Incidental Mutation 'R4209:Spns2'
| ID |
319084 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Spns2
|
| Ensembl Gene |
ENSMUSG00000040447 |
| Gene Name |
SPNS lysolipid transporter 2, sphingosine-1-phosphate |
| Synonyms |
|
| MMRRC Submission |
041038-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4209 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
72342464-72380730 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 72345012 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 492
(D492G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000044418
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000045303]
[ENSMUST00000045633]
|
| AlphaFold |
Q91VM4 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000045303
AA Change: D492G
PolyPhen 2
Score 0.071 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000044418
Gene: ENSMUSG00000040447
AA Change: D492G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
5 |
53 |
N/A |
INTRINSIC |
|
Pfam:Sugar_tr
|
104 |
308 |
7.6e-16 |
PFAM |
|
Pfam:OATP
|
106 |
427 |
7.2e-13 |
PFAM |
|
Pfam:MFS_1
|
108 |
476 |
2.7e-37 |
PFAM |
|
transmembrane domain
|
506 |
528 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000045633
|
| SMART Domains |
Protein: ENSMUSP00000044827
Gene: ENSMUSG00000040463
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
7 |
19 |
N/A |
INTRINSIC |
|
Pfam:DNA_pol_phi
|
70 |
835 |
1.2e-194 |
PFAM |
|
low complexity region
|
839 |
852 |
N/A |
INTRINSIC |
|
low complexity region
|
1080 |
1090 |
N/A |
INTRINSIC |
|
low complexity region
|
1109 |
1122 |
N/A |
INTRINSIC |
|
low complexity region
|
1259 |
1269 |
N/A |
INTRINSIC |
|
low complexity region
|
1314 |
1329 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000126452
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129274
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144374
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144923
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000144940
AA Change: D73G
|
| SMART Domains |
Protein: ENSMUSP00000120722
Gene: ENSMUSG00000040447
AA Change: D73G
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
13 |
32 |
N/A |
INTRINSIC |
|
transmembrane domain
|
37 |
59 |
N/A |
INTRINSIC |
|
transmembrane domain
|
80 |
102 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150491
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000155995
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000152894
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147418
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162048
|
| Meta Mutation Damage Score |
0.1059 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.4%
|
| Validation Efficiency |
98% (45/46) |
| 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 a transporter of sphingosine 1-phosphate, a secreted lipid that is important in cardiovascular, immunological, and neural development. Defects in this gene are a cause of early onset progressive hearing loss. [provided by RefSeq, Jul 2016]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit symblepharon and impaired egress of T and B cells from the thymus and bone marrow, respectively. Mice homozygous for a different knock-out allele exhibit abnormal immune system, abnormal eye morphology and absent pinna reflex. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aadacl2fm3 |
A |
T |
3: 59,784,577 (GRCm39) |
Y350F |
probably damaging |
Het |
| Ahnak |
G |
A |
19: 8,979,964 (GRCm39) |
G416D |
probably damaging |
Het |
| Ap3b2 |
C |
A |
7: 81,126,884 (GRCm39) |
A289S |
probably benign |
Het |
| Arhgap23 |
C |
A |
11: 97,345,322 (GRCm39) |
T657K |
probably damaging |
Het |
| Bcl9 |
A |
G |
3: 97,117,269 (GRCm39) |
L475P |
probably damaging |
Het |
| Bean1 |
T |
A |
8: 104,940,566 (GRCm39) |
M1K |
probably null |
Het |
| Cand1 |
T |
A |
10: 119,047,463 (GRCm39) |
I676F |
probably benign |
Het |
| Casp3 |
G |
T |
8: 47,088,423 (GRCm39) |
D107Y |
probably damaging |
Het |
| Cops4 |
T |
A |
5: 100,695,352 (GRCm39) |
|
probably benign |
Het |
| Dchs1 |
A |
T |
7: 105,415,397 (GRCm39) |
D626E |
probably damaging |
Het |
| Dpysl2 |
T |
C |
14: 67,052,926 (GRCm39) |
S308G |
probably damaging |
Het |
| Fezf1 |
T |
C |
6: 23,246,616 (GRCm39) |
K323E |
probably damaging |
Het |
| Gm10272 |
T |
C |
10: 77,542,665 (GRCm39) |
V69A |
possibly damaging |
Het |
| Gtf2f1 |
A |
G |
17: 57,318,003 (GRCm39) |
V11A |
probably benign |
Het |
| Hnf4a |
T |
C |
2: 163,410,809 (GRCm39) |
S378P |
probably benign |
Het |
| Inpp5j |
T |
G |
11: 3,451,107 (GRCm39) |
H514P |
probably damaging |
Het |
| Irf8 |
T |
A |
8: 121,480,208 (GRCm39) |
Y149N |
probably damaging |
Het |
| Kel |
C |
T |
6: 41,675,359 (GRCm39) |
W297* |
probably null |
Het |
| Man1c1 |
G |
C |
4: 134,430,749 (GRCm39) |
P11R |
probably damaging |
Het |
| Mcpt8 |
G |
A |
14: 56,321,375 (GRCm39) |
H30Y |
probably damaging |
Het |
| Mycl |
G |
T |
4: 122,893,715 (GRCm39) |
V172L |
possibly damaging |
Het |
| Pcgf5 |
C |
A |
19: 36,414,740 (GRCm39) |
N26K |
possibly damaging |
Het |
| Ppp2r2a |
A |
G |
14: 67,266,328 (GRCm39) |
L111S |
probably damaging |
Het |
| Prdm2 |
T |
C |
4: 142,861,007 (GRCm39) |
D761G |
probably damaging |
Het |
| Sec11a |
A |
T |
7: 80,584,790 (GRCm39) |
I49N |
probably damaging |
Het |
| Sesn3 |
T |
C |
9: 14,217,505 (GRCm39) |
I30T |
probably benign |
Het |
| Slc22a21 |
A |
G |
11: 53,846,881 (GRCm39) |
S331P |
probably benign |
Het |
| Slc38a3 |
T |
G |
9: 107,532,547 (GRCm39) |
S358R |
possibly damaging |
Het |
| Slc9a5 |
A |
G |
8: 106,085,103 (GRCm39) |
N535D |
possibly damaging |
Het |
| Tcn2 |
T |
C |
11: 3,872,114 (GRCm39) |
K338E |
possibly damaging |
Het |
| Tdp1 |
C |
A |
12: 99,864,588 (GRCm39) |
A243E |
probably damaging |
Het |
| Tex16 |
T |
A |
X: 111,030,640 (GRCm39) |
D1046E |
probably benign |
Het |
| Tmem120a |
T |
C |
5: 135,764,559 (GRCm39) |
N340S |
probably benign |
Het |
| Tnik |
A |
T |
3: 28,413,214 (GRCm39) |
|
probably benign |
Het |
| Trim36 |
A |
G |
18: 46,329,191 (GRCm39) |
L71P |
probably benign |
Het |
| Tube1 |
A |
G |
10: 39,020,930 (GRCm39) |
|
probably null |
Het |
| Urgcp |
C |
A |
11: 5,665,878 (GRCm39) |
G820V |
probably damaging |
Het |
| Veph1 |
A |
T |
3: 66,151,967 (GRCm39) |
L154Q |
probably damaging |
Het |
| Vmn1r113 |
T |
C |
7: 20,521,535 (GRCm39) |
V109A |
probably benign |
Het |
| Vmn1r152 |
A |
T |
7: 22,223,004 (GRCm39) |
T205S |
possibly damaging |
Het |
| Wdsub1 |
G |
A |
2: 59,707,149 (GRCm39) |
P28S |
probably damaging |
Het |
| Ybx2 |
G |
T |
11: 69,826,767 (GRCm39) |
|
probably benign |
Het |
| Zfyve1 |
A |
T |
12: 83,621,909 (GRCm39) |
V162E |
probably damaging |
Het |
|
| Other mutations in Spns2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01733:Spns2
|
APN |
11 |
72,347,336 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
IGL01804:Spns2
|
APN |
11 |
72,348,130 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
elderly
|
UTSW |
11 |
72,347,196 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
homely
|
UTSW |
11 |
72,347,686 (GRCm39) |
missense |
probably damaging |
1.00 |
|
whistler
|
UTSW |
11 |
72,349,513 (GRCm39) |
nonsense |
probably null |
|
|
Wrinkled
|
UTSW |
11 |
72,347,704 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R0883:Spns2
|
UTSW |
11 |
72,345,223 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1544:Spns2
|
UTSW |
11 |
72,347,193 (GRCm39) |
missense |
probably benign |
0.30 |
|
R1696:Spns2
|
UTSW |
11 |
72,347,173 (GRCm39) |
missense |
probably benign |
0.25 |
|
R2046:Spns2
|
UTSW |
11 |
72,349,866 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R2164:Spns2
|
UTSW |
11 |
72,349,497 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R2259:Spns2
|
UTSW |
11 |
72,348,094 (GRCm39) |
missense |
probably benign |
0.35 |
|
R5285:Spns2
|
UTSW |
11 |
72,380,305 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R6883:Spns2
|
UTSW |
11 |
72,347,196 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R6990:Spns2
|
UTSW |
11 |
72,380,447 (GRCm39) |
missense |
probably benign |
0.08 |
|
R7221:Spns2
|
UTSW |
11 |
72,347,742 (GRCm39) |
missense |
probably benign |
0.43 |
|
R7227:Spns2
|
UTSW |
11 |
72,349,513 (GRCm39) |
nonsense |
probably null |
|
|
R7243:Spns2
|
UTSW |
11 |
72,347,686 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7390:Spns2
|
UTSW |
11 |
72,347,704 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R7699:Spns2
|
UTSW |
11 |
72,380,443 (GRCm39) |
nonsense |
probably null |
|
|
R7700:Spns2
|
UTSW |
11 |
72,380,443 (GRCm39) |
nonsense |
probably null |
|
|
R8042:Spns2
|
UTSW |
11 |
72,345,003 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R8155:Spns2
|
UTSW |
11 |
72,347,394 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R8553:Spns2
|
UTSW |
11 |
72,348,053 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- ACAGTCCCTGCTTCACAGTG -3'
(R):5'- CATGGATCTTCTAGCCCTGACC -3'
Sequencing Primer
(F):5'- TGCTTCACAGTGCGCCC -3'
(R):5'- TGGTCATCCCCACTCGG -3'
|
| Posted On |
2015-06-10 |
Incidental Mutation