Incidental Mutation 'R5186:Sema3d'
| ID |
397869 |
| 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 |
042765-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.188)
|
| Stock # |
R5186 (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 12634875 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 647
(D647G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000030868
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030868]
|
| AlphaFold |
Q8BH34 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000030868
AA Change: D647G
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: D647G
| 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: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 95.0%
|
| 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: 72 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca8a |
T |
C |
11: 109,982,425 (GRCm39) |
I6V |
probably null |
Het |
| Aox1 |
A |
G |
1: 58,107,529 (GRCm39) |
D601G |
probably damaging |
Het |
| Asic1 |
GCACC |
GCACCACC |
15: 99,596,684 (GRCm39) |
|
probably benign |
Het |
| Cacna1g |
T |
G |
11: 94,333,674 (GRCm39) |
N931T |
probably damaging |
Het |
| Ccdc14 |
T |
C |
16: 34,541,955 (GRCm39) |
F511L |
probably damaging |
Het |
| Cd177 |
T |
A |
7: 24,444,348 (GRCm39) |
E710V |
probably benign |
Het |
| Cep112 |
T |
C |
11: 108,643,386 (GRCm39) |
C49R |
probably benign |
Het |
| Clip2 |
G |
A |
5: 134,551,645 (GRCm39) |
T159M |
possibly damaging |
Het |
| Dnah2 |
T |
C |
11: 69,326,710 (GRCm39) |
N3575S |
probably damaging |
Het |
| Dnah6 |
T |
A |
6: 73,044,410 (GRCm39) |
I3234F |
probably damaging |
Het |
| Eci3 |
G |
T |
13: 35,130,961 (GRCm39) |
A302E |
possibly damaging |
Het |
| Fam204a |
T |
C |
19: 60,188,421 (GRCm39) |
K214E |
probably damaging |
Het |
| Fam78a |
T |
C |
2: 31,972,666 (GRCm39) |
T85A |
possibly damaging |
Het |
| Flnb |
T |
C |
14: 7,909,748 (GRCm38) |
Y1401H |
probably damaging |
Het |
| Foxl2 |
A |
T |
9: 98,838,108 (GRCm39) |
D132V |
probably damaging |
Het |
| Frs2 |
C |
A |
10: 116,914,747 (GRCm39) |
W57C |
probably damaging |
Het |
| Gm26558 |
G |
T |
2: 70,491,761 (GRCm39) |
|
probably benign |
Het |
| Gpr139 |
A |
G |
7: 118,744,063 (GRCm39) |
V174A |
probably benign |
Het |
| Grik5 |
T |
C |
7: 24,715,244 (GRCm39) |
T676A |
probably damaging |
Het |
| H60c |
T |
C |
10: 3,209,273 (GRCm39) |
|
probably null |
Het |
| Hspa1l |
A |
G |
17: 35,197,445 (GRCm39) |
K495E |
probably damaging |
Het |
| Irgm1 |
C |
T |
11: 48,757,044 (GRCm39) |
V256I |
probably benign |
Het |
| Kat7 |
T |
A |
11: 95,177,242 (GRCm39) |
T293S |
probably benign |
Het |
| Lipg |
C |
T |
18: 75,094,009 (GRCm39) |
V13I |
probably benign |
Het |
| Lrrn1 |
A |
T |
6: 107,546,185 (GRCm39) |
Y661F |
probably damaging |
Het |
| Mllt3 |
A |
G |
4: 87,759,232 (GRCm39) |
V272A |
probably benign |
Het |
| Mx1 |
G |
A |
16: 97,256,694 (GRCm39) |
R162C |
probably benign |
Het |
| Myo18b |
T |
A |
5: 113,019,336 (GRCm39) |
D647V |
probably damaging |
Het |
| Naf1 |
G |
A |
8: 67,332,298 (GRCm39) |
V329I |
probably benign |
Het |
| Or4k40 |
A |
T |
2: 111,251,119 (GRCm39) |
M59K |
probably damaging |
Het |
| Or52u1 |
A |
T |
7: 104,237,418 (GRCm39) |
I153F |
probably damaging |
Het |
| Or8g22 |
A |
T |
9: 38,958,265 (GRCm39) |
C194* |
probably null |
Het |
| P2rx5 |
G |
A |
11: 73,062,616 (GRCm39) |
V442M |
possibly damaging |
Het |
| Pcdhb9 |
A |
G |
18: 37,534,285 (GRCm39) |
E93G |
probably damaging |
Het |
| Pcdhga4 |
A |
T |
18: 37,820,479 (GRCm39) |
N676I |
probably benign |
Het |
| Pgm5 |
A |
G |
19: 24,797,492 (GRCm39) |
M230T |
probably damaging |
Het |
| Pik3c2g |
T |
C |
6: 139,599,016 (GRCm39) |
V44A |
probably damaging |
Het |
| Pp2d1 |
T |
C |
17: 53,815,168 (GRCm39) |
M519V |
probably benign |
Het |
| Ppp1r10 |
A |
G |
17: 36,239,403 (GRCm39) |
E404G |
probably damaging |
Het |
| Prpf8 |
A |
T |
11: 75,380,609 (GRCm39) |
E104V |
possibly damaging |
Het |
| Ptpra |
T |
C |
2: 30,328,367 (GRCm39) |
|
probably null |
Het |
| Pygl |
A |
C |
12: 70,248,118 (GRCm39) |
N248K |
probably damaging |
Het |
| Rbm8a |
A |
G |
3: 96,538,248 (GRCm39) |
D102G |
probably damaging |
Het |
| Serpinb11 |
A |
T |
1: 107,307,484 (GRCm39) |
D305V |
probably damaging |
Het |
| Slc12a8 |
T |
C |
16: 33,437,578 (GRCm39) |
I337T |
probably damaging |
Het |
| Slc29a2 |
G |
A |
19: 5,078,995 (GRCm39) |
R286Q |
probably benign |
Het |
| Slc2a3 |
T |
A |
6: 122,712,542 (GRCm39) |
D234V |
probably damaging |
Het |
| Slco4a1 |
T |
C |
2: 180,114,901 (GRCm39) |
V608A |
probably damaging |
Het |
| Spata31d1e |
A |
T |
13: 59,891,553 (GRCm39) |
L89H |
probably damaging |
Het |
| Srrm2 |
C |
T |
17: 24,035,561 (GRCm39) |
T831I |
probably benign |
Het |
| St18 |
T |
A |
1: 6,872,541 (GRCm39) |
|
probably null |
Het |
| Tesk2 |
G |
C |
4: 116,599,093 (GRCm39) |
G67A |
probably damaging |
Het |
| Tlr1 |
A |
T |
5: 65,082,564 (GRCm39) |
L671H |
probably damaging |
Het |
| Tmem63b |
A |
T |
17: 45,972,403 (GRCm39) |
Y735N |
possibly damaging |
Het |
| Tmprss11a |
C |
T |
5: 86,567,938 (GRCm39) |
C263Y |
probably damaging |
Het |
| Trio |
A |
T |
15: 27,898,077 (GRCm39) |
V345E |
probably damaging |
Het |
| Tut7 |
A |
G |
13: 59,964,470 (GRCm39) |
|
probably null |
Het |
| Ubr5 |
A |
G |
15: 37,998,160 (GRCm39) |
S1674P |
probably damaging |
Het |
| Uchl3 |
T |
A |
14: 101,933,353 (GRCm39) |
C209S |
probably damaging |
Het |
| Uhmk1 |
T |
C |
1: 170,038,736 (GRCm39) |
N206S |
probably damaging |
Het |
| Uhrf1 |
C |
T |
17: 56,625,340 (GRCm39) |
R588W |
probably damaging |
Het |
| Usp28 |
T |
C |
9: 48,921,550 (GRCm39) |
V256A |
probably damaging |
Het |
| Utrn |
C |
A |
10: 12,604,521 (GRCm39) |
L552F |
probably damaging |
Het |
| Vmn1r55 |
A |
T |
7: 5,149,985 (GRCm39) |
M146K |
probably damaging |
Het |
| Vmn1r57 |
A |
C |
7: 5,224,107 (GRCm39) |
I211L |
probably benign |
Het |
| Zar1 |
C |
T |
5: 72,734,742 (GRCm39) |
C316Y |
probably damaging |
Het |
| Zc3h11a |
A |
T |
1: 133,549,412 (GRCm39) |
S750T |
probably damaging |
Het |
| Zfp366 |
G |
A |
13: 99,382,676 (GRCm39) |
C613Y |
probably benign |
Het |
| Zfp37 |
A |
T |
4: 62,109,493 (GRCm39) |
C524S |
probably damaging |
Het |
| Zfp516 |
T |
C |
18: 82,975,218 (GRCm39) |
V472A |
probably benign |
Het |
| Zhx1 |
A |
T |
15: 57,915,819 (GRCm39) |
M809K |
probably damaging |
Het |
| Zic1 |
T |
C |
9: 91,246,424 (GRCm39) |
Y216C |
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 |
|
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'- ACCATCTTCAACTATGGCTGAC -3'
(R):5'- GGATGTAGTCTTTGTATCTCAACCG -3'
Sequencing Primer
(F):5'- GGCTGACAATGTTATAGTTGATGAC -3'
(R):5'- GTGACTCAGCCAACAGATCCTTG -3'
|
| Posted On |
2016-07-06 |
Incidental Mutation