Incidental Mutation 'R4428:Sema3d'
ID |
328268 |
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 |
041698-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.188)
|
Stock # |
R4428 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
5 |
Chromosomal Location |
12433352-12638915 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 12498087 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Phenylalanine to Serine
at position 31
(F31S)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000142453
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030868]
[ENSMUST00000197927]
|
AlphaFold |
Q8BH34 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000030868
AA Change: F31S
PolyPhen 2
Score 0.154 (Sensitivity: 0.92; Specificity: 0.87)
|
SMART Domains |
Protein: ENSMUSP00000030868 Gene: ENSMUSG00000040254 AA Change: F31S
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: ENSMUST00000196618
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000197927
AA Change: F31S
PolyPhen 2
Score 0.316 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000142453 Gene: ENSMUSG00000040254 AA Change: F31S
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 |
0.0839 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.5%
|
Validation Efficiency |
100% (46/46) |
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: 41 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
0610040J01Rik |
G |
T |
5: 64,056,182 (GRCm39) |
|
probably benign |
Het |
Abcc1 |
T |
A |
16: 14,263,164 (GRCm39) |
V708E |
probably damaging |
Het |
Bag4 |
C |
T |
8: 26,259,516 (GRCm39) |
A228T |
probably benign |
Het |
Ccdc18 |
A |
G |
5: 108,283,943 (GRCm39) |
Y82C |
probably benign |
Het |
Cd82 |
T |
C |
2: 93,250,214 (GRCm39) |
Y266C |
probably damaging |
Het |
Chrna4 |
A |
G |
2: 180,670,413 (GRCm39) |
S448P |
probably damaging |
Het |
Cldn8 |
A |
C |
16: 88,359,619 (GRCm39) |
M102R |
probably damaging |
Het |
Cmpk1 |
T |
C |
4: 114,820,559 (GRCm39) |
E180G |
probably benign |
Het |
Dock8 |
T |
C |
19: 25,177,863 (GRCm39) |
I2066T |
probably damaging |
Het |
Dock8 |
T |
C |
19: 25,042,754 (GRCm39) |
V112A |
probably benign |
Het |
Fgf3 |
T |
C |
7: 144,394,444 (GRCm39) |
V86A |
probably damaging |
Het |
Frem2 |
A |
G |
3: 53,561,759 (GRCm39) |
I916T |
probably benign |
Het |
Gsk3b |
T |
A |
16: 38,014,298 (GRCm39) |
L252Q |
probably damaging |
Het |
Kif18a |
A |
G |
2: 109,118,466 (GRCm39) |
T94A |
probably damaging |
Het |
Klhdc1 |
T |
A |
12: 69,315,000 (GRCm39) |
|
probably benign |
Het |
Klhl25 |
T |
A |
7: 75,515,162 (GRCm39) |
F23I |
probably damaging |
Het |
Mapk7 |
T |
C |
11: 61,380,055 (GRCm39) |
D701G |
possibly damaging |
Het |
Mbd5 |
A |
T |
2: 49,169,776 (GRCm39) |
Q47L |
possibly damaging |
Het |
Nrcam |
A |
G |
12: 44,623,558 (GRCm39) |
D1049G |
possibly damaging |
Het |
Olfml2a |
G |
T |
2: 38,831,755 (GRCm39) |
M111I |
probably damaging |
Het |
Or3a1c |
T |
C |
11: 74,046,025 (GRCm39) |
F15S |
probably damaging |
Het |
Pld2 |
A |
T |
11: 70,432,160 (GRCm39) |
H93L |
probably damaging |
Het |
Pomgnt2 |
T |
C |
9: 121,811,320 (GRCm39) |
E487G |
possibly damaging |
Het |
Psg17 |
G |
T |
7: 18,550,717 (GRCm39) |
N379K |
probably benign |
Het |
Rfk |
T |
A |
19: 17,375,959 (GRCm39) |
H84Q |
possibly damaging |
Het |
Scn8a |
A |
G |
15: 100,881,784 (GRCm39) |
Y617C |
probably damaging |
Het |
Shq1 |
T |
C |
6: 100,647,889 (GRCm39) |
Y45C |
probably damaging |
Het |
Siglecg |
C |
T |
7: 43,067,350 (GRCm39) |
P639L |
possibly damaging |
Het |
Skp2 |
A |
T |
15: 9,117,034 (GRCm39) |
N325K |
probably benign |
Het |
Sost |
G |
A |
11: 101,857,670 (GRCm39) |
P44S |
probably damaging |
Het |
Sp8 |
T |
A |
12: 118,812,938 (GRCm39) |
S264R |
possibly damaging |
Het |
Sun1 |
T |
C |
5: 139,220,230 (GRCm39) |
|
probably benign |
Het |
Tardbp |
A |
G |
4: 148,709,659 (GRCm39) |
V54A |
possibly damaging |
Het |
Tert |
T |
A |
13: 73,775,594 (GRCm39) |
F115Y |
probably damaging |
Het |
Tmem181a |
T |
A |
17: 6,346,061 (GRCm39) |
L185H |
probably damaging |
Het |
Tmem68 |
A |
T |
4: 3,569,534 (GRCm39) |
I52K |
probably benign |
Het |
Trhde |
A |
T |
10: 114,339,028 (GRCm39) |
L594Q |
probably damaging |
Het |
Umps |
A |
C |
16: 33,781,956 (GRCm39) |
V322G |
probably damaging |
Het |
Vmn2r109 |
T |
C |
17: 20,773,286 (GRCm39) |
D445G |
probably benign |
Het |
Vmn2r22 |
T |
C |
6: 123,614,817 (GRCm39) |
T258A |
possibly damaging |
Het |
Vmn2r4 |
C |
T |
3: 64,322,590 (GRCm39) |
G43E |
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 |
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'- TGATGCCTTGGCAACCTGTTATC -3'
(R):5'- TCTCAGCTATTGTAGACTGTGAAAC -3'
Sequencing Primer
(F):5'- CAGAAAACTTGCTAACTCTAGGAG -3'
(R):5'- CCTTGGAATAGTAACAGTAATTAG -3'
|
Posted On |
2015-07-07 |