Incidental Mutation 'R3916:Sema3b'
ID |
309755 |
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 |
Accession Numbers |
|
Essential gene? |
Possibly non essential
(E-score: 0.321)
|
Stock # |
R3916 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
9 |
Chromosomal Location |
107474873-107486428 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 107477657 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Phenylalanine to Serine
at position 482
(F482S)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000137952
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000073448]
[ENSMUST00000102529]
[ENSMUST00000102530]
[ENSMUST00000102531]
[ENSMUST00000102532]
[ENSMUST00000123926]
[ENSMUST00000194433]
[ENSMUST00000195662]
[ENSMUST00000193180]
[ENSMUST00000195057]
[ENSMUST00000194606]
|
AlphaFold |
no structure available at present |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000073448
AA Change: F482S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000073152 Gene: ENSMUSG00000057969 AA Change: F482S
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: F482S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000099588 Gene: ENSMUSG00000057969 AA Change: F482S
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: F482S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000099589 Gene: ENSMUSG00000057969 AA Change: F482S
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: F482S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000099590 Gene: ENSMUSG00000057969 AA Change: F482S
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: F482S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000099591 Gene: ENSMUSG00000057969 AA Change: F482S
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: F482S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000137952 Gene: ENSMUSG00000057969 AA Change: F482S
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
Sema
|
55 |
497 |
6.37e-207 |
SMART |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000191791
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000193234
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000195472
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000193551
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000194433
|
SMART Domains |
Protein: ENSMUSP00000141403 Gene: ENSMUSG00000057969
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: ENSMUST00000195662
|
SMART Domains |
Protein: ENSMUSP00000141614 Gene: ENSMUSG00000057969
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
Pfam:Sema
|
55 |
137 |
8.4e-26 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000193180
|
SMART Domains |
Protein: ENSMUSP00000141726 Gene: ENSMUSG00000057969
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
24 |
N/A |
INTRINSIC |
Pfam:Sema
|
55 |
148 |
8.2e-31 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000195057
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000194606
|
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.4%
|
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: 64 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4932414N04Rik |
T |
G |
2: 68,562,329 (GRCm39) |
F319V |
possibly damaging |
Het |
Acad12 |
A |
G |
5: 121,737,277 (GRCm39) |
V498A |
probably damaging |
Het |
Adam19 |
A |
G |
11: 45,951,762 (GRCm39) |
E37G |
probably benign |
Het |
Anks3 |
A |
G |
16: 4,765,143 (GRCm39) |
Y423H |
probably damaging |
Het |
Arfgef1 |
A |
T |
1: 10,259,668 (GRCm39) |
V600D |
probably benign |
Het |
Arhgef18 |
T |
C |
8: 3,504,197 (GRCm39) |
F939L |
probably benign |
Het |
Arhgef2 |
A |
G |
3: 88,540,340 (GRCm39) |
N127S |
probably damaging |
Het |
Arid1b |
A |
G |
17: 5,392,928 (GRCm39) |
S2100G |
probably benign |
Het |
Atp1b2 |
A |
G |
11: 69,493,901 (GRCm39) |
V93A |
probably damaging |
Het |
Atrnl1 |
T |
C |
19: 57,924,084 (GRCm39) |
V1283A |
possibly damaging |
Het |
Bpifb5 |
A |
C |
2: 154,070,101 (GRCm39) |
K184Q |
probably benign |
Het |
Cadps |
C |
T |
14: 12,457,702 (GRCm38) |
A1060T |
probably benign |
Het |
Cant1 |
A |
G |
11: 118,299,572 (GRCm39) |
V259A |
probably damaging |
Het |
Ccdc89 |
A |
G |
7: 90,076,033 (GRCm39) |
D81G |
probably damaging |
Het |
Cd109 |
CATTTATTTATTTATTTATTTATTTATTTATTTAT |
CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT |
9: 78,619,782 (GRCm39) |
|
probably benign |
Het |
Cntnap4 |
C |
G |
8: 113,602,165 (GRCm39) |
P1190A |
probably benign |
Het |
Colgalt2 |
T |
A |
1: 152,384,362 (GRCm39) |
Y567* |
probably null |
Het |
Cyp4f18 |
A |
T |
8: 72,749,881 (GRCm39) |
F256Y |
probably benign |
Het |
Ddx41 |
G |
A |
13: 55,682,293 (GRCm39) |
R205W |
possibly damaging |
Het |
Dop1a |
G |
A |
9: 86,403,186 (GRCm39) |
R1462H |
probably damaging |
Het |
Dync1i2 |
A |
G |
2: 71,079,716 (GRCm39) |
T377A |
probably damaging |
Het |
F2 |
G |
A |
2: 91,455,833 (GRCm39) |
T600M |
probably damaging |
Het |
Fam91a1 |
C |
T |
15: 58,302,583 (GRCm39) |
H308Y |
probably damaging |
Het |
Fkbp2 |
C |
A |
19: 6,955,925 (GRCm39) |
|
probably null |
Het |
Gabarapl2 |
T |
A |
8: 112,679,028 (GRCm39) |
F115L |
probably benign |
Het |
Heatr3 |
T |
G |
8: 88,876,999 (GRCm39) |
|
probably null |
Het |
Ifi204 |
T |
G |
1: 173,583,341 (GRCm39) |
K292N |
possibly damaging |
Het |
Itpkc |
A |
T |
7: 26,927,728 (GRCm39) |
I62N |
probably benign |
Het |
Kcnab1 |
G |
A |
3: 65,211,585 (GRCm39) |
|
probably null |
Het |
Krt88 |
G |
A |
15: 101,350,809 (GRCm39) |
|
probably null |
Het |
Larp4 |
C |
T |
15: 99,888,284 (GRCm39) |
T107I |
probably benign |
Het |
Lmo7 |
T |
C |
14: 102,166,778 (GRCm39) |
|
probably benign |
Het |
Lrrc37a |
T |
C |
11: 103,346,344 (GRCm39) |
Y3174C |
possibly damaging |
Het |
Lyzl4 |
T |
A |
9: 121,412,101 (GRCm39) |
D105V |
probably damaging |
Het |
Mst1 |
A |
G |
9: 107,961,494 (GRCm39) |
I575V |
probably benign |
Het |
Myh7 |
C |
A |
14: 55,211,503 (GRCm39) |
E1555D |
probably damaging |
Het |
Nwd1 |
T |
A |
8: 73,394,439 (GRCm39) |
C608* |
probably null |
Het |
Obox3 |
C |
A |
7: 15,361,151 (GRCm39) |
C38F |
probably benign |
Het |
P4ha2 |
A |
G |
11: 54,017,074 (GRCm39) |
D441G |
probably benign |
Het |
Pcdhb14 |
A |
T |
18: 37,581,598 (GRCm39) |
I235F |
possibly damaging |
Het |
Rasgrf2 |
A |
G |
13: 92,167,296 (GRCm39) |
V259A |
probably damaging |
Het |
Scn1a |
T |
C |
2: 66,107,957 (GRCm39) |
T1590A |
probably damaging |
Het |
Sdk1 |
T |
A |
5: 142,036,999 (GRCm39) |
D817E |
probably damaging |
Het |
Slc35a5 |
G |
C |
16: 44,978,521 (GRCm39) |
|
probably benign |
Het |
Slc6a3 |
A |
G |
13: 73,710,427 (GRCm39) |
I346V |
probably benign |
Het |
Slu7 |
G |
T |
11: 43,331,511 (GRCm39) |
|
probably null |
Het |
Spns1 |
A |
T |
7: 125,970,711 (GRCm39) |
|
probably null |
Het |
Supv3l1 |
T |
C |
10: 62,285,199 (GRCm39) |
D89G |
possibly damaging |
Het |
Taf1c |
G |
A |
8: 120,327,244 (GRCm39) |
R412W |
probably damaging |
Het |
Tctn3 |
T |
A |
19: 40,596,093 (GRCm39) |
T305S |
possibly damaging |
Het |
Tekt1 |
A |
G |
11: 72,236,574 (GRCm39) |
I296T |
possibly damaging |
Het |
Tet2 |
T |
C |
3: 133,191,816 (GRCm39) |
K873E |
possibly damaging |
Het |
Thada |
G |
A |
17: 84,749,210 (GRCm39) |
A587V |
possibly damaging |
Het |
Tmprss15 |
T |
A |
16: 78,782,884 (GRCm39) |
N712Y |
probably damaging |
Het |
Tnks |
A |
G |
8: 35,320,515 (GRCm39) |
S719P |
probably damaging |
Het |
Tnrc6a |
A |
C |
7: 122,780,607 (GRCm39) |
Q1332H |
probably damaging |
Het |
Trpv3 |
A |
G |
11: 73,174,560 (GRCm39) |
D309G |
possibly damaging |
Het |
Tti2 |
A |
G |
8: 31,643,547 (GRCm39) |
K221E |
possibly damaging |
Het |
Uba5 |
A |
T |
9: 103,931,389 (GRCm39) |
C227S |
probably damaging |
Het |
Ugcg |
C |
T |
4: 59,207,798 (GRCm39) |
P46S |
probably benign |
Het |
Unc80 |
T |
C |
1: 66,716,654 (GRCm39) |
C2925R |
probably benign |
Het |
Vmn2r83 |
G |
A |
10: 79,314,744 (GRCm39) |
G331R |
probably benign |
Het |
Xirp2 |
G |
T |
2: 67,341,766 (GRCm39) |
V1336F |
probably benign |
Het |
Zbed5 |
T |
C |
5: 129,931,118 (GRCm39) |
Y356H |
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 |
R3971:Sema3b
|
UTSW |
9 |
107,477,567 (GRCm39) |
missense |
probably benign |
|
R4212:Sema3b
|
UTSW |
9 |
107,480,597 (GRCm39) |
missense |
probably damaging |
1.00 |
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 |
PCR Primer
(F):5'- CGGGGCTTTGAAAACCAAGG -3'
(R):5'- CCCAATCATGATGATGGTGGAG -3'
Sequencing Primer
(F):5'- CTTTGAAAACCAAGGAGAAGCTAGAC -3'
(R):5'- CAATCATGATGATGGTGGAGACAGG -3'
|
Posted On |
2015-04-17 |