Incidental Mutation 'R8754:Sema3d'
| ID |
664025 |
| 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 |
068620-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.188)
|
| Stock # |
R8754 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
12433352-12638915 bp(+) (GRCm39) |
| Type of Mutation |
critical splice donor site (2 bp from exon) |
| DNA Base Change (assembly) |
T to C
at 12603191 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000030868
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030868]
[ENSMUST00000197927]
|
| AlphaFold |
Q8BH34 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000030868
|
| SMART Domains |
Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
| 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 |
probably benign
Transcript: ENSMUST00000197927
|
| SMART Domains |
Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
| 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: 100.0%
- 3x: 99.9%
- 10x: 99.3%
- 20x: 97.5%
|
| Validation Efficiency |
100% (67/67) |
| 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: 70 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1110002E22Rik |
T |
C |
3: 137,771,798 (GRCm39) |
V329A |
probably benign |
Het |
| A830018L16Rik |
G |
T |
1: 11,615,472 (GRCm39) |
K148N |
probably benign |
Het |
| Actn3 |
A |
G |
19: 4,913,488 (GRCm39) |
F648L |
probably damaging |
Het |
| Amotl2 |
A |
G |
9: 102,597,358 (GRCm39) |
D39G |
possibly damaging |
Het |
| Anks1 |
C |
A |
17: 28,214,984 (GRCm39) |
T477K |
possibly damaging |
Het |
| Brix1 |
A |
T |
15: 10,476,664 (GRCm39) |
S271T |
probably benign |
Het |
| Ccdc88b |
T |
C |
19: 6,833,213 (GRCm39) |
E278G |
probably damaging |
Het |
| Cdc40 |
C |
T |
10: 40,717,480 (GRCm39) |
D404N |
probably damaging |
Het |
| Chrna6 |
T |
C |
8: 27,897,229 (GRCm39) |
H216R |
probably damaging |
Het |
| Col6a3 |
C |
G |
1: 90,695,328 (GRCm39) |
|
probably benign |
Het |
| Copa |
C |
T |
1: 171,935,926 (GRCm39) |
R423W |
probably damaging |
Het |
| Cttnbp2 |
A |
C |
6: 18,434,037 (GRCm39) |
I607R |
possibly damaging |
Het |
| Depdc5 |
A |
T |
5: 33,136,881 (GRCm39) |
T1384S |
probably benign |
Het |
| Dlat |
G |
T |
9: 50,560,967 (GRCm39) |
A360E |
probably damaging |
Het |
| Dusp26 |
C |
T |
8: 31,581,805 (GRCm39) |
|
probably benign |
Het |
| Eif1ad13 |
T |
A |
12: 87,762,569 (GRCm39) |
N96K |
possibly damaging |
Het |
| Fam135a |
G |
A |
1: 24,067,569 (GRCm39) |
T1100M |
probably benign |
Het |
| Fuca1 |
T |
C |
4: 135,652,889 (GRCm39) |
L171P |
probably damaging |
Het |
| Gpr158 |
G |
A |
2: 21,581,693 (GRCm39) |
V391I |
probably benign |
Het |
| Gtf2h5 |
C |
CA |
17: 6,134,833 (GRCm39) |
|
probably null |
Het |
| Heatr1 |
T |
A |
13: 12,428,175 (GRCm39) |
Y771N |
probably damaging |
Het |
| Il17ra |
A |
G |
6: 120,458,417 (GRCm39) |
T523A |
probably benign |
Het |
| Kcnv1 |
G |
A |
15: 44,977,865 (GRCm39) |
Q58* |
probably null |
Het |
| Kdm5d |
T |
C |
Y: 941,594 (GRCm39) |
V1265A |
probably damaging |
Het |
| Kifc3 |
A |
T |
8: 95,829,024 (GRCm39) |
L726Q |
probably damaging |
Het |
| Klk1b21 |
T |
A |
7: 43,755,912 (GRCm39) |
I247N |
probably benign |
Het |
| Kntc1 |
T |
A |
5: 123,897,115 (GRCm39) |
N159K |
probably benign |
Het |
| Krtap4-7 |
G |
T |
11: 99,534,667 (GRCm39) |
C65* |
probably null |
Het |
| Lama2 |
C |
T |
10: 26,877,147 (GRCm39) |
V2680M |
possibly damaging |
Het |
| Lipe |
T |
A |
7: 25,088,007 (GRCm39) |
M61L |
probably benign |
Het |
| Med17 |
A |
G |
9: 15,188,896 (GRCm39) |
M123T |
possibly damaging |
Het |
| Mrpl37 |
T |
C |
4: 106,921,611 (GRCm39) |
N206S |
probably benign |
Het |
| Muc4 |
A |
T |
16: 32,602,356 (GRCm39) |
N1390Y |
|
Het |
| Muc5ac |
C |
T |
7: 141,354,008 (GRCm39) |
A869V |
possibly damaging |
Het |
| Nckap5l |
A |
G |
15: 99,327,290 (GRCm39) |
V133A |
probably benign |
Het |
| Nin |
A |
T |
12: 70,077,787 (GRCm39) |
|
probably benign |
Het |
| Nr1h2 |
C |
T |
7: 44,200,768 (GRCm39) |
A287T |
probably damaging |
Het |
| Or8c16 |
A |
T |
9: 38,130,865 (GRCm39) |
I246L |
possibly damaging |
Het |
| Patl1 |
A |
G |
19: 11,899,898 (GRCm39) |
E230G |
probably damaging |
Het |
| Pbxip1 |
T |
C |
3: 89,355,235 (GRCm39) |
S585P |
probably damaging |
Het |
| Pde3b |
T |
A |
7: 114,015,278 (GRCm39) |
W165R |
possibly damaging |
Het |
| Pdia4 |
A |
C |
6: 47,773,464 (GRCm39) |
D628E |
probably benign |
Het |
| Pigo |
T |
A |
4: 43,024,724 (GRCm39) |
H125L |
probably benign |
Het |
| Platr25 |
A |
T |
13: 62,847,924 (GRCm39) |
*313K |
probably null |
Het |
| Plxdc1 |
A |
T |
11: 97,846,337 (GRCm39) |
M169K |
possibly damaging |
Het |
| Pxk |
T |
C |
14: 8,151,496 (GRCm38) |
I437T |
probably damaging |
Het |
| Rlf |
T |
C |
4: 121,004,010 (GRCm39) |
T1767A |
possibly damaging |
Het |
| Rnf123 |
T |
A |
9: 107,948,363 (GRCm39) |
D110V |
probably damaging |
Het |
| Rnf185 |
A |
T |
11: 3,368,052 (GRCm39) |
F209I |
probably benign |
Het |
| Rpl4 |
A |
T |
9: 64,082,242 (GRCm39) |
N47I |
probably damaging |
Het |
| Rsl1d1 |
A |
T |
16: 11,017,512 (GRCm39) |
F151L |
probably damaging |
Het |
| Serhl |
A |
G |
15: 82,986,126 (GRCm39) |
N80D |
probably benign |
Het |
| Sh3tc1 |
C |
A |
5: 35,863,802 (GRCm39) |
R795L |
probably benign |
Het |
| Slc2a12 |
A |
T |
10: 22,521,116 (GRCm39) |
T7S |
probably benign |
Het |
| Snrnp200 |
A |
G |
2: 127,068,005 (GRCm39) |
Y834C |
probably damaging |
Het |
| Ss18 |
G |
C |
18: 14,774,016 (GRCm39) |
Q258E |
probably damaging |
Het |
| Telo2 |
G |
A |
17: 25,321,041 (GRCm39) |
L725F |
probably damaging |
Het |
| Tnxb |
A |
G |
17: 34,934,882 (GRCm39) |
E2497G |
probably damaging |
Het |
| Tox2 |
A |
G |
2: 163,163,360 (GRCm39) |
D111G |
|
Het |
| Trim16 |
G |
A |
11: 62,731,763 (GRCm39) |
E545K |
probably benign |
Het |
| Trpm7 |
A |
G |
2: 126,664,623 (GRCm39) |
W919R |
probably damaging |
Het |
| Ttbk1 |
G |
T |
17: 46,756,127 (GRCm39) |
S1301* |
probably null |
Het |
| Txk |
T |
C |
5: 72,889,122 (GRCm39) |
N144S |
probably damaging |
Het |
| Ubqln4 |
T |
A |
3: 88,473,090 (GRCm39) |
V515E |
probably benign |
Het |
| Ush2a |
C |
T |
1: 188,581,162 (GRCm39) |
R3681* |
probably null |
Het |
| Ythdf3 |
A |
T |
3: 16,258,138 (GRCm39) |
N106I |
probably damaging |
Het |
| Zfp367 |
A |
T |
13: 64,292,069 (GRCm39) |
C187* |
probably null |
Het |
| Zfp735 |
A |
G |
11: 73,603,000 (GRCm39) |
D648G |
possibly damaging |
Het |
| Zic1 |
T |
C |
9: 91,244,701 (GRCm39) |
|
probably benign |
Het |
| Zik1 |
A |
G |
7: 10,223,826 (GRCm39) |
S424P |
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 |
|
|
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 |
|
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'- CAGGAGAATGAATGGGTCATCTTC -3'
(R):5'- CATCACAACATAGTCCAGTGTG -3'
Sequencing Primer
(F):5'- GAGAATGAATGGGTCATCTTCCTCTC -3'
(R):5'- CAACATAGTCCAGTGTGTTCTTTAG -3'
|
| Posted On |
2021-03-08 |
Incidental Mutation