Incidental Mutation 'R1946:Sema3d'
| ID |
216661 |
| 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 |
039964-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.188)
|
| Stock # |
R1946 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
5 |
| Chromosomal Location |
12433352-12638915 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 12623810 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamine to Arginine
at position 573
(Q573R)
|
| 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: Q573R
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: Q573R
| 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: Q573R
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
AA Change: Q573R
| 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 |
0.4223 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.7%
- 20x: 93.8%
|
| 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: 76 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aasdh |
A |
G |
5: 77,039,551 (GRCm39) |
S253P |
probably damaging |
Het |
| Adamts5 |
C |
A |
16: 85,696,131 (GRCm39) |
C342F |
probably damaging |
Het |
| Adgrv1 |
C |
T |
13: 81,522,368 (GRCm39) |
C5923Y |
probably damaging |
Het |
| Aen |
G |
C |
7: 78,552,420 (GRCm39) |
E32Q |
probably damaging |
Het |
| Apba2 |
T |
C |
7: 64,394,378 (GRCm39) |
|
probably null |
Het |
| Arhgap44 |
A |
G |
11: 64,902,922 (GRCm39) |
M509T |
probably damaging |
Het |
| Arpc1b |
A |
G |
5: 145,059,443 (GRCm39) |
T56A |
probably null |
Het |
| Atoh1 |
T |
C |
6: 64,706,443 (GRCm39) |
V46A |
probably benign |
Het |
| Bmpr2 |
T |
C |
1: 59,907,556 (GRCm39) |
V883A |
possibly damaging |
Het |
| Bpifa1 |
A |
T |
2: 153,987,554 (GRCm39) |
I135F |
probably damaging |
Het |
| Bsn |
A |
G |
9: 107,991,850 (GRCm39) |
F1301L |
probably damaging |
Het |
| Capn13 |
T |
C |
17: 73,657,520 (GRCm39) |
E240G |
possibly damaging |
Het |
| Ccdc18 |
A |
G |
5: 108,376,861 (GRCm39) |
E1434G |
probably damaging |
Het |
| Coq8b |
G |
A |
7: 26,939,299 (GRCm39) |
V150I |
possibly damaging |
Het |
| Cpn1 |
G |
A |
19: 43,944,957 (GRCm39) |
T450M |
probably benign |
Het |
| Dlg4 |
A |
G |
11: 69,930,401 (GRCm39) |
Y432C |
probably damaging |
Het |
| Dnah8 |
C |
A |
17: 30,931,359 (GRCm39) |
T1458K |
probably benign |
Het |
| Dock5 |
A |
T |
14: 68,023,765 (GRCm39) |
M1132K |
probably damaging |
Het |
| Dsg2 |
A |
G |
18: 20,713,605 (GRCm39) |
D192G |
probably damaging |
Het |
| F930017D23Rik |
G |
A |
10: 43,469,440 (GRCm39) |
|
noncoding transcript |
Het |
| Fndc11 |
A |
T |
2: 180,863,627 (GRCm39) |
D144V |
probably benign |
Het |
| Fut2 |
A |
G |
7: 45,300,748 (GRCm39) |
F8S |
probably damaging |
Het |
| Gad2 |
A |
T |
2: 22,575,440 (GRCm39) |
T515S |
probably benign |
Het |
| Ganab |
T |
A |
19: 8,888,172 (GRCm39) |
D439E |
probably damaging |
Het |
| Gm10228 |
C |
A |
16: 88,838,241 (GRCm39) |
G21V |
unknown |
Het |
| Grm3 |
A |
G |
5: 9,562,123 (GRCm39) |
W576R |
probably damaging |
Het |
| Gsdmc4 |
C |
A |
15: 63,774,629 (GRCm39) |
D51Y |
probably benign |
Het |
| Hmcn2 |
T |
C |
2: 31,295,647 (GRCm39) |
S2619P |
probably damaging |
Het |
| Kcnq2 |
T |
A |
2: 180,730,244 (GRCm39) |
D446V |
probably benign |
Het |
| Kera |
A |
G |
10: 97,445,009 (GRCm39) |
K123E |
probably benign |
Het |
| Kmt2c |
A |
T |
5: 25,520,152 (GRCm39) |
V1986E |
probably benign |
Het |
| Lrp11 |
T |
C |
10: 7,499,540 (GRCm39) |
Y244H |
probably damaging |
Het |
| Lrp1b |
T |
A |
2: 40,555,159 (GRCm39) |
D320V |
unknown |
Het |
| Lrrcc1 |
A |
G |
3: 14,615,453 (GRCm39) |
R394G |
probably benign |
Het |
| Lrrk2 |
G |
A |
15: 91,620,864 (GRCm39) |
|
probably null |
Het |
| Map4k5 |
A |
T |
12: 69,892,529 (GRCm39) |
D133E |
probably damaging |
Het |
| Megf11 |
A |
T |
9: 64,586,558 (GRCm39) |
D461V |
probably damaging |
Het |
| Msrb3 |
A |
G |
10: 120,687,913 (GRCm39) |
V54A |
probably damaging |
Het |
| Muc21 |
A |
T |
17: 35,933,416 (GRCm39) |
|
probably benign |
Het |
| Ncoa3 |
T |
A |
2: 165,901,097 (GRCm39) |
N896K |
possibly damaging |
Het |
| Ncor2 |
G |
A |
5: 125,111,476 (GRCm39) |
T1314I |
probably damaging |
Het |
| Nes |
A |
G |
3: 87,885,821 (GRCm39) |
Q1316R |
possibly damaging |
Het |
| Nfe2l3 |
A |
C |
6: 51,434,295 (GRCm39) |
Q285P |
probably damaging |
Het |
| Nkd1 |
C |
T |
8: 89,318,745 (GRCm39) |
H357Y |
probably damaging |
Het |
| Nmt2 |
T |
A |
2: 3,323,672 (GRCm39) |
I355N |
probably benign |
Het |
| Or10ak11 |
T |
C |
4: 118,687,223 (GRCm39) |
N139S |
probably benign |
Het |
| Or1n1b |
A |
T |
2: 36,780,458 (GRCm39) |
M134K |
possibly damaging |
Het |
| Or5ae1 |
T |
C |
7: 84,565,487 (GRCm39) |
S167P |
probably benign |
Het |
| Or5b3 |
T |
C |
19: 13,388,143 (GRCm39) |
V70A |
possibly damaging |
Het |
| Or7a38 |
T |
A |
10: 78,752,758 (GRCm39) |
I28N |
probably damaging |
Het |
| Or8b3 |
T |
A |
9: 38,314,182 (GRCm39) |
M1K |
probably null |
Het |
| Otx1 |
G |
T |
11: 21,948,482 (GRCm39) |
T46K |
probably damaging |
Het |
| Panx1 |
A |
G |
9: 14,918,822 (GRCm39) |
C346R |
probably benign |
Het |
| Pcdhb16 |
T |
A |
18: 37,611,952 (GRCm39) |
L304* |
probably null |
Het |
| Plet1 |
A |
G |
9: 50,415,652 (GRCm39) |
|
probably null |
Het |
| Plod2 |
A |
G |
9: 92,489,188 (GRCm39) |
S707G |
probably damaging |
Het |
| Plscr4 |
G |
A |
9: 92,365,889 (GRCm39) |
V120I |
probably damaging |
Het |
| Ppp1r12b |
A |
G |
1: 134,820,008 (GRCm39) |
V245A |
probably damaging |
Het |
| Ppp2r2d |
A |
G |
7: 138,470,196 (GRCm39) |
D19G |
probably damaging |
Het |
| Pramel31 |
T |
A |
4: 144,088,435 (GRCm39) |
V77E |
probably benign |
Het |
| Rimbp3 |
G |
A |
16: 17,028,291 (GRCm39) |
V572I |
probably benign |
Het |
| Ror2 |
T |
C |
13: 53,285,885 (GRCm39) |
I110V |
probably damaging |
Het |
| Sec24d |
A |
T |
3: 123,147,043 (GRCm39) |
H667L |
probably benign |
Het |
| Snx19 |
T |
A |
9: 30,343,620 (GRCm39) |
N593K |
probably damaging |
Het |
| Sulf1 |
T |
C |
1: 12,867,131 (GRCm39) |
V105A |
probably benign |
Het |
| Syngr3 |
T |
C |
17: 24,906,680 (GRCm39) |
N45S |
probably benign |
Het |
| Tenm4 |
A |
T |
7: 96,385,015 (GRCm39) |
H524L |
probably damaging |
Het |
| Tex30 |
C |
T |
1: 44,130,564 (GRCm39) |
G68D |
probably damaging |
Het |
| Tmem43 |
A |
T |
6: 91,463,891 (GRCm39) |
I389F |
probably benign |
Het |
| Trpm1 |
A |
T |
7: 63,873,556 (GRCm39) |
N488Y |
probably damaging |
Het |
| Usf2 |
T |
C |
7: 30,655,663 (GRCm39) |
T1A |
probably null |
Het |
| Vill |
A |
T |
9: 118,887,560 (GRCm39) |
H108L |
probably benign |
Het |
| Vmn1r16 |
T |
C |
6: 57,299,885 (GRCm39) |
I246V |
probably benign |
Het |
| Vmn1r188 |
T |
G |
13: 22,272,815 (GRCm39) |
S256R |
possibly damaging |
Het |
| Zfp12 |
G |
A |
5: 143,231,133 (GRCm39) |
E487K |
probably damaging |
Het |
| Zfp24 |
AC |
A |
18: 24,147,476 (GRCm39) |
|
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 |
|
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 |
|
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'- CTGATCATCTTAATGCAAGACAGG -3'
(R):5'- CCTGTTACTTTTCTAGAACATACGC -3'
Sequencing Primer
(F):5'- TCATCTTAATGCAAGACAGGATTTG -3'
(R):5'- AGAACATACGCATTATACAGAATGAG -3'
|
| Posted On |
2014-08-01 |
Incidental Mutation