Incidental Mutation 'R4694:Sema3b'
| ID |
355571 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sema3b
|
| Ensembl Gene |
ENSMUSG00000057969 |
| Gene Name |
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B |
| Synonyms |
SemA, sema5, semaV, Semaa, LUCA-1, SemA |
| MMRRC Submission |
041945-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.434)
|
| Stock # |
R4694 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
9 |
| Chromosomal Location |
107597674-107609229 bp(-) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 107605002 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Proline to Serine
at position 26
(P26S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141928
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000073448]
[ENSMUST00000102529]
[ENSMUST00000102530]
[ENSMUST00000102531]
[ENSMUST00000102532]
[ENSMUST00000123926]
[ENSMUST00000193180]
[ENSMUST00000194433]
[ENSMUST00000194606]
[ENSMUST00000195662]
[ENSMUST00000195057]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000073448
AA Change: P26S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000073152
Gene: ENSMUSG00000057969
AA Change: P26S
| 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 benign
Transcript: ENSMUST00000102529
AA Change: P26S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000099588
Gene: ENSMUSG00000057969
AA Change: P26S
| 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 benign
Transcript: ENSMUST00000102530
AA Change: P26S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000099589
Gene: ENSMUSG00000057969
AA Change: P26S
| 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 benign
Transcript: ENSMUST00000102531
AA Change: P26S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000099590
Gene: ENSMUSG00000057969
AA Change: P26S
| 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 benign
Transcript: ENSMUST00000102532
AA Change: P26S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000099591
Gene: ENSMUSG00000057969
AA Change: P26S
| 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 benign
Transcript: ENSMUST00000123926
AA Change: P26S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000137952
Gene: ENSMUSG00000057969
AA Change: P26S
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Sema
|
55 |
497 |
6.37e-207 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000193180
AA Change: P26S
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000141726
Gene: ENSMUSG00000057969
AA Change: P26S
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
55 |
148 |
8.2e-31 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000193234
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000193551
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194433
AA Change: P26S
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000141403
Gene: ENSMUSG00000057969
AA Change: P26S
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
55 |
172 |
3.5e-36 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194606
AA Change: P26S
PolyPhen 2
Score 0.034 (Sensitivity: 0.95; Specificity: 0.82)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000195662
AA Change: P26S
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000141614
Gene: ENSMUSG00000057969
AA Change: P26S
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
55 |
137 |
8.4e-26 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000195472
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000195057
|
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 96.9%
- 20x: 94.3%
|
| 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: 67 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcg5 |
A |
T |
17: 84,672,158 (GRCm38) |
F258Y |
probably damaging |
Het |
| Adamtsl4 |
C |
T |
3: 95,679,745 (GRCm38) |
R765H |
probably damaging |
Het |
| Bicd1 |
T |
A |
6: 149,409,553 (GRCm38) |
L42Q |
probably damaging |
Het |
| Cacna1e |
C |
T |
1: 154,437,266 (GRCm38) |
|
probably null |
Het |
| Capn1 |
T |
A |
19: 5,994,731 (GRCm38) |
K504* |
probably null |
Het |
| Cdh15 |
G |
A |
8: 122,862,024 (GRCm38) |
R279Q |
probably damaging |
Het |
| Cep350 |
T |
C |
1: 155,928,586 (GRCm38) |
K917R |
probably damaging |
Het |
| Cp |
A |
T |
3: 19,974,885 (GRCm38) |
T509S |
probably benign |
Het |
| Cyp2d10 |
T |
C |
15: 82,404,483 (GRCm38) |
D266G |
probably damaging |
Het |
| Dhodh |
C |
G |
8: 109,606,416 (GRCm38) |
R7P |
probably damaging |
Het |
| Dmxl2 |
A |
G |
9: 54,446,905 (GRCm38) |
L419P |
probably benign |
Het |
| Epb41l4b |
A |
T |
4: 57,019,875 (GRCm38) |
M84K |
probably benign |
Het |
| Fbln7 |
A |
G |
2: 128,880,425 (GRCm38) |
|
probably null |
Het |
| Fbxw11 |
C |
T |
11: 32,642,820 (GRCm38) |
|
probably benign |
Het |
| Flnc |
C |
A |
6: 29,443,448 (GRCm38) |
P543T |
probably damaging |
Het |
| Gm13103 |
T |
C |
4: 143,852,960 (GRCm38) |
S372P |
probably damaging |
Het |
| Grid1 |
T |
C |
14: 35,026,780 (GRCm38) |
S186P |
probably damaging |
Het |
| Hcfc2 |
C |
T |
10: 82,723,700 (GRCm38) |
T382M |
probably damaging |
Het |
| Hdac9 |
G |
T |
12: 34,437,247 (GRCm38) |
L73I |
probably damaging |
Het |
| Hnrnpa2b1 |
A |
T |
6: 51,464,183 (GRCm38) |
D302E |
probably damaging |
Het |
| Ifi204 |
C |
T |
1: 173,749,259 (GRCm38) |
C592Y |
probably damaging |
Het |
| Jph1 |
T |
A |
1: 16,997,505 (GRCm38) |
I653F |
probably damaging |
Het |
| Kcnj3 |
A |
G |
2: 55,594,906 (GRCm38) |
K339E |
probably benign |
Het |
| Kcp |
G |
A |
6: 29,493,197 (GRCm38) |
T838I |
probably benign |
Het |
| Krtap26-1 |
A |
T |
16: 88,647,220 (GRCm38) |
V171E |
possibly damaging |
Het |
| Lck |
G |
T |
4: 129,548,972 (GRCm38) |
N452K |
possibly damaging |
Het |
| Madd |
A |
G |
2: 91,160,328 (GRCm38) |
L1134S |
probably damaging |
Het |
| Mafk |
T |
C |
5: 139,800,493 (GRCm38) |
S149P |
probably damaging |
Het |
| Man1c1 |
T |
C |
4: 134,703,189 (GRCm38) |
D94G |
probably benign |
Het |
| Me2 |
T |
A |
18: 73,801,859 (GRCm38) |
M38L |
probably benign |
Het |
| Muc2 |
A |
C |
7: 141,752,345 (GRCm38) |
D257A |
probably damaging |
Het |
| Myh11 |
T |
C |
16: 14,200,702 (GRCm38) |
K1927E |
probably damaging |
Het |
| Naaladl1 |
C |
T |
19: 6,108,890 (GRCm38) |
P324S |
probably damaging |
Het |
| Ndufa10 |
T |
C |
1: 92,452,102 (GRCm38) |
E303G |
probably benign |
Het |
| Nedd1 |
C |
T |
10: 92,719,582 (GRCm38) |
V14I |
probably benign |
Het |
| Nwd1 |
T |
G |
8: 72,667,330 (GRCm38) |
V407G |
probably damaging |
Het |
| Olfr1136 |
T |
A |
2: 87,693,760 (GRCm38) |
T41S |
probably benign |
Het |
| Olfr132 |
A |
C |
17: 38,130,857 (GRCm38) |
C112G |
probably damaging |
Het |
| Olfr32 |
T |
A |
2: 90,138,249 (GRCm38) |
K297* |
probably null |
Het |
| Olfr726 |
T |
C |
14: 50,084,019 (GRCm38) |
I221V |
probably benign |
Het |
| Olfr847 |
A |
G |
9: 19,375,398 (GRCm38) |
L161P |
probably damaging |
Het |
| Pgrmc2 |
T |
C |
3: 41,070,405 (GRCm38) |
D144G |
probably damaging |
Het |
| Ppp3cb |
T |
C |
14: 20,501,515 (GRCm38) |
N516S |
probably benign |
Het |
| Prelp |
A |
G |
1: 133,914,747 (GRCm38) |
M220T |
probably damaging |
Het |
| Prss36 |
A |
G |
7: 127,935,615 (GRCm38) |
W465R |
probably damaging |
Het |
| Pth2r |
C |
A |
1: 65,336,761 (GRCm38) |
F59L |
probably benign |
Het |
| Rab20 |
C |
T |
8: 11,454,485 (GRCm38) |
G72R |
probably damaging |
Het |
| Rab4a |
G |
T |
8: 123,829,030 (GRCm38) |
G49W |
probably damaging |
Het |
| Rad9a |
G |
A |
19: 4,200,561 (GRCm38) |
R85C |
probably damaging |
Het |
| Rhox2c |
A |
C |
X: 37,453,698 (GRCm38) |
Q4H |
probably benign |
Het |
| Rock1 |
A |
T |
18: 10,136,152 (GRCm38) |
Y178* |
probably null |
Het |
| Scaf8 |
C |
A |
17: 3,197,404 (GRCm38) |
L1001I |
probably damaging |
Het |
| Slc23a1 |
A |
G |
18: 35,619,580 (GRCm38) |
L548P |
probably damaging |
Het |
| Sncaip |
A |
C |
18: 52,906,557 (GRCm38) |
T548P |
probably benign |
Het |
| Stpg2 |
C |
T |
3: 139,317,416 (GRCm38) |
P398S |
possibly damaging |
Het |
| Stpg3 |
A |
C |
2: 25,213,297 (GRCm38) |
V260G |
probably damaging |
Het |
| Tbc1d9 |
T |
A |
8: 83,234,246 (GRCm38) |
F242I |
probably damaging |
Het |
| Tnks1bp1 |
G |
A |
2: 85,071,722 (GRCm38) |
R992Q |
probably damaging |
Het |
| Tom1l1 |
T |
G |
11: 90,646,849 (GRCm38) |
H394P |
possibly damaging |
Het |
| Topors |
T |
G |
4: 40,261,442 (GRCm38) |
N614T |
possibly damaging |
Het |
| Trank1 |
A |
T |
9: 111,392,061 (GRCm38) |
Q2622L |
probably benign |
Het |
| Trub2 |
A |
G |
2: 29,778,846 (GRCm38) |
S186P |
probably damaging |
Het |
| Unc13c |
T |
A |
9: 73,572,354 (GRCm38) |
H1756L |
probably benign |
Het |
| Vmn1r9 |
A |
T |
6: 57,071,329 (GRCm38) |
I130F |
probably benign |
Het |
| Wdr72 |
A |
T |
9: 74,179,555 (GRCm38) |
I602F |
probably damaging |
Het |
| Zfand3 |
T |
A |
17: 30,135,388 (GRCm38) |
F60I |
possibly damaging |
Het |
| Zfp946 |
G |
A |
17: 22,455,711 (GRCm38) |
G482E |
probably benign |
Het |
|
| Other mutations in Sema3b |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00674:Sema3b
|
APN |
9 |
107,604,041 (GRCm38) |
critical splice donor site |
probably null |
|
|
IGL02750:Sema3b
|
APN |
9 |
107,603,164 (GRCm38) |
missense |
probably benign |
0.02 |
|
IGL02878:Sema3b
|
APN |
9 |
107,600,993 (GRCm38) |
missense |
probably damaging |
0.97 |
|
IGL03004:Sema3b
|
APN |
9 |
107,602,915 (GRCm38) |
missense |
possibly damaging |
0.72 |
|
IGL03026:Sema3b
|
APN |
9 |
107,602,063 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL03129:Sema3b
|
APN |
9 |
107,599,796 (GRCm38) |
unclassified |
probably benign |
|
|
IGL03334:Sema3b
|
APN |
9 |
107,604,077 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R0373:Sema3b
|
UTSW |
9 |
107,602,918 (GRCm38) |
missense |
probably benign |
0.05 |
|
R0384:Sema3b
|
UTSW |
9 |
107,600,966 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R0883:Sema3b
|
UTSW |
9 |
107,604,156 (GRCm38) |
missense |
possibly damaging |
0.77 |
|
R3916:Sema3b
|
UTSW |
9 |
107,600,458 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R3971:Sema3b
|
UTSW |
9 |
107,600,368 (GRCm38) |
missense |
probably benign |
|
|
R4212:Sema3b
|
UTSW |
9 |
107,603,398 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4647:Sema3b
|
UTSW |
9 |
107,599,051 (GRCm38) |
missense |
possibly damaging |
0.79 |
|
R4791:Sema3b
|
UTSW |
9 |
107,603,813 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4853:Sema3b
|
UTSW |
9 |
107,602,067 (GRCm38) |
splice site |
probably null |
|
|
R5305:Sema3b
|
UTSW |
9 |
107,603,337 (GRCm38) |
missense |
probably null |
1.00 |
|
R5487:Sema3b
|
UTSW |
9 |
107,600,962 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5745:Sema3b
|
UTSW |
9 |
107,601,429 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R5751:Sema3b
|
UTSW |
9 |
107,599,714 (GRCm38) |
missense |
probably benign |
|
|
R6086:Sema3b
|
UTSW |
9 |
107,600,848 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R6306:Sema3b
|
UTSW |
9 |
107,600,920 (GRCm38) |
missense |
possibly damaging |
0.88 |
|
R6594:Sema3b
|
UTSW |
9 |
107,598,826 (GRCm38) |
missense |
probably benign |
0.01 |
|
R6816:Sema3b
|
UTSW |
9 |
107,600,350 (GRCm38) |
missense |
probably benign |
0.08 |
|
R6833:Sema3b
|
UTSW |
9 |
107,603,316 (GRCm38) |
missense |
probably benign |
0.04 |
|
R7320:Sema3b
|
UTSW |
9 |
107,600,942 (GRCm38) |
missense |
probably benign |
|
|
R7448:Sema3b
|
UTSW |
9 |
107,602,963 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7687:Sema3b
|
UTSW |
9 |
107,603,814 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R8839:Sema3b
|
UTSW |
9 |
107,601,353 (GRCm38) |
unclassified |
probably benign |
|
|
R9090:Sema3b
|
UTSW |
9 |
107,598,955 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R9123:Sema3b
|
UTSW |
9 |
107,600,974 (GRCm38) |
missense |
possibly damaging |
0.64 |
|
R9271:Sema3b
|
UTSW |
9 |
107,598,955 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R9442:Sema3b
|
UTSW |
9 |
107,601,758 (GRCm38) |
critical splice donor site |
probably null |
|
|
R9682:Sema3b
|
UTSW |
9 |
107,603,814 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R9755:Sema3b
|
UTSW |
9 |
107,601,585 (GRCm38) |
missense |
probably damaging |
1.00 |
|
Z1088:Sema3b
|
UTSW |
9 |
107,599,034 (GRCm38) |
splice site |
probably null |
|
|
Z1176:Sema3b
|
UTSW |
9 |
107,599,639 (GRCm38) |
missense |
possibly damaging |
0.89 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGGGTTAACTGGAGATGGCC -3'
(R):5'- AATCTGATCCCTTGGGACTCC -3'
Sequencing Primer
(F):5'- CTGGAGATGGCCCAAGAAAACC -3'
(R):5'- TCTGCTTTGCTGCGGAC -3'
|
| Posted On |
2015-10-21 |
Incidental Mutation