171 |
N/A |
INTRINSIC |
CH
|
509 |
606 |
4.18e-13 |
SMART |
low complexity region
|
649 |
666 |
N/A |
INTRINSIC |
LIM
|
682 |
736 |
2.07e-3 |
SMART |
low complexity region
|
766 |
785 |
N/A |
INTRINSIC |
low complexity region
|
787 |
803 |
N/A |
INTRINSIC |
low complexity region
|
855 |
877 |
N/A |
INTRINSIC |
DUF3585
|
912 |
1048 |
3.07e-44 |
SMART |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000099934
|
SMART Domains |
Protein: ENSMUSP00000097519 Gene: ENSMUSG00000019823
Domain | Start | End | E-Value | Type |
PDB:2C4C|B
|
1 |
86 |
5e-49 |
PDB |
low complexity region
|
87 |
98 |
N/A |
INTRINSIC |
PDB:2C4C|B
|
99 |
416 |
N/A |
PDB |
CH
|
436 |
533 |
4.18e-13 |
SMART |
low complexity region
|
576 |
593 |
N/A |
INTRINSIC |
LIM
|
609 |
663 |
2.07e-3 |
SMART |
low complexity region
|
693 |
712 |
N/A |
INTRINSIC |
low complexity region
|
714 |
730 |
N/A |
INTRINSIC |
low complexity region
|
782 |
804 |
N/A |
INTRINSIC |
DUF3585
|
839 |
975 |
3.07e-44 |
SMART |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000105507
|
SMART Domains |
Protein: ENSMUSP00000101146 Gene: ENSMUSG00000078451
Domain | Start | End | E-Value | Type |
low complexity region
|
20 |
33 |
N/A |
INTRINSIC |
Pfam:Pro_isomerase
|
147 |
310 |
1.3e-41 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000119962
|
SMART Domains |
Protein: ENSMUSP00000113783 Gene: ENSMUSG00000019823
Domain | Start | End | E-Value | Type |
Pfam:FAD_binding_3
|
84 |
140 |
7.2e-8 |
PFAM |
Pfam:FAD_binding_2
|
86 |
125 |
3.8e-6 |
PFAM |
low complexity region
|
160 |
171 |
N/A |
INTRINSIC |
CH
|
509 |
606 |
4.18e-13 |
SMART |
low complexity region
|
649 |
666 |
N/A |
INTRINSIC |
LIM
|
682 |
736 |
2.07e-3 |
SMART |
low complexity region
|
766 |
785 |
N/A |
INTRINSIC |
low complexity region
|
787 |
803 |
N/A |
INTRINSIC |
low complexity region
|
855 |
877 |
N/A |
INTRINSIC |
DUF3585
|
912 |
1048 |
3.07e-44 |
SMART |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000122997
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000123798
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000143470
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000155411
|
SMART Domains |
Protein: ENSMUSP00000115461 Gene: ENSMUSG00000019822
Domain | Start | End | E-Value | Type |
SCOP:d2dnja_
|
9 |
81 |
2e-4 |
SMART |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000155411
|
SMART Domains |
Protein: ENSMUSP00000115461 Gene: ENSMUSG00000019822
Domain | Start | End | E-Value | Type |
SCOP:d2dnja_
|
9 |
81 |
2e-4 |
SMART |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000132170
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141542
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000138657
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000125099
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000126833
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147367
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147738
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000134010
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000215608
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000126436
|
SMART Domains |
Protein: ENSMUSP00000114969 Gene: ENSMUSG00000019823
Domain | Start | End | E-Value | Type |
Pfam:FAD_binding_3
|
84 |
140 |
1.1e-7 |
PFAM |
Pfam:FAD_binding_2
|
86 |
125 |
3.2e-6 |
PFAM |
low complexity region
|
160 |
171 |
N/A |
INTRINSIC |
CH
|
509 |
606 |
4.18e-13 |
SMART |
low complexity region
|
649 |
666 |
N/A |
INTRINSIC |
LIM
|
682 |
736 |
2.07e-3 |
SMART |
low complexity region
|
766 |
785 |
N/A |
INTRINSIC |
low complexity region
|
787 |
803 |
N/A |
INTRINSIC |
low complexity region
|
855 |
877 |
N/A |
INTRINSIC |
|
Meta Mutation Damage Score |
0.9755 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.8%
- 10x: 97.5%
- 20x: 95.9%
|
Validation Efficiency |
98% (57/58) |
MGI Phenotype |
FUNCTION: This gene encodes a protein with similarity to the human nSMase1 protein. In humans, the nSMase1 protein was initially identified as a sphingomyelinase based on sequence similarity between bacterial sphingomyelinases and a yeast protein. Subsequent studies showed that its biological function is less likely to be as a sphingomyelinase and instead as a lysophospholipase. [provided by RefSeq, Oct 2009] PHENOTYPE: Mice homozygous for a knock-out allele are phenotypically normal, have a normal lifespan, and display neither lipid accumulation nor changes in sphingomyelin levels despite grossly reduced enzyme activity in all organs except brain. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 54 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca16 |
T |
C |
7: 120,139,969 (GRCm39) |
|
probably null |
Het |
Acap2 |
C |
A |
16: 30,928,543 (GRCm39) |
C475F |
probably damaging |
Het |
Ace |
C |
A |
11: 105,879,284 (GRCm39) |
P603Q |
possibly damaging |
Het |
Adamts20 |
C |
G |
15: 94,243,659 (GRCm39) |
V657L |
possibly damaging |
Het |
Antxr2 |
A |
G |
5: 98,125,458 (GRCm39) |
|
probably null |
Het |
Atp6v1b2 |
G |
A |
8: 69,554,089 (GRCm39) |
V89I |
probably benign |
Het |
Cacna1e |
G |
A |
1: 154,353,542 (GRCm39) |
P676L |
probably damaging |
Het |
Camsap3 |
A |
T |
8: 3,654,276 (GRCm39) |
I649F |
probably damaging |
Het |
Camta1 |
G |
T |
4: 151,159,695 (GRCm39) |
S490R |
probably damaging |
Het |
Celsr1 |
A |
G |
15: 85,809,719 (GRCm39) |
I2221T |
probably damaging |
Het |
Cfd |
A |
T |
10: 79,727,959 (GRCm39) |
D164V |
probably damaging |
Het |
Cfdp1 |
T |
C |
8: 112,495,384 (GRCm39) |
D278G |
probably damaging |
Het |
Cntn6 |
A |
T |
6: 104,809,523 (GRCm39) |
L519F |
probably damaging |
Het |
Col4a4 |
C |
T |
1: 82,471,312 (GRCm39) |
G681E |
unknown |
Het |
Cybrd1 |
T |
C |
2: 70,967,989 (GRCm39) |
|
probably null |
Het |
Cyp2e1 |
T |
C |
7: 140,343,906 (GRCm39) |
L48P |
probably damaging |
Het |
Eddm13 |
T |
C |
7: 6,269,346 (GRCm39) |
|
probably null |
Het |
Ep400 |
G |
A |
5: 110,849,594 (GRCm39) |
T1409I |
unknown |
Het |
Exosc7 |
A |
T |
9: 122,947,972 (GRCm39) |
D47V |
probably damaging |
Het |
Fgr |
T |
C |
4: 132,722,342 (GRCm39) |
F204L |
probably damaging |
Het |
Gm10100 |
G |
A |
10: 77,562,560 (GRCm39) |
V81M |
probably benign |
Het |
Gm12367 |
T |
C |
4: 35,235,690 (GRCm39) |
|
noncoding transcript |
Het |
Grxcr1 |
C |
A |
5: 68,323,538 (GRCm39) |
T272K |
probably damaging |
Het |
Kcna5 |
C |
T |
6: 126,511,859 (GRCm39) |
D90N |
probably benign |
Het |
Kdm5b |
T |
A |
1: 134,536,635 (GRCm39) |
Y618* |
probably null |
Het |
Lama5 |
T |
A |
2: 179,832,539 (GRCm39) |
H1670L |
possibly damaging |
Het |
Mtus2 |
C |
T |
5: 148,243,518 (GRCm39) |
Q113* |
probably null |
Het |
Ncam1 |
A |
C |
9: 49,456,054 (GRCm39) |
D521E |
probably benign |
Het |
Nkapl |
T |
C |
13: 21,651,740 (GRCm39) |
H291R |
possibly damaging |
Het |
Nlrp1b |
T |
G |
11: 71,062,967 (GRCm39) |
N695H |
probably damaging |
Het |
Npc1l1 |
T |
A |
11: 6,164,733 (GRCm39) |
Q1105H |
probably damaging |
Het |
Paxip1 |
C |
G |
5: 27,986,453 (GRCm39) |
|
probably benign |
Het |
Pign |
A |
T |
1: 105,583,695 (GRCm39) |
W136R |
probably damaging |
Het |
Pira1 |
T |
C |
7: 3,741,856 (GRCm39) |
T175A |
possibly damaging |
Het |
Pkn3 |
T |
A |
2: 29,971,086 (GRCm39) |
S222T |
probably damaging |
Het |
Polr3a |
T |
C |
14: 24,505,009 (GRCm39) |
I1084V |
possibly damaging |
Het |
Ppfibp1 |
T |
A |
6: 146,898,338 (GRCm39) |
I98N |
probably damaging |
Het |
Ppfibp1 |
T |
G |
6: 146,917,828 (GRCm39) |
S484A |
probably damaging |
Het |
Ppp1r7 |
T |
C |
1: 93,280,312 (GRCm39) |
F127L |
probably damaging |
Het |
Pramel1 |
T |
C |
4: 143,123,954 (GRCm39) |
Y210H |
probably benign |
Het |
Rad21l |
C |
T |
2: 151,495,403 (GRCm39) |
V427I |
probably benign |
Het |
Ripply1 |
TTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT |
TTCCTCCTCCTCCTCCTCCTCCTCCTCCT |
X: 138,680,599 (GRCm39) |
|
probably benign |
Het |
Rnf225 |
A |
G |
7: 12,661,932 (GRCm39) |
D37G |
probably damaging |
Het |
Spata31h1 |
T |
C |
10: 82,119,561 (GRCm39) |
Q4483R |
probably damaging |
Het |
Tmem38b |
C |
T |
4: 53,859,945 (GRCm39) |
R242W |
probably benign |
Het |
Topaz1 |
A |
T |
9: 122,603,158 (GRCm39) |
K1035I |
possibly damaging |
Het |
Trhr |
T |
C |
15: 44,060,873 (GRCm39) |
I131T |
possibly damaging |
Het |
Usp1 |
A |
G |
4: 98,819,294 (GRCm39) |
D252G |
probably benign |
Het |
Usp14 |
C |
T |
18: 10,018,023 (GRCm39) |
E90K |
probably damaging |
Het |
Yme1l1 |
T |
G |
2: 23,052,569 (GRCm39) |
D74E |
probably benign |
Het |
Ythdc2 |
T |
A |
18: 44,990,092 (GRCm39) |
L732Q |
possibly damaging |
Het |
Zbbx |
G |
T |
3: 74,990,977 (GRCm39) |
A289D |
probably damaging |
Het |
Zfhx3 |
G |
A |
8: 109,673,446 (GRCm39) |
V1499I |
possibly damaging |
Het |
Zfp622 |
T |
C |
15: 25,996,285 (GRCm39) |
V184A |
possibly damaging |
Het |
|
Other mutations in Smpd2 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL01581:Smpd2
|
APN |
10 |
41,365,524 (GRCm39) |
missense |
possibly damaging |
0.52 |
IGL02797:Smpd2
|
APN |
10 |
41,364,074 (GRCm39) |
missense |
possibly damaging |
0.90 |
clumsy
|
UTSW |
10 |
41,363,967 (GRCm39) |
splice site |
probably null |
|
R1170:Smpd2
|
UTSW |
10 |
41,364,728 (GRCm39) |
critical splice donor site |
probably null |
|
R1832:Smpd2
|
UTSW |
10 |
41,364,232 (GRCm39) |
missense |
probably benign |
0.01 |
R5383:Smpd2
|
UTSW |
10 |
41,364,698 (GRCm39) |
intron |
probably benign |
|
R5905:Smpd2
|
UTSW |
10 |
41,365,344 (GRCm39) |
missense |
probably damaging |
1.00 |
R6028:Smpd2
|
UTSW |
10 |
41,365,344 (GRCm39) |
missense |
probably damaging |
1.00 |
R6833:Smpd2
|
UTSW |
10 |
41,364,442 (GRCm39) |
missense |
probably damaging |
0.98 |
R7440:Smpd2
|
UTSW |
10 |
41,365,012 (GRCm39) |
missense |
probably benign |
0.13 |
R7505:Smpd2
|
UTSW |
10 |
41,363,350 (GRCm39) |
missense |
probably benign |
0.09 |
R8869:Smpd2
|
UTSW |
10 |
41,365,301 (GRCm39) |
missense |
probably benign |
|
R9200:Smpd2
|
UTSW |
10 |
41,363,561 (GRCm39) |
missense |
probably benign |
0.03 |
R9275:Smpd2
|
UTSW |
10 |
41,363,685 (GRCm39) |
missense |
probably benign |
|
R9621:Smpd2
|
UTSW |
10 |
41,364,283 (GRCm39) |
missense |
probably benign |
0.01 |
|
Predicted Primers |
PCR Primer
(F):5'- CAGACGTGGAACTCAGAGAC -3'
(R):5'- GCTTTCGTTGAGACTGAGGAC -3'
Sequencing Primer
(F):5'- CGTGGAACTCAGAGACTGCCTAG -3'
(R):5'- TAAGGTGAGAGACTGTTTCCCACC -3'
|
Posted On |
2016-08-04 |