Incidental Mutation 'R0145:Sema4a'
| ID |
22550 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sema4a
|
| Ensembl Gene |
ENSMUSG00000028064 |
| Gene Name |
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A |
| Synonyms |
SemB, SemB, Semab |
| MMRRC Submission |
038430-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.902)
|
| Stock # |
R0145 (G1)
of strain
722
|
| Quality Score |
178 |
|
Status
|
Validated
(trace)
|
| Chromosome |
3 |
| Chromosomal Location |
88343266-88368489 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 88358729 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Asparagine
at position 10
(I10N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000138858
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029700]
[ENSMUST00000107531]
[ENSMUST00000123753]
[ENSMUST00000125526]
[ENSMUST00000127436]
[ENSMUST00000169222]
[ENSMUST00000184876]
[ENSMUST00000147200]
[ENSMUST00000185137]
[ENSMUST00000165898]
[ENSMUST00000184487]
[ENSMUST00000166237]
[ENSMUST00000141471]
|
| AlphaFold |
Q62178 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000029700
AA Change: I164N
PolyPhen 2
Score 0.098 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000029700
Gene: ENSMUSG00000028064
AA Change: I164N
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Sema
|
64 |
478 |
1.96e-166 |
SMART |
|
PSI
|
496 |
547 |
9.33e-13 |
SMART |
|
transmembrane domain
|
680 |
702 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000107531
AA Change: I32N
PolyPhen 2
Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000103155
Gene: ENSMUSG00000028064
AA Change: I32N
| Domain | Start | End | E-Value | Type |
|---|
|
Sema
|
2 |
346 |
2.06e-101 |
SMART |
|
PSI
|
364 |
415 |
9.33e-13 |
SMART |
|
transmembrane domain
|
548 |
570 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000123753
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000125526
|
| SMART Domains |
Protein: ENSMUSP00000119028
Gene: ENSMUSG00000028064
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
113 |
8.2e-9 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000127436
AA Change: I164N
PolyPhen 2
Score 0.205 (Sensitivity: 0.92; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000118706
Gene: ENSMUSG00000028064
AA Change: I164N
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
234 |
5.5e-53 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000135539
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000135732
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000169222
AA Change: I164N
PolyPhen 2
Score 0.098 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000128887
Gene: ENSMUSG00000028064
AA Change: I164N
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Sema
|
64 |
478 |
1.96e-166 |
SMART |
|
PSI
|
496 |
547 |
9.33e-13 |
SMART |
|
transmembrane domain
|
680 |
702 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000184876
AA Change: S180T
|
| SMART Domains |
Protein: ENSMUSP00000139159
Gene: ENSMUSG00000028064
AA Change: S180T
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
179 |
7.7e-31 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000147200
AA Change: I164N
PolyPhen 2
Score 0.869 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000123061
Gene: ENSMUSG00000028064
AA Change: I164N
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
203 |
3.5e-45 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000185137
AA Change: I10N
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000165898
AA Change: I164N
PolyPhen 2
Score 0.098 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000128510
Gene: ENSMUSG00000028064
AA Change: I164N
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Sema
|
64 |
478 |
1.96e-166 |
SMART |
|
PSI
|
496 |
547 |
9.33e-13 |
SMART |
|
transmembrane domain
|
680 |
702 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000184487
AA Change: S170T
PolyPhen 2
Score 0.177 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000139126
Gene: ENSMUSG00000028064
AA Change: S170T
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
168 |
1.5e-30 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000166237
AA Change: I164N
PolyPhen 2
Score 0.098 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000125909
Gene: ENSMUSG00000028064
AA Change: I164N
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Sema
|
64 |
478 |
1.96e-166 |
SMART |
|
PSI
|
496 |
547 |
9.33e-13 |
SMART |
|
transmembrane domain
|
680 |
702 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149145
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000184972
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146921
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000141471
|
| SMART Domains |
Protein: ENSMUSP00000114330
Gene: ENSMUSG00000028064
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.2108 |
| Coding Region Coverage |
- 1x: 98.9%
- 3x: 97.8%
- 10x: 93.7%
- 20x: 82.1%
|
| Validation Efficiency |
96% (109/113) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the semaphorin family of soluble and transmembrane proteins. Semaphorins are involved in numerous functions, including axon guidance, morphogenesis, carcinogenesis, and immunomodulation. The encoded protein is a single-pass type I membrane protein containing an immunoglobulin-like C2-type domain, a PSI domain and a sema domain. It inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons. It is an activator of T-cell-mediated immunity and suppresses vascular endothelial growth factor (VEGF)-mediated endothelial cell migration and proliferation in vitro and angiogenesis in vivo. Mutations in this gene are associated with retinal degenerative diseases including retinitis pigmentosa type 35 (RP35) and cone-rod dystrophy type 10 (CORD10). Multiple alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]
PHENOTYPE: Homozygotes for a knock-out allele show no obvious brain defects but exhibit impaired T cell priming and defective Th1 responses. Homozygotes for a gene trap allele show severe retinal degeneration with reduced retinal vessels, depigmentation and dysfunction of both rod and cone photoreceptors. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 80 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700017N19Rik |
A |
G |
10: 100,437,783 (GRCm39) |
E64G |
probably damaging |
Het |
| Actr6 |
A |
T |
10: 89,564,040 (GRCm39) |
Y77* |
probably null |
Het |
| Aldoart1 |
A |
T |
4: 72,769,576 (GRCm39) |
S411T |
probably benign |
Het |
| Aqp1 |
C |
T |
6: 55,323,672 (GRCm39) |
R234C |
probably damaging |
Het |
| Arsb |
G |
A |
13: 93,998,795 (GRCm39) |
G368R |
possibly damaging |
Het |
| Asxl3 |
G |
A |
18: 22,586,662 (GRCm39) |
A151T |
probably damaging |
Het |
| Bcas3 |
T |
C |
11: 85,250,436 (GRCm39) |
|
probably benign |
Het |
| Bmpr2 |
AACACA |
AACA |
1: 59,906,739 (GRCm39) |
|
probably null |
Het |
| Bst1 |
A |
G |
5: 43,976,414 (GRCm39) |
Y49C |
probably damaging |
Het |
| Btrc |
T |
A |
19: 45,411,612 (GRCm39) |
L12Q |
probably damaging |
Het |
| Cd248 |
T |
C |
19: 5,119,051 (GRCm39) |
F300L |
possibly damaging |
Het |
| Cdk11b |
G |
T |
4: 155,726,076 (GRCm39) |
|
probably benign |
Het |
| Cfap410 |
T |
C |
10: 77,819,390 (GRCm39) |
S196P |
probably benign |
Het |
| Cfap44 |
A |
T |
16: 44,288,735 (GRCm39) |
D1495V |
probably damaging |
Het |
| Chil3 |
T |
A |
3: 106,067,794 (GRCm39) |
I124F |
probably damaging |
Het |
| Cnot2 |
A |
T |
10: 116,353,273 (GRCm39) |
S63T |
possibly damaging |
Het |
| Cox8a |
G |
T |
19: 7,192,783 (GRCm39) |
H61N |
probably benign |
Het |
| Cpne9 |
T |
C |
6: 113,277,562 (GRCm39) |
V427A |
probably damaging |
Het |
| Ctsll3 |
C |
A |
13: 60,946,409 (GRCm39) |
G301C |
probably damaging |
Het |
| Cubn |
T |
A |
2: 13,311,243 (GRCm39) |
D3094V |
probably damaging |
Het |
| Cyba |
A |
T |
8: 123,153,977 (GRCm39) |
M65K |
possibly damaging |
Het |
| Cyp4f39 |
T |
A |
17: 32,705,934 (GRCm39) |
S342T |
possibly damaging |
Het |
| Daam2 |
T |
C |
17: 49,787,806 (GRCm39) |
I436V |
probably benign |
Het |
| Daglb |
T |
C |
5: 143,460,363 (GRCm39) |
|
probably benign |
Het |
| Dnah7b |
T |
G |
1: 46,262,338 (GRCm39) |
L2067R |
probably damaging |
Het |
| Ep300 |
T |
C |
15: 81,500,328 (GRCm39) |
|
probably null |
Het |
| Esm1 |
A |
G |
13: 113,353,230 (GRCm39) |
N171D |
probably damaging |
Het |
| Fbxl2 |
T |
C |
9: 113,814,393 (GRCm39) |
E266G |
probably damaging |
Het |
| Ficd |
G |
T |
5: 113,876,880 (GRCm39) |
A352S |
probably damaging |
Het |
| H2-Q2 |
A |
G |
17: 35,564,152 (GRCm39) |
D302G |
probably benign |
Het |
| Hacd3 |
A |
T |
9: 64,911,524 (GRCm39) |
|
probably benign |
Het |
| Kbtbd6 |
T |
A |
14: 79,690,464 (GRCm39) |
N386K |
probably benign |
Het |
| Lct |
T |
C |
1: 128,255,632 (GRCm39) |
M137V |
probably benign |
Het |
| Lilrb4b |
T |
G |
10: 51,360,614 (GRCm39) |
N176K |
probably benign |
Het |
| Macf1 |
T |
A |
4: 123,281,190 (GRCm39) |
H4340L |
probably damaging |
Het |
| Mcidas |
A |
G |
13: 113,130,906 (GRCm39) |
D77G |
probably damaging |
Het |
| Mmrn1 |
C |
A |
6: 60,949,994 (GRCm39) |
Q315K |
probably damaging |
Het |
| Mon2 |
C |
A |
10: 122,849,417 (GRCm39) |
L1294F |
possibly damaging |
Het |
| Muc5ac |
A |
G |
7: 141,349,012 (GRCm39) |
T483A |
possibly damaging |
Het |
| Nacc1 |
T |
C |
8: 85,401,504 (GRCm39) |
|
probably benign |
Het |
| Nanos3 |
C |
T |
8: 84,902,763 (GRCm39) |
R133Q |
probably damaging |
Het |
| Ngef |
A |
G |
1: 87,468,370 (GRCm39) |
|
probably benign |
Het |
| Nol8 |
C |
T |
13: 49,815,923 (GRCm39) |
A677V |
possibly damaging |
Het |
| Ogfod3 |
A |
T |
11: 121,085,896 (GRCm39) |
|
probably benign |
Het |
| Or6c8 |
A |
T |
10: 128,915,232 (GRCm39) |
V200E |
probably damaging |
Het |
| Or8i2 |
A |
C |
2: 86,852,134 (GRCm39) |
Y251* |
probably null |
Het |
| Parpbp |
T |
C |
10: 87,928,871 (GRCm39) |
Y523C |
possibly damaging |
Het |
| Pik3cg |
C |
A |
12: 32,254,321 (GRCm39) |
L555F |
probably benign |
Het |
| Pkp3 |
T |
G |
7: 140,669,676 (GRCm39) |
|
probably null |
Het |
| Pole |
G |
T |
5: 110,472,291 (GRCm39) |
R1518L |
probably damaging |
Het |
| Prkab1 |
T |
C |
5: 116,156,144 (GRCm39) |
|
probably benign |
Het |
| Prrc2a |
T |
C |
17: 35,374,796 (GRCm39) |
T1285A |
probably benign |
Het |
| Pus1 |
C |
A |
5: 110,922,720 (GRCm39) |
V222L |
probably benign |
Het |
| Rab11fip1 |
A |
G |
8: 27,633,352 (GRCm39) |
L1118P |
probably damaging |
Het |
| Ranbp2 |
T |
A |
10: 58,315,868 (GRCm39) |
I2196N |
probably damaging |
Het |
| Rims3 |
T |
C |
4: 120,744,223 (GRCm39) |
L151P |
probably damaging |
Het |
| Rnf130 |
A |
G |
11: 49,962,046 (GRCm39) |
D164G |
possibly damaging |
Het |
| Rps6ka2 |
C |
A |
17: 7,529,585 (GRCm39) |
L293I |
probably benign |
Het |
| Ruvbl1 |
A |
G |
6: 88,461,441 (GRCm39) |
T269A |
possibly damaging |
Het |
| Serpinb6e |
A |
T |
13: 34,025,043 (GRCm39) |
S83T |
probably benign |
Het |
| Slc12a9 |
C |
A |
5: 137,313,550 (GRCm39) |
W803L |
probably damaging |
Het |
| Slc3a2 |
A |
G |
19: 8,685,437 (GRCm39) |
S188P |
probably damaging |
Het |
| Slc7a13 |
G |
A |
4: 19,818,782 (GRCm39) |
|
probably benign |
Het |
| Spart |
A |
T |
3: 55,035,092 (GRCm39) |
K493* |
probably null |
Het |
| Spata31e2 |
A |
G |
1: 26,726,413 (GRCm39) |
M32T |
probably benign |
Het |
| Sun1 |
T |
C |
5: 139,227,166 (GRCm39) |
V574A |
probably damaging |
Het |
| Supt6 |
A |
G |
11: 78,099,062 (GRCm39) |
V1603A |
probably benign |
Het |
| Tgm5 |
A |
G |
2: 120,908,062 (GRCm39) |
V38A |
possibly damaging |
Het |
| Tm6sf2 |
T |
C |
8: 70,530,518 (GRCm39) |
|
probably benign |
Het |
| Tnfaip2 |
T |
A |
12: 111,412,292 (GRCm39) |
V231E |
possibly damaging |
Het |
| Tube1 |
T |
A |
10: 39,021,598 (GRCm39) |
M281K |
possibly damaging |
Het |
| Tubgcp3 |
A |
G |
8: 12,707,561 (GRCm39) |
Y143H |
probably benign |
Het |
| Tyrp1 |
A |
G |
4: 80,759,015 (GRCm39) |
Y296C |
probably damaging |
Het |
| Utp4 |
A |
G |
8: 107,621,301 (GRCm39) |
N26S |
probably benign |
Het |
| Vgf |
T |
A |
5: 137,060,336 (GRCm39) |
|
probably benign |
Het |
| Zfat |
T |
C |
15: 68,058,948 (GRCm39) |
K196E |
possibly damaging |
Het |
| Zfp366 |
G |
T |
13: 99,366,048 (GRCm39) |
S403I |
probably damaging |
Het |
| Zfp462 |
G |
A |
4: 55,010,529 (GRCm39) |
G832R |
probably damaging |
Het |
| Zfp955a |
T |
A |
17: 33,461,430 (GRCm39) |
Q234L |
probably damaging |
Het |
| Zup1 |
T |
C |
10: 33,819,709 (GRCm39) |
T202A |
probably damaging |
Het |
|
| Other mutations in Sema4a |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00913:Sema4a
|
APN |
3 |
88,357,117 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01722:Sema4a
|
APN |
3 |
88,345,491 (GRCm39) |
missense |
probably benign |
0.14 |
|
IGL01769:Sema4a
|
APN |
3 |
88,357,063 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
IGL02076:Sema4a
|
APN |
3 |
88,357,829 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02202:Sema4a
|
APN |
3 |
88,357,050 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0386:Sema4a
|
UTSW |
3 |
88,344,107 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R0837:Sema4a
|
UTSW |
3 |
88,360,405 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R0863:Sema4a
|
UTSW |
3 |
88,355,456 (GRCm39) |
unclassified |
probably benign |
|
|
R1567:Sema4a
|
UTSW |
3 |
88,359,353 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1675:Sema4a
|
UTSW |
3 |
88,362,073 (GRCm39) |
missense |
possibly damaging |
0.66 |
|
R1739:Sema4a
|
UTSW |
3 |
88,344,145 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R1801:Sema4a
|
UTSW |
3 |
88,344,056 (GRCm39) |
missense |
probably benign |
0.04 |
|
R1961:Sema4a
|
UTSW |
3 |
88,345,483 (GRCm39) |
splice site |
probably benign |
|
|
R2029:Sema4a
|
UTSW |
3 |
88,358,668 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4934:Sema4a
|
UTSW |
3 |
88,345,568 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5006:Sema4a
|
UTSW |
3 |
88,344,091 (GRCm39) |
missense |
probably benign |
|
|
R5309:Sema4a
|
UTSW |
3 |
88,344,343 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5312:Sema4a
|
UTSW |
3 |
88,344,343 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5338:Sema4a
|
UTSW |
3 |
88,358,804 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5481:Sema4a
|
UTSW |
3 |
88,360,347 (GRCm39) |
nonsense |
probably null |
|
|
R5510:Sema4a
|
UTSW |
3 |
88,357,293 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6046:Sema4a
|
UTSW |
3 |
88,348,008 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7242:Sema4a
|
UTSW |
3 |
88,357,416 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8403:Sema4a
|
UTSW |
3 |
88,359,341 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8798:Sema4a
|
UTSW |
3 |
88,344,004 (GRCm39) |
missense |
possibly damaging |
0.76 |
|
R9328:Sema4a
|
UTSW |
3 |
88,345,613 (GRCm39) |
nonsense |
probably null |
|
|
R9638:Sema4a
|
UTSW |
3 |
88,357,066 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9728:Sema4a
|
UTSW |
3 |
88,348,187 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
Z1176:Sema4a
|
UTSW |
3 |
88,344,500 (GRCm39) |
missense |
probably damaging |
0.97 |
|
| Predicted Primers |
PCR Primer
(F):5'- CATGTGTAGGCCATTCGAGAGAGTC -3'
(R):5'- CTGTCCTCCGTAGCTTTGGGAATC -3'
Sequencing Primer
(F):5'- GTTAAACAAGTGGCTGAACCTC -3'
(R):5'- GAATCTCTGGTCCCTGCG -3'
|
| Posted On |
2013-04-16 |
Incidental Mutation