Incidental Mutation 'R0384:Sema3b'
| ID |
31181 |
| 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 |
038590-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.341)
|
| Stock # |
R0384 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
9 |
| Chromosomal Location |
107474873-107486428 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 107478165 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Phenylalanine
at position 407
(L407F)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000137952
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000073448]
[ENSMUST00000102529]
[ENSMUST00000102530]
[ENSMUST00000102531]
[ENSMUST00000102532]
[ENSMUST00000123926]
[ENSMUST00000194606]
[ENSMUST00000194433]
[ENSMUST00000195057]
[ENSMUST00000195662]
[ENSMUST00000193180]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000073448
AA Change: L407F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000073152
Gene: ENSMUSG00000057969
AA Change: L407F
| 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: L407F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000099588
Gene: ENSMUSG00000057969
AA Change: L407F
| 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: L407F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000099589
Gene: ENSMUSG00000057969
AA Change: L407F
| 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: L407F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000099590
Gene: ENSMUSG00000057969
AA Change: L407F
| 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: L407F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000099591
Gene: ENSMUSG00000057969
AA Change: L407F
| 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: L407F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000137952
Gene: ENSMUSG00000057969
AA Change: L407F
| 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: ENSMUST00000193551
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000193234
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000195472
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194606
|
| 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: ENSMUST00000195057
|
| 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 |
|
| Meta Mutation Damage Score |
0.7259 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.1%
- 10x: 95.8%
- 20x: 91.7%
|
| Validation Efficiency |
100% (72/72) |
| 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: 69 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam8 |
T |
A |
7: 139,566,725 (GRCm39) |
|
probably benign |
Het |
| Akr1b8 |
T |
C |
6: 34,341,265 (GRCm39) |
|
probably benign |
Het |
| Arhgef39 |
A |
G |
4: 43,498,613 (GRCm39) |
L117P |
probably damaging |
Het |
| Atp13a1 |
A |
T |
8: 70,249,974 (GRCm39) |
Q356L |
possibly damaging |
Het |
| Bmp2k |
T |
A |
5: 97,178,984 (GRCm39) |
|
probably benign |
Het |
| Ccdc141 |
A |
G |
2: 76,857,992 (GRCm39) |
V1063A |
probably damaging |
Het |
| Col20a1 |
T |
C |
2: 180,640,955 (GRCm39) |
Y568H |
probably benign |
Het |
| Crabp2 |
T |
C |
3: 87,860,328 (GRCm39) |
V134A |
possibly damaging |
Het |
| Cyp19a1 |
T |
C |
9: 54,080,025 (GRCm39) |
K265E |
probably benign |
Het |
| Cyp2j9 |
T |
C |
4: 96,474,122 (GRCm39) |
H106R |
probably benign |
Het |
| Dcps |
T |
C |
9: 35,087,239 (GRCm39) |
K9R |
probably damaging |
Het |
| Dnajc6 |
C |
T |
4: 101,456,153 (GRCm39) |
T47I |
probably damaging |
Het |
| Dnhd1 |
T |
G |
7: 105,369,321 (GRCm39) |
S4315A |
possibly damaging |
Het |
| Dnmt3l |
A |
T |
10: 77,888,571 (GRCm39) |
I158F |
possibly damaging |
Het |
| Dock3 |
A |
G |
9: 106,779,094 (GRCm39) |
|
probably benign |
Het |
| Eefsec |
A |
G |
6: 88,258,632 (GRCm39) |
|
probably null |
Het |
| Fam204a |
T |
C |
19: 60,209,728 (GRCm39) |
M1V |
probably null |
Het |
| Fam98b |
T |
C |
2: 117,098,328 (GRCm39) |
V266A |
possibly damaging |
Het |
| Fat2 |
A |
T |
11: 55,160,291 (GRCm39) |
I3274N |
possibly damaging |
Het |
| Fbh1 |
A |
G |
2: 11,754,389 (GRCm39) |
I198T |
probably damaging |
Het |
| Fer |
T |
C |
17: 64,231,179 (GRCm39) |
|
probably benign |
Het |
| Fhad1 |
T |
A |
4: 141,729,737 (GRCm39) |
M89L |
probably benign |
Het |
| Fjx1 |
C |
A |
2: 102,281,452 (GRCm39) |
C161F |
probably damaging |
Het |
| Fkbp7 |
T |
A |
2: 76,496,168 (GRCm39) |
|
probably benign |
Het |
| Gm42669 |
T |
A |
5: 107,656,664 (GRCm39) |
C976S |
probably benign |
Het |
| Gm4845 |
T |
C |
1: 141,184,823 (GRCm39) |
|
noncoding transcript |
Het |
| Herc1 |
T |
A |
9: 66,388,332 (GRCm39) |
|
probably benign |
Het |
| Hook3 |
C |
T |
8: 26,534,263 (GRCm39) |
|
probably null |
Het |
| Idh2 |
C |
T |
7: 79,748,005 (GRCm39) |
A232T |
probably damaging |
Het |
| Itga2b |
A |
T |
11: 102,356,188 (GRCm39) |
|
probably null |
Het |
| Klk1b21 |
T |
C |
7: 43,754,917 (GRCm39) |
Y71H |
probably benign |
Het |
| Kndc1 |
A |
T |
7: 139,490,515 (GRCm39) |
N339I |
possibly damaging |
Het |
| Ky |
C |
T |
9: 102,419,289 (GRCm39) |
T432I |
probably benign |
Het |
| Map4 |
C |
T |
9: 109,863,696 (GRCm39) |
T307I |
probably damaging |
Het |
| Matn1 |
T |
C |
4: 130,671,787 (GRCm39) |
L18P |
probably benign |
Het |
| Mindy4 |
G |
A |
6: 55,193,669 (GRCm39) |
D121N |
probably damaging |
Het |
| Mpv17l |
A |
T |
16: 13,758,863 (GRCm39) |
I96L |
probably benign |
Het |
| Msto1 |
G |
A |
3: 88,817,646 (GRCm39) |
Q441* |
probably null |
Het |
| Muc5ac |
A |
G |
7: 141,365,988 (GRCm39) |
H2048R |
possibly damaging |
Het |
| Musk |
T |
C |
4: 58,373,711 (GRCm39) |
*879Q |
probably null |
Het |
| Nat8f2 |
T |
C |
6: 85,845,350 (GRCm39) |
Y4C |
possibly damaging |
Het |
| Ncaph2 |
T |
A |
15: 89,253,594 (GRCm39) |
I282N |
probably benign |
Het |
| Nid1 |
A |
G |
13: 13,638,421 (GRCm39) |
T114A |
probably benign |
Het |
| Npr1 |
C |
A |
3: 90,372,474 (GRCm39) |
G113C |
probably damaging |
Het |
| Nrxn1 |
G |
A |
17: 90,515,775 (GRCm39) |
P193S |
probably damaging |
Het |
| Nwd2 |
T |
C |
5: 63,963,025 (GRCm39) |
F870L |
probably benign |
Het |
| Or10h1b |
A |
G |
17: 33,395,522 (GRCm39) |
I45V |
probably damaging |
Het |
| Or4c122 |
A |
G |
2: 89,079,414 (GRCm39) |
I208T |
possibly damaging |
Het |
| Or6c5c |
T |
A |
10: 129,298,909 (GRCm39) |
Y121* |
probably null |
Het |
| Or8k30 |
T |
A |
2: 86,339,727 (GRCm39) |
I308K |
possibly damaging |
Het |
| Phf14 |
A |
G |
6: 11,997,019 (GRCm39) |
|
probably benign |
Het |
| Pnpla5 |
G |
T |
15: 84,004,920 (GRCm39) |
L144M |
probably damaging |
Het |
| Prdm2 |
T |
C |
4: 142,862,258 (GRCm39) |
E344G |
probably benign |
Het |
| Psmd12 |
T |
C |
11: 107,376,547 (GRCm39) |
V61A |
probably benign |
Het |
| Relt |
T |
C |
7: 100,496,712 (GRCm39) |
D385G |
probably benign |
Het |
| Rif1 |
GCCACCA |
GCCA |
2: 52,000,336 (GRCm39) |
|
probably benign |
Het |
| Scg2 |
T |
A |
1: 79,413,266 (GRCm39) |
I446F |
probably benign |
Het |
| Slc25a13 |
A |
T |
6: 6,042,600 (GRCm39) |
Y601* |
probably null |
Het |
| Sun5 |
C |
T |
2: 153,700,885 (GRCm39) |
V270I |
probably benign |
Het |
| Tex52 |
A |
G |
6: 128,356,496 (GRCm39) |
Y63C |
probably damaging |
Het |
| Tmem138 |
A |
G |
19: 10,552,186 (GRCm39) |
|
probably benign |
Het |
| Tnpo3 |
A |
G |
6: 29,582,163 (GRCm39) |
|
probably null |
Het |
| Tspoap1 |
A |
T |
11: 87,657,280 (GRCm39) |
Q364L |
probably damaging |
Het |
| Ttc41 |
T |
C |
10: 86,599,811 (GRCm39) |
L1037P |
probably damaging |
Het |
| Ugcg |
T |
A |
4: 59,220,387 (GRCm39) |
D393E |
possibly damaging |
Het |
| Vmn1r184 |
T |
C |
7: 25,967,076 (GRCm39) |
I274T |
probably benign |
Het |
| Vmn2r27 |
A |
G |
6: 124,200,871 (GRCm39) |
V362A |
probably benign |
Het |
| Vmn2r87 |
T |
A |
10: 130,307,712 (GRCm39) |
Y842F |
probably benign |
Het |
| Vps8 |
T |
A |
16: 21,325,575 (GRCm39) |
|
probably benign |
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 |
|
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 |
|
|
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'- TTGTGATGAGACCCTGACCTGTACC -3'
(R):5'- AAAGATAGAGCTGTGCCCCTCAGAG -3'
Sequencing Primer
(F):5'- CCTGACCTGTACCAATGAAGAG -3'
(R):5'- TTCGCCAAGGAAAGGCTC -3'
|
| Posted On |
2013-04-24 |
Incidental Mutation