Incidental Mutation 'R5056:Sgms1'
| ID |
390878 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sgms1
|
| Ensembl Gene |
ENSMUSG00000040451 |
| Gene Name |
sphingomyelin synthase 1 |
| Synonyms |
SMS1beta, SMS1gamma, SMS1alpha2, 9530058O11Rik, SMS1, Tmem23, SMS1alpha1 |
| MMRRC Submission |
042646-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.925)
|
| Stock # |
R5056 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
32100127-32367114 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 32137087 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Proline
at position 160
(S160P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000119869
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000099514]
[ENSMUST00000134415]
[ENSMUST00000142618]
[ENSMUST00000151289]
[ENSMUST00000152340]
[ENSMUST00000151822]
|
| AlphaFold |
Q8VCQ6 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000099514
AA Change: S160P
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000097114
Gene: ENSMUSG00000040451
AA Change: S160P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SAM_1
|
11 |
74 |
1.3e-6 |
PFAM |
|
transmembrane domain
|
141 |
163 |
N/A |
INTRINSIC |
|
transmembrane domain
|
186 |
208 |
N/A |
INTRINSIC |
|
Pfam:PAP2
|
216 |
362 |
4.5e-10 |
PFAM |
|
Pfam:PAP2_C
|
282 |
355 |
4.9e-34 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000124012
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000131768
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000134415
AA Change: S160P
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000115785
Gene: ENSMUSG00000040451
AA Change: S160P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SAM_1
|
11 |
74 |
4.3e-7 |
PFAM |
|
transmembrane domain
|
141 |
163 |
N/A |
INTRINSIC |
|
transmembrane domain
|
188 |
210 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141655
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000142618
AA Change: S160P
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000117336
Gene: ENSMUSG00000040451
AA Change: S160P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SAM_1
|
11 |
74 |
1.3e-6 |
PFAM |
|
transmembrane domain
|
141 |
163 |
N/A |
INTRINSIC |
|
transmembrane domain
|
186 |
208 |
N/A |
INTRINSIC |
|
Pfam:PAP2
|
216 |
362 |
4.5e-10 |
PFAM |
|
Pfam:PAP2_C
|
282 |
355 |
4.9e-34 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149107
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000151289
AA Change: S160P
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000123395
Gene: ENSMUSG00000040451
AA Change: S160P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SAM_1
|
11 |
74 |
1.5e-6 |
PFAM |
|
transmembrane domain
|
141 |
163 |
N/A |
INTRINSIC |
|
transmembrane domain
|
186 |
208 |
N/A |
INTRINSIC |
|
transmembrane domain
|
221 |
243 |
N/A |
INTRINSIC |
|
Pfam:PAP2_C
|
282 |
355 |
1.7e-30 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000152340
AA Change: S160P
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000119869
Gene: ENSMUSG00000040451
AA Change: S160P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SAM_1
|
11 |
74 |
4.7e-7 |
PFAM |
|
transmembrane domain
|
141 |
163 |
N/A |
INTRINSIC |
|
transmembrane domain
|
188 |
210 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000151822
|
| Meta Mutation Damage Score |
0.3606 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.0%
- 20x: 91.2%
|
| Validation Efficiency |
99% (73/74) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is predicted to be a five-pass transmembrane protein. This gene may be predominately expressed in brain. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit premature death, impaired insulin tolerance, increased insulin sensitivity, decreased insulin secretion, and abnormal pancreatic islet cell mitochondria morphology. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 66 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700030J22Rik |
T |
A |
8: 117,698,421 (GRCm39) |
K229* |
probably null |
Het |
| Adora2a |
T |
A |
10: 75,161,992 (GRCm39) |
S44T |
probably damaging |
Het |
| Agap3 |
T |
C |
5: 24,682,860 (GRCm39) |
V459A |
probably damaging |
Het |
| Apc2 |
T |
C |
10: 80,137,148 (GRCm39) |
V31A |
probably benign |
Het |
| Asic2 |
T |
A |
11: 80,862,429 (GRCm39) |
K189N |
possibly damaging |
Het |
| Bbs10 |
C |
T |
10: 111,136,401 (GRCm39) |
P505S |
probably benign |
Het |
| Brd10 |
A |
T |
19: 29,694,759 (GRCm39) |
I1578K |
probably benign |
Het |
| Cdh20 |
G |
T |
1: 104,881,722 (GRCm39) |
V396L |
probably benign |
Het |
| Cenpb |
C |
T |
2: 131,020,091 (GRCm39) |
|
probably benign |
Het |
| Chil6 |
T |
A |
3: 106,301,659 (GRCm39) |
Y147F |
probably damaging |
Het |
| Cluh |
C |
T |
11: 74,552,772 (GRCm39) |
R606C |
probably damaging |
Het |
| Cmtr1 |
A |
G |
17: 29,909,302 (GRCm39) |
T404A |
possibly damaging |
Het |
| Cnot1 |
T |
C |
8: 96,467,636 (GRCm39) |
N1499S |
probably damaging |
Het |
| Dmkn |
T |
C |
7: 30,463,529 (GRCm39) |
S61P |
probably damaging |
Het |
| Dmxl1 |
T |
C |
18: 50,003,990 (GRCm39) |
C872R |
probably benign |
Het |
| Dnah3 |
A |
G |
7: 119,620,169 (GRCm39) |
Y1587H |
probably damaging |
Het |
| Dsc2 |
A |
T |
18: 20,183,199 (GRCm39) |
V73D |
probably damaging |
Het |
| F5 |
A |
T |
1: 164,019,601 (GRCm39) |
Y692F |
possibly damaging |
Het |
| Fam184a |
A |
T |
10: 53,550,670 (GRCm39) |
L80I |
probably damaging |
Het |
| Foxj2 |
A |
G |
6: 122,810,833 (GRCm39) |
H271R |
probably benign |
Het |
| Grm7 |
A |
G |
6: 111,057,404 (GRCm39) |
T335A |
probably damaging |
Het |
| Hspa9 |
A |
G |
18: 35,071,734 (GRCm39) |
L622P |
probably damaging |
Het |
| Kcna7 |
G |
A |
7: 45,056,015 (GRCm39) |
R77H |
probably damaging |
Het |
| Kcnd3 |
T |
A |
3: 105,574,244 (GRCm39) |
|
probably benign |
Het |
| Klhdc8b |
ACACGCACGCACGCACGCACGCACGCACGCACGCACGCAC |
ACACGCACGCACGCACGCACGCACGCACGCACGCACGCACGCAC |
9: 108,326,184 (GRCm39) |
|
probably benign |
Het |
| Klk14 |
G |
A |
7: 43,341,501 (GRCm39) |
C51Y |
probably damaging |
Het |
| Lrch4 |
C |
G |
5: 137,635,113 (GRCm39) |
N237K |
probably damaging |
Het |
| Lss |
T |
G |
10: 76,388,760 (GRCm39) |
|
probably null |
Het |
| Map6 |
T |
C |
7: 98,985,859 (GRCm39) |
F588L |
probably benign |
Het |
| Mbd6 |
C |
T |
10: 127,122,310 (GRCm39) |
V173I |
probably benign |
Het |
| Med13 |
A |
T |
11: 86,219,391 (GRCm39) |
S352T |
probably benign |
Het |
| Mettl16 |
T |
A |
11: 74,707,766 (GRCm39) |
V320E |
probably benign |
Het |
| Myh7b |
G |
C |
2: 155,474,293 (GRCm39) |
R1669S |
possibly damaging |
Het |
| Nup188 |
T |
A |
2: 30,194,143 (GRCm39) |
D149E |
probably damaging |
Het |
| Ogfrl1 |
A |
G |
1: 23,418,130 (GRCm39) |
S83P |
probably damaging |
Het |
| Or52l1 |
T |
A |
7: 104,829,779 (GRCm39) |
H262L |
probably damaging |
Het |
| Or5m13 |
T |
A |
2: 85,748,480 (GRCm39) |
D70E |
probably damaging |
Het |
| Or8k36-ps1 |
T |
A |
2: 86,437,364 (GRCm39) |
I184F |
unknown |
Het |
| Or9m1 |
T |
C |
2: 87,733,915 (GRCm39) |
Y35C |
probably damaging |
Het |
| Pafah1b3 |
C |
T |
7: 24,994,764 (GRCm39) |
R98Q |
probably damaging |
Het |
| Pde6b |
A |
T |
5: 108,571,357 (GRCm39) |
K437* |
probably null |
Het |
| Ppp1r12b |
A |
T |
1: 134,762,130 (GRCm39) |
|
probably benign |
Het |
| Ppp1r12b |
G |
T |
1: 134,883,471 (GRCm39) |
A17E |
probably benign |
Het |
| Pramel34 |
T |
C |
5: 93,786,784 (GRCm39) |
|
probably benign |
Het |
| Prdm9 |
T |
C |
17: 15,782,679 (GRCm39) |
Q104R |
possibly damaging |
Het |
| Rgs22 |
A |
T |
15: 36,050,391 (GRCm39) |
|
probably null |
Het |
| Rnf14 |
C |
T |
18: 38,441,441 (GRCm39) |
P277L |
probably damaging |
Het |
| Robo4 |
T |
C |
9: 37,316,102 (GRCm39) |
S258P |
probably benign |
Het |
| Sfrp1 |
T |
A |
8: 23,907,420 (GRCm39) |
F207I |
probably damaging |
Het |
| Sil1 |
T |
C |
18: 35,402,755 (GRCm39) |
K263R |
probably benign |
Het |
| St14 |
A |
G |
9: 31,008,847 (GRCm39) |
|
probably null |
Het |
| Syne2 |
A |
G |
12: 75,955,905 (GRCm39) |
|
probably benign |
Het |
| Tbc1d9 |
T |
C |
8: 83,995,835 (GRCm39) |
S1013P |
probably benign |
Het |
| Tent5b |
C |
T |
4: 133,207,749 (GRCm39) |
R47W |
possibly damaging |
Het |
| Tmem67 |
T |
C |
4: 12,070,471 (GRCm39) |
S352G |
probably benign |
Het |
| Trib2 |
C |
A |
12: 15,843,795 (GRCm39) |
K282N |
possibly damaging |
Het |
| Trnau1ap |
T |
C |
4: 132,054,482 (GRCm39) |
|
probably benign |
Het |
| Trpm4 |
T |
C |
7: 44,958,054 (GRCm39) |
D952G |
probably damaging |
Het |
| Unc93b1 |
A |
G |
19: 3,992,762 (GRCm39) |
N305D |
possibly damaging |
Het |
| Usp32 |
A |
G |
11: 84,917,621 (GRCm39) |
V802A |
probably benign |
Het |
| Vmn2r48 |
T |
A |
7: 9,676,251 (GRCm39) |
H410L |
probably damaging |
Het |
| Wfs1 |
T |
C |
5: 37,132,931 (GRCm39) |
N116S |
probably benign |
Het |
| Wif1 |
A |
T |
10: 120,935,684 (GRCm39) |
H333L |
probably benign |
Het |
| Zfp109 |
T |
C |
7: 23,928,162 (GRCm39) |
T416A |
possibly damaging |
Het |
| Zfp808 |
T |
A |
13: 62,320,444 (GRCm39) |
C558S |
probably damaging |
Het |
| Zpbp |
T |
C |
11: 11,409,734 (GRCm39) |
D116G |
possibly damaging |
Het |
|
| Other mutations in Sgms1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00486:Sgms1
|
APN |
19 |
32,137,025 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01585:Sgms1
|
APN |
19 |
32,120,245 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02490:Sgms1
|
APN |
19 |
32,137,543 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL02970:Sgms1
|
APN |
19 |
32,137,165 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1051:Sgms1
|
UTSW |
19 |
32,137,439 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1871:Sgms1
|
UTSW |
19 |
32,137,282 (GRCm39) |
missense |
probably benign |
0.01 |
|
R1971:Sgms1
|
UTSW |
19 |
32,137,357 (GRCm39) |
missense |
probably benign |
0.05 |
|
R2001:Sgms1
|
UTSW |
19 |
32,137,083 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R2404:Sgms1
|
UTSW |
19 |
32,137,072 (GRCm39) |
nonsense |
probably null |
|
|
R2405:Sgms1
|
UTSW |
19 |
32,137,072 (GRCm39) |
nonsense |
probably null |
|
|
R2408:Sgms1
|
UTSW |
19 |
32,137,072 (GRCm39) |
nonsense |
probably null |
|
|
R2410:Sgms1
|
UTSW |
19 |
32,137,072 (GRCm39) |
nonsense |
probably null |
|
|
R3747:Sgms1
|
UTSW |
19 |
32,136,994 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
R4016:Sgms1
|
UTSW |
19 |
32,120,192 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R4710:Sgms1
|
UTSW |
19 |
32,137,537 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5422:Sgms1
|
UTSW |
19 |
32,137,232 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6023:Sgms1
|
UTSW |
19 |
32,101,773 (GRCm39) |
missense |
probably benign |
0.12 |
|
R6106:Sgms1
|
UTSW |
19 |
32,101,825 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R6932:Sgms1
|
UTSW |
19 |
32,120,193 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7207:Sgms1
|
UTSW |
19 |
32,120,147 (GRCm39) |
missense |
probably null |
1.00 |
|
R7382:Sgms1
|
UTSW |
19 |
32,137,182 (GRCm39) |
missense |
possibly damaging |
0.68 |
|
R7494:Sgms1
|
UTSW |
19 |
32,107,091 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7712:Sgms1
|
UTSW |
19 |
32,120,169 (GRCm39) |
missense |
probably benign |
0.05 |
|
R7759:Sgms1
|
UTSW |
19 |
32,137,276 (GRCm39) |
missense |
probably benign |
|
|
R7872:Sgms1
|
UTSW |
19 |
32,102,765 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8283:Sgms1
|
UTSW |
19 |
32,137,035 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8377:Sgms1
|
UTSW |
19 |
32,101,821 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8487:Sgms1
|
UTSW |
19 |
32,102,697 (GRCm39) |
missense |
probably benign |
0.30 |
|
R8507:Sgms1
|
UTSW |
19 |
32,137,109 (GRCm39) |
missense |
probably benign |
0.06 |
|
R9007:Sgms1
|
UTSW |
19 |
32,137,227 (GRCm39) |
missense |
probably benign |
0.03 |
|
R9182:Sgms1
|
UTSW |
19 |
32,101,758 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- CTGGATCCCTGTGTGCAAAC -3'
(R):5'- ATGGCAGCTTCAGCATCAAGAC -3'
Sequencing Primer
(F):5'- CCTTCATGGCTGGATCTCAAGAG -3'
(R):5'- GGCAGCTTCAGCATCAAGACTAAAC -3'
|
| Posted On |
2016-06-06 |
Incidental Mutation