Incidental Mutation 'R4063:Sema3d'
ID |
315952 |
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 |
041619-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.188)
|
Stock # |
R4063 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
5 |
Chromosomal Location |
12433352-12638915 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 12635091 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Isoleucine to Asparagine
at position 719
(I719N)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000030868
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030868]
|
AlphaFold |
Q8BH34 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000030868
AA Change: I719N
PolyPhen 2
Score 0.252 (Sensitivity: 0.91; Specificity: 0.88)
|
SMART Domains |
Protein: ENSMUSP00000030868 Gene: ENSMUSG00000040254 AA Change: I719N
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
|
Meta Mutation Damage Score |
0.2932 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.9%
|
Validation Efficiency |
97% (59/61) |
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: 54 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700034J05Rik |
A |
T |
6: 146,854,606 (GRCm39) |
F145L |
probably benign |
Het |
Abcc9 |
T |
C |
6: 142,551,645 (GRCm39) |
D1221G |
possibly damaging |
Het |
Adamtsl4 |
T |
C |
3: 95,584,864 (GRCm39) |
K935E |
probably benign |
Het |
Ago4 |
A |
T |
4: 126,409,655 (GRCm39) |
|
probably benign |
Het |
Arhgef28 |
T |
C |
13: 98,130,575 (GRCm39) |
D421G |
probably benign |
Het |
Armh4 |
T |
A |
14: 50,011,444 (GRCm39) |
M88L |
probably benign |
Het |
Atl2 |
T |
C |
17: 80,157,588 (GRCm39) |
*413W |
probably null |
Het |
B4galt7 |
C |
A |
13: 55,756,152 (GRCm39) |
|
probably null |
Het |
Bltp3b |
A |
G |
10: 89,651,917 (GRCm39) |
N247S |
probably benign |
Het |
C8g |
A |
T |
2: 25,389,425 (GRCm39) |
S147T |
probably damaging |
Het |
Clstn3 |
A |
T |
6: 124,426,792 (GRCm39) |
Y510N |
possibly damaging |
Het |
Cnot2 |
A |
G |
10: 116,373,301 (GRCm39) |
V34A |
possibly damaging |
Het |
Cyb5d2 |
A |
T |
11: 72,686,606 (GRCm39) |
|
probably benign |
Het |
Dnah5 |
T |
C |
15: 28,421,144 (GRCm39) |
I3827T |
probably damaging |
Het |
Dnah7a |
G |
T |
1: 53,464,376 (GRCm39) |
Q3672K |
probably benign |
Het |
Dock1 |
A |
T |
7: 134,717,021 (GRCm39) |
Y1219F |
possibly damaging |
Het |
Espl1 |
A |
G |
15: 102,221,424 (GRCm39) |
I944V |
probably damaging |
Het |
Fat1 |
A |
T |
8: 45,478,518 (GRCm39) |
E2521D |
probably benign |
Het |
Gm10719 |
G |
T |
9: 3,019,043 (GRCm39) |
W96L |
probably damaging |
Het |
H2-M2 |
G |
A |
17: 37,792,399 (GRCm39) |
H291Y |
probably damaging |
Het |
Hmgcl |
T |
C |
4: 135,686,035 (GRCm39) |
Y167H |
probably damaging |
Het |
Il22ra2 |
A |
T |
10: 19,502,400 (GRCm39) |
D73V |
possibly damaging |
Het |
Incenp |
A |
T |
19: 9,861,142 (GRCm39) |
M480K |
unknown |
Het |
Irag1 |
G |
T |
7: 110,522,984 (GRCm39) |
A359D |
probably benign |
Het |
Kdm6a |
A |
G |
X: 18,117,114 (GRCm39) |
T266A |
probably benign |
Het |
Lipf |
A |
G |
19: 33,942,965 (GRCm39) |
N91S |
probably benign |
Het |
M1ap |
A |
T |
6: 82,980,756 (GRCm39) |
N214I |
probably damaging |
Het |
Mast3 |
A |
G |
8: 71,233,838 (GRCm39) |
V969A |
probably damaging |
Het |
Mdga1 |
A |
G |
17: 30,057,005 (GRCm39) |
C826R |
probably damaging |
Het |
Msx1 |
C |
A |
5: 37,981,365 (GRCm39) |
A105S |
probably benign |
Het |
Or5ac23 |
A |
C |
16: 59,149,243 (GRCm39) |
S210A |
probably benign |
Het |
Otogl |
A |
T |
10: 107,626,510 (GRCm39) |
D1451E |
probably benign |
Het |
Otop2 |
G |
A |
11: 115,220,201 (GRCm39) |
G347D |
probably damaging |
Het |
Ppp1r13l |
A |
T |
7: 19,103,978 (GRCm39) |
H153L |
probably benign |
Het |
Pramel21 |
A |
G |
4: 143,342,559 (GRCm39) |
D222G |
possibly damaging |
Het |
Pramel29 |
T |
C |
4: 143,935,265 (GRCm39) |
K161E |
possibly damaging |
Het |
Proz |
A |
G |
8: 13,114,621 (GRCm39) |
Y85C |
probably damaging |
Het |
Prss50 |
A |
G |
9: 110,687,480 (GRCm39) |
D141G |
probably benign |
Het |
Rad54l2 |
T |
A |
9: 106,597,613 (GRCm39) |
Q131L |
probably benign |
Het |
Sdha |
A |
G |
13: 74,472,077 (GRCm39) |
|
probably benign |
Het |
Slc18b1 |
A |
T |
10: 23,681,879 (GRCm39) |
I148L |
probably benign |
Het |
Tacc2 |
G |
T |
7: 130,330,852 (GRCm39) |
D2086Y |
probably damaging |
Het |
Tchh |
T |
C |
3: 93,354,298 (GRCm39) |
L1246P |
unknown |
Het |
Tmprss11d |
T |
C |
5: 86,457,177 (GRCm39) |
I161V |
probably benign |
Het |
Trpc3 |
T |
C |
3: 36,725,172 (GRCm39) |
D268G |
probably damaging |
Het |
Trpm8 |
G |
A |
1: 88,289,727 (GRCm39) |
R895H |
probably damaging |
Het |
Txndc2 |
A |
G |
17: 65,945,079 (GRCm39) |
I366T |
possibly damaging |
Het |
Ugt2a3 |
T |
C |
5: 87,484,725 (GRCm39) |
I100V |
probably benign |
Het |
Upp1 |
C |
A |
11: 9,081,709 (GRCm39) |
P82Q |
probably damaging |
Het |
Vim |
A |
G |
2: 13,584,827 (GRCm39) |
|
probably null |
Het |
Vmn2r12 |
A |
T |
5: 109,240,058 (GRCm39) |
N168K |
possibly damaging |
Het |
Zdhhc14 |
G |
T |
17: 5,802,983 (GRCm39) |
C362F |
probably damaging |
Het |
Zfp292 |
A |
G |
4: 34,810,863 (GRCm39) |
V727A |
probably damaging |
Het |
Zswim5 |
G |
A |
4: 116,735,177 (GRCm39) |
G174D |
unknown |
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 |
R0085:Sema3d
|
UTSW |
5 |
12,620,953 (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 |
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'- TATTACTGCAAAGCACAGGAGC -3'
(R):5'- GACATTATTTGTGCAGGCAGG -3'
Sequencing Primer
(F):5'- GCACAGGAGCACACTTTCATC -3'
(R):5'- GTGCAGGCAGGTAAATAATTCCCTC -3'
|
Posted On |
2015-05-15 |