Incidental Mutation 'R1657:Sema3d'
| ID |
186453 |
| 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 |
039693-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.210)
|
| Stock # |
R1657 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
5 |
| Chromosomal Location |
12383385-12588948 bp(+) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 12584974 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Glycine
at position 669
(E669G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000030868
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030868]
|
| AlphaFold |
Q8BH34 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000030868
AA Change: E669G
PolyPhen 2
Score 0.823 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: E669G
| 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
|
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.5%
- 20x: 93.2%
|
| 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: 55 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 0610009B22Rik |
T |
C |
11: 51,685,678 (GRCm38) |
Q131R |
probably benign |
Het |
| 3632451O06Rik |
G |
C |
14: 49,773,560 (GRCm38) |
T230S |
probably damaging |
Het |
| Acaca |
T |
G |
11: 84,264,084 (GRCm38) |
D988E |
probably benign |
Het |
| Als2 |
A |
G |
1: 59,180,601 (GRCm38) |
V1185A |
probably damaging |
Het |
| Amdhd2 |
A |
G |
17: 24,156,055 (GRCm38) |
V391A |
probably damaging |
Het |
| Caprin1 |
A |
T |
2: 103,769,506 (GRCm38) |
V608E |
probably damaging |
Het |
| Celsr3 |
T |
A |
9: 108,842,952 (GRCm38) |
C2512* |
probably null |
Het |
| Cfl1 |
A |
T |
19: 5,493,555 (GRCm38) |
R187W |
probably damaging |
Het |
| Cgnl1 |
C |
T |
9: 71,725,944 (GRCm38) |
V42I |
probably damaging |
Het |
| Chd2 |
A |
G |
7: 73,480,430 (GRCm38) |
Y826H |
probably damaging |
Het |
| Col9a2 |
C |
A |
4: 121,040,974 (GRCm38) |
P28T |
unknown |
Het |
| Cyp3a44 |
G |
A |
5: 145,779,743 (GRCm38) |
P346S |
probably damaging |
Het |
| Dact2 |
A |
G |
17: 14,197,990 (GRCm38) |
V151A |
probably benign |
Het |
| Dhx29 |
T |
C |
13: 112,952,843 (GRCm38) |
I716T |
probably damaging |
Het |
| Esam |
T |
C |
9: 37,537,621 (GRCm38) |
S342P |
probably damaging |
Het |
| Fam189a2 |
C |
A |
19: 23,975,635 (GRCm38) |
C437F |
probably damaging |
Het |
| Fer1l4 |
A |
G |
2: 156,035,598 (GRCm38) |
V1053A |
possibly damaging |
Het |
| Grk3 |
A |
G |
5: 112,966,982 (GRCm38) |
F124S |
probably damaging |
Het |
| H2-DMa |
G |
A |
17: 34,137,399 (GRCm38) |
|
probably null |
Het |
| Hsd3b5 |
T |
A |
3: 98,619,720 (GRCm38) |
I137F |
possibly damaging |
Het |
| Itgav |
A |
T |
2: 83,801,779 (GRCm38) |
I902F |
probably benign |
Het |
| Itsn1 |
G |
T |
16: 91,909,223 (GRCm38) |
C179F |
probably damaging |
Het |
| Kcnh8 |
G |
A |
17: 52,839,125 (GRCm38) |
R347H |
probably damaging |
Het |
| Kif9 |
T |
C |
9: 110,489,966 (GRCm38) |
M166T |
possibly damaging |
Het |
| Kmt5c |
C |
T |
7: 4,746,454 (GRCm38) |
Q324* |
probably null |
Het |
| Lcn9 |
G |
A |
2: 25,824,710 (GRCm38) |
E154K |
probably benign |
Het |
| Mfge8 |
A |
T |
7: 79,141,773 (GRCm38) |
L227Q |
probably benign |
Het |
| Mroh2b |
A |
T |
15: 4,931,043 (GRCm38) |
R753* |
probably null |
Het |
| Mtif2 |
G |
A |
11: 29,540,721 (GRCm38) |
R475Q |
probably benign |
Het |
| Nln |
C |
T |
13: 104,036,947 (GRCm38) |
V584I |
possibly damaging |
Het |
| Nr2e3 |
T |
C |
9: 59,948,767 (GRCm38) |
E129G |
probably benign |
Het |
| Ocstamp |
T |
C |
2: 165,397,516 (GRCm38) |
D250G |
probably damaging |
Het |
| Olfr1065 |
A |
C |
2: 86,445,218 (GRCm38) |
L255V |
probably damaging |
Het |
| Olfr403 |
A |
T |
11: 74,195,896 (GRCm38) |
H131L |
probably damaging |
Het |
| Olfr503 |
T |
C |
7: 108,545,377 (GRCm38) |
I284T |
possibly damaging |
Het |
| Pld1 |
A |
T |
3: 28,071,187 (GRCm38) |
I417L |
probably benign |
Het |
| Polr1a |
A |
T |
6: 71,941,535 (GRCm38) |
K692N |
probably damaging |
Het |
| Qsox2 |
A |
T |
2: 26,220,747 (GRCm38) |
Y152* |
probably null |
Het |
| Rpap1 |
T |
C |
2: 119,783,778 (GRCm38) |
D46G |
possibly damaging |
Het |
| Rpe65 |
A |
G |
3: 159,614,448 (GRCm38) |
T246A |
probably damaging |
Het |
| Scn5a |
T |
C |
9: 119,562,380 (GRCm38) |
D82G |
probably damaging |
Het |
| Serpinb6c |
T |
C |
13: 33,880,226 (GRCm38) |
N282S |
probably benign |
Het |
| Snap47 |
A |
T |
11: 59,428,770 (GRCm38) |
S181T |
probably benign |
Het |
| Snx9 |
A |
C |
17: 5,918,436 (GRCm38) |
T336P |
possibly damaging |
Het |
| Sphkap |
G |
A |
1: 83,277,515 (GRCm38) |
R838* |
probably null |
Het |
| Terb1 |
A |
T |
8: 104,488,491 (GRCm38) |
D284E |
possibly damaging |
Het |
| Tmem266 |
C |
T |
9: 55,418,008 (GRCm38) |
A153V |
probably damaging |
Het |
| Ttn |
T |
C |
2: 76,742,804 (GRCm38) |
E25915G |
possibly damaging |
Het |
| Tubal3 |
A |
G |
13: 3,933,011 (GRCm38) |
T264A |
possibly damaging |
Het |
| Vldlr |
G |
A |
19: 27,245,670 (GRCm38) |
R747Q |
probably benign |
Het |
| Zc3h8 |
G |
T |
2: 128,929,957 (GRCm38) |
|
probably benign |
Het |
| Zfp184 |
C |
T |
13: 21,959,273 (GRCm38) |
T383M |
probably damaging |
Het |
| Zfp455 |
T |
C |
13: 67,198,639 (GRCm38) |
F38S |
possibly damaging |
Het |
| Zfp746 |
A |
G |
6: 48,082,174 (GRCm38) |
V167A |
possibly damaging |
Het |
| Zfp985 |
T |
A |
4: 147,584,110 (GRCm38) |
N478K |
probably benign |
Het |
|
| Other mutations in Sema3d |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00559:Sema3d
|
APN |
5 |
12,563,222 (GRCm38) |
missense |
probably benign |
0.01 |
|
IGL00582:Sema3d
|
APN |
5 |
12,585,195 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL00661:Sema3d
|
APN |
5 |
12,505,839 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL00780:Sema3d
|
APN |
5 |
12,524,326 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL01531:Sema3d
|
APN |
5 |
12,541,080 (GRCm38) |
missense |
probably benign |
|
|
IGL01957:Sema3d
|
APN |
5 |
12,563,315 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL02100:Sema3d
|
APN |
5 |
12,584,991 (GRCm38) |
missense |
probably benign |
0.29 |
|
IGL02676:Sema3d
|
APN |
5 |
12,570,978 (GRCm38) |
missense |
probably benign |
0.38 |
|
IGL02749:Sema3d
|
APN |
5 |
12,563,145 (GRCm38) |
splice site |
probably benign |
|
|
IGL02827:Sema3d
|
APN |
5 |
12,585,118 (GRCm38) |
missense |
probably benign |
0.04 |
|
IGL03325:Sema3d
|
APN |
5 |
12,463,222 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R0050:Sema3d
|
UTSW |
5 |
12,584,953 (GRCm38) |
missense |
probably benign |
0.00 |
|
R0085:Sema3d
|
UTSW |
5 |
12,570,986 (GRCm38) |
missense |
probably benign |
0.00 |
|
R0095:Sema3d
|
UTSW |
5 |
12,563,347 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R0157:Sema3d
|
UTSW |
5 |
12,508,137 (GRCm38) |
missense |
possibly damaging |
0.95 |
|
R0328:Sema3d
|
UTSW |
5 |
12,448,075 (GRCm38) |
missense |
possibly damaging |
0.48 |
|
R0924:Sema3d
|
UTSW |
5 |
12,463,216 (GRCm38) |
missense |
possibly damaging |
0.69 |
|
R0930:Sema3d
|
UTSW |
5 |
12,463,216 (GRCm38) |
missense |
possibly damaging |
0.69 |
|
R1609:Sema3d
|
UTSW |
5 |
12,541,056 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1669:Sema3d
|
UTSW |
5 |
12,508,084 (GRCm38) |
splice site |
probably benign |
|
|
R1795:Sema3d
|
UTSW |
5 |
12,584,887 (GRCm38) |
missense |
probably benign |
0.02 |
|
R1861:Sema3d
|
UTSW |
5 |
12,497,603 (GRCm38) |
missense |
probably benign |
0.00 |
|
R1889:Sema3d
|
UTSW |
5 |
12,485,021 (GRCm38) |
splice site |
probably null |
|
|
R1895:Sema3d
|
UTSW |
5 |
12,573,843 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1946:Sema3d
|
UTSW |
5 |
12,573,843 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1975:Sema3d
|
UTSW |
5 |
12,584,998 (GRCm38) |
missense |
probably benign |
|
|
R1975:Sema3d
|
UTSW |
5 |
12,563,318 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R2117:Sema3d
|
UTSW |
5 |
12,563,273 (GRCm38) |
missense |
probably benign |
|
|
R2148:Sema3d
|
UTSW |
5 |
12,484,959 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R2276:Sema3d
|
UTSW |
5 |
12,542,582 (GRCm38) |
missense |
possibly damaging |
0.63 |
|
R3761:Sema3d
|
UTSW |
5 |
12,571,037 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4063:Sema3d
|
UTSW |
5 |
12,585,124 (GRCm38) |
missense |
probably benign |
0.25 |
|
R4428:Sema3d
|
UTSW |
5 |
12,448,120 (GRCm38) |
missense |
probably benign |
0.32 |
|
R4903:Sema3d
|
UTSW |
5 |
12,563,158 (GRCm38) |
missense |
probably benign |
0.00 |
|
R4999:Sema3d
|
UTSW |
5 |
12,508,087 (GRCm38) |
splice site |
probably null |
|
|
R5000:Sema3d
|
UTSW |
5 |
12,448,038 (GRCm38) |
missense |
probably benign |
0.01 |
|
R5022:Sema3d
|
UTSW |
5 |
12,584,956 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5186:Sema3d
|
UTSW |
5 |
12,584,908 (GRCm38) |
missense |
probably benign |
|
|
R5584:Sema3d
|
UTSW |
5 |
12,570,987 (GRCm38) |
missense |
possibly damaging |
0.73 |
|
R5584:Sema3d
|
UTSW |
5 |
12,566,008 (GRCm38) |
missense |
possibly damaging |
0.49 |
|
R6270:Sema3d
|
UTSW |
5 |
12,448,107 (GRCm38) |
missense |
probably benign |
|
|
R6368:Sema3d
|
UTSW |
5 |
12,571,013 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R6426:Sema3d
|
UTSW |
5 |
12,563,264 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R6750:Sema3d
|
UTSW |
5 |
12,585,100 (GRCm38) |
nonsense |
probably null |
|
|
R7403:Sema3d
|
UTSW |
5 |
12,497,584 (GRCm38) |
missense |
probably damaging |
0.97 |
|
R7450:Sema3d
|
UTSW |
5 |
12,584,934 (GRCm38) |
nonsense |
probably null |
|
|
R7470:Sema3d
|
UTSW |
5 |
12,508,185 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7548:Sema3d
|
UTSW |
5 |
12,577,816 (GRCm38) |
missense |
unknown |
|
|
R7593:Sema3d
|
UTSW |
5 |
12,508,145 (GRCm38) |
missense |
probably benign |
0.02 |
|
R7683:Sema3d
|
UTSW |
5 |
12,573,856 (GRCm38) |
nonsense |
probably null |
|
|
R8155:Sema3d
|
UTSW |
5 |
12,448,181 (GRCm38) |
critical splice donor site |
probably null |
|
|
R8442:Sema3d
|
UTSW |
5 |
12,542,641 (GRCm38) |
missense |
probably damaging |
0.99 |
|
R8725:Sema3d
|
UTSW |
5 |
12,505,855 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R8754:Sema3d
|
UTSW |
5 |
12,553,224 (GRCm38) |
critical splice donor site |
probably null |
|
|
R9293:Sema3d
|
UTSW |
5 |
12,553,214 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R9771:Sema3d
|
UTSW |
5 |
12,563,240 (GRCm38) |
missense |
probably damaging |
0.99 |
|
Z1176:Sema3d
|
UTSW |
5 |
12,585,059 (GRCm38) |
nonsense |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- AGCAGGTTATATCTTGGGGACTACTACC -3'
(R):5'- GTACTGGTCCAGGCTGAAGTTCG -3'
Sequencing Primer
(F):5'- tctttctttcttcctttcttccttc -3'
(R):5'- TCGGGCTGCTAAGGATTTG -3'
|
| Posted On |
2014-05-09 |
Incidental Mutation