Incidental Mutation 'R0924:Sema3d'
| ID |
83068 |
| 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 |
039071-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.188)
|
| Stock # |
R0924 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
12433352-12638915 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to C
at 12513183 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Alanine
at position 51
(D51A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000142453
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030868]
[ENSMUST00000197927]
|
| AlphaFold |
Q8BH34 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000030868
AA Change: D51A
PolyPhen 2
Score 0.467 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: D51A
| 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 |
possibly damaging
Transcript: ENSMUST00000197927
AA Change: D51A
PolyPhen 2
Score 0.690 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
AA Change: D51A
| 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 |
0.4737 |
| Coding Region Coverage |
- 1x: 99.5%
- 3x: 98.9%
- 10x: 97.7%
- 20x: 96.2%
|
| Validation Efficiency |
97% (69/71) |
| 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 |
|---|
| Adamts18 |
A |
T |
8: 114,432,028 (GRCm39) |
|
probably null |
Het |
| Ahcyl2 |
A |
C |
6: 29,870,627 (GRCm39) |
|
probably null |
Het |
| Ajap1 |
T |
A |
4: 153,470,929 (GRCm39) |
I293F |
probably damaging |
Het |
| Akap10 |
T |
C |
11: 61,795,689 (GRCm39) |
|
probably benign |
Het |
| Aldh3b2 |
T |
C |
19: 4,029,350 (GRCm39) |
V241A |
probably benign |
Het |
| Anxa6 |
A |
T |
11: 54,885,214 (GRCm39) |
|
probably null |
Het |
| Atpaf1 |
T |
A |
4: 115,652,635 (GRCm39) |
V12D |
probably damaging |
Het |
| Aurkb |
C |
A |
11: 68,936,822 (GRCm39) |
Y12* |
probably null |
Het |
| Bicdl1 |
A |
G |
5: 115,799,587 (GRCm39) |
|
probably benign |
Het |
| Bnc1 |
A |
T |
7: 81,628,156 (GRCm39) |
|
probably benign |
Het |
| Bpi |
A |
G |
2: 158,103,346 (GRCm39) |
I114V |
possibly damaging |
Het |
| Cacna1c |
A |
T |
6: 118,652,857 (GRCm39) |
I772N |
probably damaging |
Het |
| Cacna2d1 |
A |
G |
5: 16,570,860 (GRCm39) |
N1045D |
possibly damaging |
Het |
| Ccrl2 |
A |
G |
9: 110,885,036 (GRCm39) |
V154A |
probably benign |
Het |
| Celsr3 |
C |
A |
9: 108,723,224 (GRCm39) |
Q2831K |
possibly damaging |
Het |
| Cplane1 |
T |
C |
15: 8,280,554 (GRCm39) |
|
probably benign |
Het |
| Cul3 |
A |
T |
1: 80,267,835 (GRCm39) |
M102K |
probably damaging |
Het |
| Cwf19l2 |
T |
C |
9: 3,441,047 (GRCm39) |
|
probably benign |
Het |
| Dlg5 |
G |
A |
14: 24,185,645 (GRCm39) |
P1920L |
probably damaging |
Het |
| Dnah2 |
T |
C |
11: 69,312,134 (GRCm39) |
H4393R |
probably damaging |
Het |
| Eif2b3 |
T |
A |
4: 116,938,775 (GRCm39) |
V408D |
possibly damaging |
Het |
| Eml3 |
T |
C |
19: 8,910,675 (GRCm39) |
|
probably null |
Het |
| Enpp2 |
T |
C |
15: 54,770,355 (GRCm39) |
|
probably benign |
Het |
| Fcgbpl1 |
A |
T |
7: 27,839,555 (GRCm39) |
Y456F |
probably damaging |
Het |
| Gm14178 |
T |
A |
11: 99,638,326 (GRCm39) |
T18S |
|
Het |
| H2bc12 |
G |
A |
13: 22,220,210 (GRCm39) |
D52N |
probably damaging |
Het |
| H2-M11 |
A |
G |
17: 36,860,106 (GRCm39) |
M324V |
probably benign |
Het |
| H2-T13 |
A |
T |
17: 36,394,824 (GRCm39) |
V33E |
probably damaging |
Het |
| Hdac10 |
T |
C |
15: 89,010,065 (GRCm39) |
T298A |
probably benign |
Het |
| Hepacam |
A |
C |
9: 37,295,224 (GRCm39) |
|
probably benign |
Het |
| Hmx3 |
A |
T |
7: 131,144,813 (GRCm39) |
H41L |
probably benign |
Het |
| Ifi27l2a |
A |
G |
12: 103,408,639 (GRCm39) |
V68A |
probably damaging |
Het |
| Itga11 |
A |
G |
9: 62,683,956 (GRCm39) |
E1079G |
probably benign |
Het |
| Krt6a |
T |
C |
15: 101,599,235 (GRCm39) |
|
probably benign |
Het |
| L1td1 |
A |
G |
4: 98,625,862 (GRCm39) |
N686D |
probably damaging |
Het |
| Lrrtm2 |
G |
A |
18: 35,346,808 (GRCm39) |
R165C |
probably damaging |
Het |
| Macf1 |
G |
T |
4: 123,279,271 (GRCm39) |
A3910E |
probably damaging |
Het |
| Muc5ac |
A |
T |
7: 141,361,252 (GRCm39) |
Y1521F |
possibly damaging |
Het |
| Myo7a |
A |
T |
7: 97,747,463 (GRCm39) |
I129N |
probably damaging |
Het |
| Ncam1 |
A |
T |
9: 49,473,476 (GRCm39) |
|
probably benign |
Het |
| Nckap1 |
A |
T |
2: 80,384,593 (GRCm39) |
C114S |
probably benign |
Het |
| Nf1 |
T |
G |
11: 79,344,692 (GRCm39) |
W1260G |
probably damaging |
Het |
| Or3a1d |
T |
C |
11: 74,237,624 (GRCm39) |
Y262C |
probably damaging |
Het |
| Or6b2b |
A |
G |
1: 92,419,127 (GRCm39) |
S117P |
possibly damaging |
Het |
| Or6c76b |
A |
T |
10: 129,692,515 (GRCm39) |
I43F |
probably damaging |
Het |
| Oxtr |
A |
T |
6: 112,466,598 (GRCm39) |
|
probably null |
Het |
| Pabpc4 |
C |
T |
4: 123,188,458 (GRCm39) |
R356C |
possibly damaging |
Het |
| Pcbp2 |
T |
A |
15: 102,398,197 (GRCm39) |
D182E |
probably damaging |
Het |
| Pgm2 |
A |
T |
5: 64,269,490 (GRCm39) |
I526F |
possibly damaging |
Het |
| Rab43 |
A |
T |
6: 87,769,752 (GRCm39) |
Y151* |
probably null |
Het |
| Rbm19 |
A |
G |
5: 120,264,269 (GRCm39) |
E343G |
probably benign |
Het |
| Rel |
A |
T |
11: 23,692,439 (GRCm39) |
D531E |
probably benign |
Het |
| Rfx4 |
T |
A |
10: 84,704,291 (GRCm39) |
V262E |
probably damaging |
Het |
| Rnf31 |
T |
C |
14: 55,830,459 (GRCm39) |
|
probably benign |
Het |
| Robo3 |
T |
A |
9: 37,340,778 (GRCm39) |
|
probably benign |
Het |
| Ryr3 |
A |
G |
2: 112,672,178 (GRCm39) |
L1431P |
probably damaging |
Het |
| Sema6a |
A |
G |
18: 47,381,559 (GRCm39) |
L996P |
probably damaging |
Het |
| Sh2d4a |
T |
A |
8: 68,787,775 (GRCm39) |
F294I |
probably damaging |
Het |
| Sorl1 |
T |
A |
9: 41,919,470 (GRCm39) |
|
probably benign |
Het |
| Sox1ot |
G |
T |
8: 12,480,455 (GRCm39) |
|
noncoding transcript |
Het |
| Spsb3 |
A |
T |
17: 25,110,358 (GRCm39) |
N395I |
probably damaging |
Het |
| Sptan1 |
A |
G |
2: 29,906,040 (GRCm39) |
N1662S |
probably damaging |
Het |
| Srd5a2 |
G |
T |
17: 74,331,516 (GRCm39) |
N160K |
probably damaging |
Het |
| Sting1 |
A |
G |
18: 35,868,154 (GRCm39) |
|
probably null |
Het |
| Tmem132d |
G |
A |
5: 128,061,503 (GRCm39) |
|
probably benign |
Het |
| Unc80 |
A |
T |
1: 66,549,800 (GRCm39) |
Q686L |
possibly damaging |
Het |
| Vmn2r93 |
A |
G |
17: 18,524,443 (GRCm39) |
T146A |
probably benign |
Het |
| Wdr19 |
A |
G |
5: 65,413,782 (GRCm39) |
|
probably benign |
Het |
| Zfp646 |
C |
T |
7: 127,482,982 (GRCm39) |
Q1500* |
probably null |
Het |
| Zfp683 |
T |
C |
4: 133,783,138 (GRCm39) |
Y201H |
probably benign |
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 |
|
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 |
|
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'- GGTTAGGAGGAGAGCCAAGATACTGTAATA -3'
(R):5'- GCACACAGAAGAAATTCAGTGAATCTACCAA -3'
Sequencing Primer
(F):5'- tttataCACAGAATAGGGTTAAGCAC -3'
(R):5'- GAAATTCAGTGAATCTACCAATGATG -3'
|
| Posted On |
2013-11-08 |
Incidental Mutation