Incidental Mutation 'R4212:Sema3b'
| ID |
319252 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sema3b
|
| Ensembl Gene |
ENSMUSG00000057969 |
| Gene Name |
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B |
| Synonyms |
semaV, Semaa, SemA, sema5, SemA, LUCA-1 |
| MMRRC Submission |
041641-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.341)
|
| Stock # |
R4212 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
9 |
| Chromosomal Location |
107474873-107486428 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 107480597 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Methionine
at position 117
(V117M)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141614
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000073448]
[ENSMUST00000102529]
[ENSMUST00000102530]
[ENSMUST00000102531]
[ENSMUST00000102532]
[ENSMUST00000123926]
[ENSMUST00000193180]
[ENSMUST00000195662]
[ENSMUST00000194433]
[ENSMUST00000194606]
[ENSMUST00000195057]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000073448
AA Change: V117M
PolyPhen 2
Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000073152
Gene: ENSMUSG00000057969
AA Change: V117M
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Sema
|
55 |
497 |
6.37e-207 |
SMART |
|
PSI
|
515 |
567 |
1.77e-13 |
SMART |
|
IG
|
577 |
660 |
7.7e-5 |
SMART |
|
low complexity region
|
665 |
683 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000102529
AA Change: V117M
PolyPhen 2
Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000099588
Gene: ENSMUSG00000057969
AA Change: V117M
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Sema
|
55 |
497 |
6.37e-207 |
SMART |
|
PSI
|
515 |
567 |
1.77e-13 |
SMART |
|
IG
|
577 |
660 |
7.7e-5 |
SMART |
|
low complexity region
|
665 |
683 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000102530
AA Change: V117M
PolyPhen 2
Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000099589
Gene: ENSMUSG00000057969
AA Change: V117M
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Sema
|
55 |
497 |
6.37e-207 |
SMART |
|
PSI
|
515 |
567 |
1.77e-13 |
SMART |
|
IG
|
577 |
660 |
7.7e-5 |
SMART |
|
low complexity region
|
665 |
683 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000102531
AA Change: V117M
PolyPhen 2
Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000099590
Gene: ENSMUSG00000057969
AA Change: V117M
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Sema
|
55 |
497 |
6.37e-207 |
SMART |
|
PSI
|
515 |
567 |
1.77e-13 |
SMART |
|
IG
|
577 |
660 |
7.7e-5 |
SMART |
|
low complexity region
|
665 |
683 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000102532
AA Change: V117M
PolyPhen 2
Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000099591
Gene: ENSMUSG00000057969
AA Change: V117M
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Sema
|
55 |
497 |
6.37e-207 |
SMART |
|
PSI
|
515 |
567 |
1.77e-13 |
SMART |
|
IG
|
577 |
660 |
7.7e-5 |
SMART |
|
low complexity region
|
665 |
683 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000123926
AA Change: V117M
PolyPhen 2
Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000137952
Gene: ENSMUSG00000057969
AA Change: V117M
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Sema
|
55 |
497 |
6.37e-207 |
SMART |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000193180
AA Change: V117M
PolyPhen 2
Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000141726
Gene: ENSMUSG00000057969
AA Change: V117M
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
55 |
148 |
8.2e-31 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000195662
AA Change: V117M
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000141614
Gene: ENSMUSG00000057969
AA Change: V117M
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
55 |
137 |
8.4e-26 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000194433
AA Change: V117M
PolyPhen 2
Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000141403
Gene: ENSMUSG00000057969
AA Change: V117M
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
55 |
172 |
3.5e-36 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000195472
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000193234
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000193551
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194606
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000195057
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.8%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: This gene encodes a secreted protein that belongs to the class 3 semaphorin/collapsin family. Members of this family play a role in growth cone guidance during neurogenesis. The encoded protein inhibits axonal extension. This protein is thought to be an osteoblast protein that regulates bone mass and affects skeletal homeostasis. A similar gene in humans functions as a tumor suppressor gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]
PHENOTYPE: Mice homozygous for one knock-out allele are viable and fertile with no obvious pathological abnormalities. Mice homozygous for a second knock-out allele exhibit improper positioning of a major brain commissural projection, the anterior commissure. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A1bg |
G |
T |
15: 60,791,585 (GRCm39) |
L284M |
possibly damaging |
Het |
| Adamts15 |
A |
G |
9: 30,817,470 (GRCm39) |
V536A |
probably damaging |
Het |
| Arsi |
A |
T |
18: 61,049,773 (GRCm39) |
I219F |
probably damaging |
Het |
| Atg7 |
G |
A |
6: 114,680,386 (GRCm39) |
G447E |
probably benign |
Het |
| Bdp1 |
T |
A |
13: 100,196,093 (GRCm39) |
H1223L |
probably benign |
Het |
| Cep152 |
A |
G |
2: 125,461,921 (GRCm39) |
M87T |
probably benign |
Het |
| Chrm3 |
T |
C |
13: 9,927,791 (GRCm39) |
D415G |
probably benign |
Het |
| Chrnb2 |
A |
T |
3: 89,668,851 (GRCm39) |
C155S |
probably damaging |
Het |
| Col6a4 |
T |
A |
9: 105,952,569 (GRCm39) |
Q443L |
probably benign |
Het |
| Ct45a |
C |
T |
X: 55,590,568 (GRCm39) |
V78I |
probably benign |
Het |
| D5Ertd579e |
A |
T |
5: 36,771,823 (GRCm39) |
D857E |
probably damaging |
Het |
| Efcab6 |
T |
C |
15: 83,777,064 (GRCm39) |
D1124G |
probably damaging |
Het |
| F830045P16Rik |
C |
T |
2: 129,302,273 (GRCm39) |
A440T |
probably benign |
Het |
| Gc |
T |
C |
5: 89,583,434 (GRCm39) |
K370E |
probably benign |
Het |
| Gm11559 |
A |
G |
11: 99,755,726 (GRCm39) |
Q125R |
unknown |
Het |
| Gm3985 |
A |
T |
8: 33,432,484 (GRCm39) |
|
noncoding transcript |
Het |
| Gucy2e |
A |
G |
11: 69,118,949 (GRCm39) |
F681S |
probably damaging |
Het |
| Hip1r |
A |
G |
5: 124,137,953 (GRCm39) |
I760V |
probably benign |
Het |
| Islr2 |
C |
T |
9: 58,106,603 (GRCm39) |
G219D |
probably damaging |
Het |
| Itgae |
A |
G |
11: 73,010,178 (GRCm39) |
H556R |
probably benign |
Het |
| Jag1 |
T |
C |
2: 136,926,990 (GRCm39) |
D923G |
probably benign |
Het |
| Kmt2c |
A |
G |
5: 25,552,357 (GRCm39) |
|
probably null |
Het |
| Kmt2d |
A |
G |
15: 98,742,884 (GRCm39) |
|
probably benign |
Het |
| Krtap17-1 |
A |
G |
11: 99,884,740 (GRCm39) |
L9P |
unknown |
Het |
| Lats2 |
C |
T |
14: 57,933,712 (GRCm39) |
D802N |
possibly damaging |
Het |
| Lrfn5 |
A |
T |
12: 61,890,606 (GRCm39) |
T632S |
probably benign |
Het |
| Myo9a |
C |
T |
9: 59,813,349 (GRCm39) |
R2183* |
probably null |
Het |
| Myorg |
T |
C |
4: 41,498,307 (GRCm39) |
E441G |
probably benign |
Het |
| Naip1 |
T |
C |
13: 100,563,383 (GRCm39) |
|
probably null |
Het |
| Nf1 |
T |
A |
11: 79,360,624 (GRCm39) |
V1434E |
probably damaging |
Het |
| Nlrc4 |
T |
C |
17: 74,754,110 (GRCm39) |
Y91C |
possibly damaging |
Het |
| Or4l1 |
A |
T |
14: 50,166,346 (GRCm39) |
Y218* |
probably null |
Het |
| Or5b102 |
T |
G |
19: 13,041,123 (GRCm39) |
M116R |
probably damaging |
Het |
| Or5k1 |
T |
A |
16: 58,617,732 (GRCm39) |
H159L |
possibly damaging |
Het |
| Pard3 |
T |
A |
8: 128,336,939 (GRCm39) |
I1143K |
probably benign |
Het |
| Pcdha7 |
A |
G |
18: 37,108,027 (GRCm39) |
T351A |
probably benign |
Het |
| Phf2 |
C |
A |
13: 48,974,089 (GRCm39) |
G318V |
unknown |
Het |
| Plch1 |
T |
A |
3: 63,778,180 (GRCm39) |
|
probably benign |
Het |
| Polr1c |
A |
G |
17: 46,557,046 (GRCm39) |
I79T |
probably damaging |
Het |
| Ppp2r5e |
A |
G |
12: 75,516,325 (GRCm39) |
I244T |
probably damaging |
Het |
| Psmd12 |
T |
C |
11: 107,376,585 (GRCm39) |
C74R |
probably damaging |
Het |
| Qng1 |
C |
T |
13: 58,529,805 (GRCm39) |
G269E |
probably damaging |
Het |
| Ralgapa1 |
A |
G |
12: 55,786,115 (GRCm39) |
|
probably null |
Het |
| Robo3 |
C |
T |
9: 37,333,194 (GRCm39) |
G781D |
probably damaging |
Het |
| Scn8a |
T |
C |
15: 100,854,954 (GRCm39) |
V147A |
possibly damaging |
Het |
| Sfxn5 |
A |
T |
6: 85,309,288 (GRCm39) |
L139* |
probably null |
Het |
| Slc2a12 |
A |
T |
10: 22,577,993 (GRCm39) |
K596N |
probably benign |
Het |
| Sorcs1 |
G |
A |
19: 50,213,613 (GRCm39) |
R705C |
probably damaging |
Het |
| Spata31e4 |
C |
T |
13: 50,854,388 (GRCm39) |
T82I |
possibly damaging |
Het |
| Tlr4 |
T |
A |
4: 66,758,563 (GRCm39) |
I452N |
probably damaging |
Het |
| Tshz3 |
A |
G |
7: 36,469,544 (GRCm39) |
D511G |
probably damaging |
Het |
| Usp44 |
A |
G |
10: 93,682,632 (GRCm39) |
K314E |
possibly damaging |
Het |
|
| Other mutations in Sema3b |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00674:Sema3b
|
APN |
9 |
107,481,240 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL02750:Sema3b
|
APN |
9 |
107,480,363 (GRCm39) |
missense |
probably benign |
0.02 |
|
IGL02878:Sema3b
|
APN |
9 |
107,478,192 (GRCm39) |
missense |
probably damaging |
0.97 |
|
IGL03004:Sema3b
|
APN |
9 |
107,480,114 (GRCm39) |
missense |
possibly damaging |
0.72 |
|
IGL03026:Sema3b
|
APN |
9 |
107,479,262 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03129:Sema3b
|
APN |
9 |
107,476,995 (GRCm39) |
unclassified |
probably benign |
|
|
IGL03334:Sema3b
|
APN |
9 |
107,481,276 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0373:Sema3b
|
UTSW |
9 |
107,480,117 (GRCm39) |
missense |
probably benign |
0.05 |
|
R0384:Sema3b
|
UTSW |
9 |
107,478,165 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0883:Sema3b
|
UTSW |
9 |
107,481,355 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R3916:Sema3b
|
UTSW |
9 |
107,477,657 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3971:Sema3b
|
UTSW |
9 |
107,477,567 (GRCm39) |
missense |
probably benign |
|
|
R4647:Sema3b
|
UTSW |
9 |
107,476,250 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
R4694:Sema3b
|
UTSW |
9 |
107,482,201 (GRCm39) |
missense |
probably benign |
0.03 |
|
R4791:Sema3b
|
UTSW |
9 |
107,481,012 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4853:Sema3b
|
UTSW |
9 |
107,479,266 (GRCm39) |
splice site |
probably null |
|
|
R5305:Sema3b
|
UTSW |
9 |
107,480,536 (GRCm39) |
missense |
probably null |
1.00 |
|
R5487:Sema3b
|
UTSW |
9 |
107,478,161 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5745:Sema3b
|
UTSW |
9 |
107,478,628 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5751:Sema3b
|
UTSW |
9 |
107,476,913 (GRCm39) |
missense |
probably benign |
|
|
R6086:Sema3b
|
UTSW |
9 |
107,478,047 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6306:Sema3b
|
UTSW |
9 |
107,478,119 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R6594:Sema3b
|
UTSW |
9 |
107,476,025 (GRCm39) |
missense |
probably benign |
0.01 |
|
R6816:Sema3b
|
UTSW |
9 |
107,477,549 (GRCm39) |
missense |
probably benign |
0.08 |
|
R6833:Sema3b
|
UTSW |
9 |
107,480,515 (GRCm39) |
missense |
probably benign |
0.04 |
|
R7320:Sema3b
|
UTSW |
9 |
107,478,141 (GRCm39) |
missense |
probably benign |
|
|
R7448:Sema3b
|
UTSW |
9 |
107,480,162 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7687:Sema3b
|
UTSW |
9 |
107,481,013 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8839:Sema3b
|
UTSW |
9 |
107,478,552 (GRCm39) |
unclassified |
probably benign |
|
|
R9090:Sema3b
|
UTSW |
9 |
107,476,154 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9123:Sema3b
|
UTSW |
9 |
107,478,173 (GRCm39) |
missense |
possibly damaging |
0.64 |
|
R9271:Sema3b
|
UTSW |
9 |
107,476,154 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9442:Sema3b
|
UTSW |
9 |
107,478,957 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9682:Sema3b
|
UTSW |
9 |
107,481,013 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9755:Sema3b
|
UTSW |
9 |
107,478,784 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1088:Sema3b
|
UTSW |
9 |
107,476,233 (GRCm39) |
splice site |
probably null |
|
|
Z1176:Sema3b
|
UTSW |
9 |
107,476,838 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
| Predicted Primers |
|
| Posted On |
2015-06-10 |
Incidental Mutation