Incidental Mutation 'R6368:Sema3d'
ID |
512781 |
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 |
044518-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.207)
|
Stock # |
R6368 (G1)
|
Quality Score |
225.009 |
Status
|
Not validated
|
Chromosome |
5 |
Chromosomal Location |
12433352-12638915 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 12620980 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Leucine to Phenylalanine
at position 529
(L529F)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000142453
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030868]
[ENSMUST00000197927]
|
AlphaFold |
Q8BH34 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000030868
AA Change: L529F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000030868 Gene: ENSMUSG00000040254 AA Change: L529F
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 damaging
Transcript: ENSMUST00000197927
AA Change: L529F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000142453 Gene: ENSMUSG00000040254 AA Change: L529F
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 |
|
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 98.4%
- 20x: 95.6%
|
Validation Efficiency |
|
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: 58 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4930563M21Rik |
C |
A |
9: 55,897,416 (GRCm39) |
E272D |
possibly damaging |
Het |
Abi2 |
A |
G |
1: 60,492,810 (GRCm39) |
T158A |
possibly damaging |
Het |
Acacb |
T |
C |
5: 114,354,884 (GRCm39) |
S1221P |
probably damaging |
Het |
Agbl1 |
A |
G |
7: 76,069,578 (GRCm39) |
D370G |
probably benign |
Het |
Apeh |
A |
G |
9: 107,964,442 (GRCm39) |
I487T |
probably damaging |
Het |
Arid1b |
C |
A |
17: 5,382,808 (GRCm39) |
N1297K |
possibly damaging |
Het |
Ascc3 |
G |
A |
10: 50,576,081 (GRCm39) |
G779S |
probably damaging |
Het |
Atp7b |
A |
C |
8: 22,510,771 (GRCm39) |
|
probably null |
Het |
Bsn |
C |
T |
9: 107,988,513 (GRCm39) |
|
probably benign |
Het |
Caps2 |
C |
T |
10: 112,030,873 (GRCm39) |
Q268* |
probably null |
Het |
Cnfn |
C |
T |
7: 25,067,386 (GRCm39) |
|
probably null |
Het |
Cr2 |
A |
G |
1: 194,850,780 (GRCm39) |
S229P |
probably damaging |
Het |
Cubn |
T |
C |
2: 13,435,806 (GRCm39) |
Y1050C |
probably damaging |
Het |
Cubn |
T |
C |
2: 13,480,934 (GRCm39) |
E307G |
probably damaging |
Het |
Cyb5r3 |
A |
C |
15: 83,044,325 (GRCm39) |
Y182D |
possibly damaging |
Het |
Dclre1a |
A |
T |
19: 56,535,223 (GRCm39) |
H120Q |
probably benign |
Het |
Ddx6 |
T |
C |
9: 44,547,073 (GRCm39) |
I457T |
probably damaging |
Het |
E2f1 |
A |
T |
2: 154,406,396 (GRCm39) |
H93Q |
possibly damaging |
Het |
Fam186a |
T |
C |
15: 99,841,198 (GRCm39) |
K1682R |
possibly damaging |
Het |
Farsb |
A |
G |
1: 78,443,602 (GRCm39) |
|
probably null |
Het |
Flii |
A |
T |
11: 60,611,962 (GRCm39) |
L347Q |
probably damaging |
Het |
Galntl6 |
T |
G |
8: 59,364,475 (GRCm39) |
T12P |
probably damaging |
Het |
Gm11595 |
G |
A |
11: 99,663,381 (GRCm39) |
R100C |
unknown |
Het |
Gm21680 |
T |
C |
5: 26,174,034 (GRCm39) |
N190S |
probably damaging |
Het |
Ifit1bl2 |
T |
C |
19: 34,596,525 (GRCm39) |
S364G |
probably benign |
Het |
Kdm2a |
A |
G |
19: 4,400,345 (GRCm39) |
I234T |
probably damaging |
Het |
Kdm5b |
T |
C |
1: 134,526,945 (GRCm39) |
C356R |
probably damaging |
Het |
Kel |
A |
T |
6: 41,665,785 (GRCm39) |
C174* |
probably null |
Het |
Krt16 |
T |
A |
11: 100,137,502 (GRCm39) |
D401V |
probably damaging |
Het |
Ltb4r1 |
A |
C |
14: 56,005,200 (GRCm39) |
I168L |
probably benign |
Het |
Luzp1 |
T |
A |
4: 136,269,091 (GRCm39) |
M438K |
probably benign |
Het |
Mtf1 |
C |
T |
4: 124,718,145 (GRCm39) |
T281M |
probably damaging |
Het |
Myo9a |
T |
A |
9: 59,832,231 (GRCm39) |
S2587T |
probably benign |
Het |
Or13a21 |
G |
T |
7: 139,999,580 (GRCm39) |
Y35* |
probably null |
Het |
Or1ad1 |
T |
A |
11: 50,875,613 (GRCm39) |
F28L |
probably benign |
Het |
Or4f58 |
A |
T |
2: 111,851,896 (GRCm39) |
I101N |
probably damaging |
Het |
Or7e169 |
T |
C |
9: 19,757,705 (GRCm39) |
D70G |
probably damaging |
Het |
Pcm1 |
T |
A |
8: 41,746,581 (GRCm39) |
F1221Y |
probably benign |
Het |
Pnldc1 |
A |
T |
17: 13,124,751 (GRCm39) |
N90K |
probably damaging |
Het |
Prickle2 |
A |
T |
6: 92,397,218 (GRCm39) |
L169Q |
probably damaging |
Het |
Ralgps2 |
A |
T |
1: 156,712,144 (GRCm39) |
L147I |
probably damaging |
Het |
Rfx3 |
A |
T |
19: 27,746,009 (GRCm39) |
L674Q |
possibly damaging |
Het |
Rpl3 |
C |
A |
15: 79,966,745 (GRCm39) |
L14F |
probably damaging |
Het |
Rrbp1 |
C |
T |
2: 143,831,475 (GRCm39) |
G231R |
probably damaging |
Het |
Slain1 |
A |
T |
14: 103,894,391 (GRCm39) |
T193S |
probably benign |
Het |
Slc2a6 |
G |
T |
2: 26,914,599 (GRCm39) |
Q256K |
possibly damaging |
Het |
Slk |
A |
G |
19: 47,608,622 (GRCm39) |
E525G |
possibly damaging |
Het |
Spsb4 |
G |
T |
9: 96,826,698 (GRCm39) |
Q252K |
probably benign |
Het |
Taf1b |
A |
G |
12: 24,608,256 (GRCm39) |
T552A |
possibly damaging |
Het |
Tmprss15 |
T |
C |
16: 78,802,945 (GRCm39) |
|
probably null |
Het |
Tph2 |
T |
C |
10: 115,015,231 (GRCm39) |
H177R |
probably damaging |
Het |
Ttll1 |
A |
G |
15: 83,373,818 (GRCm39) |
S332P |
probably damaging |
Het |
Twf2 |
T |
G |
9: 106,090,032 (GRCm39) |
N128K |
probably benign |
Het |
Vegfc |
T |
A |
8: 54,634,265 (GRCm39) |
C315S |
probably damaging |
Het |
Vmn2r111 |
T |
A |
17: 22,790,889 (GRCm39) |
K136N |
probably benign |
Het |
Wnk2 |
T |
C |
13: 49,214,814 (GRCm39) |
E496G |
probably damaging |
Het |
Zfp148 |
C |
A |
16: 33,317,568 (GRCm39) |
Q705K |
probably damaging |
Het |
Zw10 |
C |
T |
9: 48,984,535 (GRCm39) |
A539V |
probably damaging |
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 |
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 |
|
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'- TCAATACAGAGTCAGGCCAGGG -3'
(R):5'- AGCGTCCCTCATGTAAGAAACC -3'
Sequencing Primer
(F):5'- GAAGAGCTTGACTTGTCTTACTACTC -3'
(R):5'- CTCATGTAAGAAACCCGTCGTGTG -3'
|
Posted On |
2018-04-27 |