Incidental Mutation 'R0085:Sema3d'
| ID |
19846 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sema3d
|
| Ensembl Gene |
ENSMUSG00000040254 |
| Gene Name |
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D |
| Synonyms |
4631426B19Rik |
| MMRRC Submission |
038372-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.188)
|
| Stock # |
R0085 (G1)
|
| Quality Score |
172 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
12433352-12638915 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 12620953 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Isoleucine
at position 520
(V520I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000142453
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030868]
[ENSMUST00000197927]
|
| AlphaFold |
Q8BH34 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000030868
AA Change: V520I
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: V520I
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
16 |
35 |
N/A |
INTRINSIC |
|
Sema
|
70 |
515 |
2.97e-207 |
SMART |
|
PSI
|
533 |
585 |
2.03e-13 |
SMART |
|
IG
|
598 |
682 |
1.39e-2 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000195923
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000197927
AA Change: V520I
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
| SMART Domains |
Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
AA Change: V520I
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
37 |
N/A |
INTRINSIC |
|
Sema
|
70 |
515 |
1e-209 |
SMART |
|
PSI
|
533 |
585 |
8.5e-16 |
SMART |
|
Blast:Sema
|
590 |
622 |
1e-9 |
BLAST |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.1%
- 10x: 95.6%
- 20x: 90.4%
|
| Validation Efficiency |
95% (71/75) |
| 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 III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit pulmonary vein connection to the right atrium and atrial septal defect. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acad12 |
A |
G |
5: 121,742,357 (GRCm39) |
I417T |
possibly damaging |
Het |
| Adcy9 |
T |
C |
16: 4,106,088 (GRCm39) |
T1009A |
probably benign |
Het |
| Ass1 |
A |
T |
2: 31,404,831 (GRCm39) |
N371Y |
probably damaging |
Het |
| Baat |
T |
C |
4: 49,490,425 (GRCm39) |
|
probably benign |
Het |
| Bpi |
T |
A |
2: 158,115,072 (GRCm39) |
L311* |
probably null |
Het |
| Brd2 |
A |
C |
17: 34,332,233 (GRCm39) |
F294L |
probably damaging |
Het |
| Carmil1 |
T |
A |
13: 24,209,850 (GRCm39) |
E804D |
probably benign |
Het |
| Cd209g |
A |
T |
8: 4,184,785 (GRCm39) |
|
probably benign |
Het |
| Cfi |
A |
G |
3: 129,668,635 (GRCm39) |
I554V |
probably benign |
Het |
| Clvs2 |
G |
C |
10: 33,498,542 (GRCm39) |
S129R |
possibly damaging |
Het |
| Dst |
T |
C |
1: 34,268,268 (GRCm39) |
S2897P |
probably damaging |
Het |
| Efcab7 |
T |
C |
4: 99,761,877 (GRCm39) |
|
probably benign |
Het |
| Fbxo2 |
T |
C |
4: 148,249,367 (GRCm39) |
|
probably null |
Het |
| Fgfr2 |
C |
A |
7: 129,797,993 (GRCm39) |
R400L |
probably damaging |
Het |
| Hsd17b14 |
T |
C |
7: 45,205,834 (GRCm39) |
|
probably benign |
Het |
| Il23r |
T |
C |
6: 67,463,206 (GRCm39) |
N96D |
probably damaging |
Het |
| Ints13 |
T |
A |
6: 146,476,285 (GRCm39) |
|
probably benign |
Het |
| Khdc4 |
T |
A |
3: 88,619,046 (GRCm39) |
S583R |
probably damaging |
Het |
| Lig1 |
A |
G |
7: 13,041,495 (GRCm39) |
I776V |
possibly damaging |
Het |
| Madd |
T |
C |
2: 90,993,083 (GRCm39) |
I997V |
probably benign |
Het |
| Mgat4b |
C |
T |
11: 50,121,826 (GRCm39) |
H116Y |
possibly damaging |
Het |
| Myh11 |
C |
A |
16: 14,041,883 (GRCm39) |
Q720H |
probably damaging |
Het |
| Myo5b |
A |
C |
18: 74,834,751 (GRCm39) |
D937A |
probably benign |
Het |
| Nox3 |
T |
C |
17: 3,685,556 (GRCm39) |
N584S |
probably benign |
Het |
| Ogfr |
A |
G |
2: 180,232,830 (GRCm39) |
|
probably null |
Het |
| Or11g25 |
T |
A |
14: 50,723,791 (GRCm39) |
M292K |
probably benign |
Het |
| Or13p3 |
T |
C |
4: 118,567,078 (GRCm39) |
V158A |
probably benign |
Het |
| Or8b1b |
T |
C |
9: 38,375,958 (GRCm39) |
I207T |
probably benign |
Het |
| Osbpl6 |
G |
T |
2: 76,423,758 (GRCm39) |
V728F |
probably benign |
Het |
| Picalm |
T |
A |
7: 89,831,525 (GRCm39) |
S453T |
probably benign |
Het |
| Piezo1 |
A |
G |
8: 123,228,354 (GRCm39) |
L310P |
probably damaging |
Het |
| Pitrm1 |
C |
T |
13: 6,599,604 (GRCm39) |
|
probably benign |
Het |
| Pkd1 |
T |
C |
17: 24,805,197 (GRCm39) |
F3250L |
probably damaging |
Het |
| Plekha4 |
C |
T |
7: 45,193,373 (GRCm39) |
R376* |
probably null |
Het |
| Pnma8b |
A |
T |
7: 16,679,474 (GRCm39) |
S153C |
unknown |
Het |
| Rp1l1 |
C |
T |
14: 64,259,744 (GRCm39) |
R129W |
probably damaging |
Het |
| Ryr3 |
A |
G |
2: 112,690,108 (GRCm39) |
V1147A |
probably damaging |
Het |
| Sgsm1 |
A |
G |
5: 113,427,136 (GRCm39) |
|
probably benign |
Het |
| Slc13a2 |
A |
G |
11: 78,297,694 (GRCm39) |
V58A |
probably damaging |
Het |
| Slc1a4 |
A |
G |
11: 20,254,510 (GRCm39) |
|
probably benign |
Het |
| Slc4a10 |
G |
A |
2: 62,074,690 (GRCm39) |
|
probably benign |
Het |
| Tab1 |
G |
T |
15: 80,040,094 (GRCm39) |
A305S |
probably benign |
Het |
| Tmem30a |
T |
A |
9: 79,678,576 (GRCm39) |
T327S |
probably benign |
Het |
| Tpr |
A |
C |
1: 150,293,164 (GRCm39) |
E863A |
possibly damaging |
Het |
| Upk3bl |
A |
G |
5: 136,088,969 (GRCm39) |
N161D |
probably benign |
Het |
| Ush1c |
T |
A |
7: 45,874,979 (GRCm39) |
I131F |
probably benign |
Het |
| Wdfy4 |
C |
A |
14: 32,800,200 (GRCm39) |
R1975S |
possibly damaging |
Het |
| Zbtb18 |
C |
T |
1: 177,275,501 (GRCm39) |
A287V |
probably benign |
Het |
| Zfp712 |
T |
C |
13: 67,189,256 (GRCm39) |
T424A |
probably benign |
Het |
| Zfp791 |
G |
T |
8: 85,838,862 (GRCm39) |
Y56* |
probably null |
Het |
|
| Other mutations in Sema3d |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00559:Sema3d
|
APN |
5 |
12,613,189 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL00582:Sema3d
|
APN |
5 |
12,635,162 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL00661:Sema3d
|
APN |
5 |
12,555,806 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL00780:Sema3d
|
APN |
5 |
12,574,293 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01531:Sema3d
|
APN |
5 |
12,591,047 (GRCm39) |
missense |
probably benign |
|
|
IGL01957:Sema3d
|
APN |
5 |
12,613,282 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02100:Sema3d
|
APN |
5 |
12,634,958 (GRCm39) |
missense |
probably benign |
0.29 |
|
IGL02676:Sema3d
|
APN |
5 |
12,620,945 (GRCm39) |
missense |
probably benign |
0.38 |
|
IGL02749:Sema3d
|
APN |
5 |
12,613,112 (GRCm39) |
splice site |
probably benign |
|
|
IGL02827:Sema3d
|
APN |
5 |
12,635,085 (GRCm39) |
missense |
probably benign |
0.04 |
|
IGL03325:Sema3d
|
APN |
5 |
12,513,189 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0050:Sema3d
|
UTSW |
5 |
12,634,920 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0095:Sema3d
|
UTSW |
5 |
12,613,314 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0157:Sema3d
|
UTSW |
5 |
12,558,104 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R0328:Sema3d
|
UTSW |
5 |
12,498,042 (GRCm39) |
missense |
possibly damaging |
0.48 |
|
R0924:Sema3d
|
UTSW |
5 |
12,513,183 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R0930:Sema3d
|
UTSW |
5 |
12,513,183 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R1609:Sema3d
|
UTSW |
5 |
12,591,023 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1657:Sema3d
|
UTSW |
5 |
12,634,941 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R1669:Sema3d
|
UTSW |
5 |
12,558,051 (GRCm39) |
splice site |
probably benign |
|
|
R1795:Sema3d
|
UTSW |
5 |
12,634,854 (GRCm39) |
missense |
probably benign |
0.02 |
|
R1861:Sema3d
|
UTSW |
5 |
12,547,570 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1889:Sema3d
|
UTSW |
5 |
12,534,988 (GRCm39) |
splice site |
probably null |
|
|
R1895:Sema3d
|
UTSW |
5 |
12,623,810 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1946:Sema3d
|
UTSW |
5 |
12,623,810 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1975:Sema3d
|
UTSW |
5 |
12,634,965 (GRCm39) |
missense |
probably benign |
|
|
R1975:Sema3d
|
UTSW |
5 |
12,613,285 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2117:Sema3d
|
UTSW |
5 |
12,613,240 (GRCm39) |
missense |
probably benign |
|
|
R2148:Sema3d
|
UTSW |
5 |
12,534,926 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2276:Sema3d
|
UTSW |
5 |
12,592,549 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
R3761:Sema3d
|
UTSW |
5 |
12,621,004 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4063:Sema3d
|
UTSW |
5 |
12,635,091 (GRCm39) |
missense |
probably benign |
0.25 |
|
R4428:Sema3d
|
UTSW |
5 |
12,498,087 (GRCm39) |
missense |
probably benign |
0.32 |
|
R4903:Sema3d
|
UTSW |
5 |
12,613,125 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4999:Sema3d
|
UTSW |
5 |
12,558,054 (GRCm39) |
splice site |
probably null |
|
|
R5000:Sema3d
|
UTSW |
5 |
12,498,005 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5022:Sema3d
|
UTSW |
5 |
12,634,923 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5186:Sema3d
|
UTSW |
5 |
12,634,875 (GRCm39) |
missense |
probably benign |
|
|
R5584:Sema3d
|
UTSW |
5 |
12,620,954 (GRCm39) |
missense |
possibly damaging |
0.73 |
|
R5584:Sema3d
|
UTSW |
5 |
12,615,975 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R6270:Sema3d
|
UTSW |
5 |
12,498,074 (GRCm39) |
missense |
probably benign |
|
|
R6368:Sema3d
|
UTSW |
5 |
12,620,980 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6426:Sema3d
|
UTSW |
5 |
12,613,231 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6750:Sema3d
|
UTSW |
5 |
12,635,067 (GRCm39) |
nonsense |
probably null |
|
|
R7403:Sema3d
|
UTSW |
5 |
12,547,551 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R7450:Sema3d
|
UTSW |
5 |
12,634,901 (GRCm39) |
nonsense |
probably null |
|
|
R7470:Sema3d
|
UTSW |
5 |
12,558,152 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7548:Sema3d
|
UTSW |
5 |
12,627,783 (GRCm39) |
missense |
unknown |
|
|
R7593:Sema3d
|
UTSW |
5 |
12,558,112 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7683:Sema3d
|
UTSW |
5 |
12,623,823 (GRCm39) |
nonsense |
probably null |
|
|
R8155:Sema3d
|
UTSW |
5 |
12,498,148 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8442:Sema3d
|
UTSW |
5 |
12,592,608 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8725:Sema3d
|
UTSW |
5 |
12,555,822 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8754:Sema3d
|
UTSW |
5 |
12,603,191 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9293:Sema3d
|
UTSW |
5 |
12,603,181 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9771:Sema3d
|
UTSW |
5 |
12,613,207 (GRCm39) |
missense |
probably damaging |
0.99 |
|
Z1176:Sema3d
|
UTSW |
5 |
12,635,026 (GRCm39) |
nonsense |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- GTGTTCAATACAGAGTCAGGCCAGG -3'
(R):5'- CGTCCCTCATGTAAGAAACCCGTC -3'
Sequencing Primer
(F):5'- GTAGAAGAGCTTGACTTGTCTTAC -3'
(R):5'- ACCCGTCGTGTGGAAAG -3'
|
| Posted On |
2013-04-11 |
Incidental Mutation