Incidental Mutation 'R1975:Sema3d'
| ID |
221550 |
| 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 |
039988-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.188)
|
| Stock # |
R1975 (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 12634965 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 677
(V677A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000030868
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030868]
|
| AlphaFold |
Q8BH34 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000030868
AA Change: V677A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: V677A
| 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
|
| Meta Mutation Damage Score |
0.0748 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.3%
|
| Validation Efficiency |
96% (71/74) |
| 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: 69 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acad12 |
T |
C |
5: 121,742,322 (GRCm39) |
T429A |
probably benign |
Het |
| Afmid |
A |
C |
11: 117,727,300 (GRCm39) |
I275L |
probably benign |
Het |
| Aimp1 |
A |
C |
3: 132,382,860 (GRCm39) |
D5E |
possibly damaging |
Het |
| Aldob |
G |
A |
4: 49,538,171 (GRCm39) |
A319V |
probably benign |
Het |
| Ankar |
C |
T |
1: 72,697,600 (GRCm39) |
V1068I |
possibly damaging |
Het |
| Ccr2 |
C |
T |
9: 123,906,830 (GRCm39) |
S370L |
probably benign |
Het |
| Chrnb4 |
A |
G |
9: 54,942,102 (GRCm39) |
Y391H |
probably damaging |
Het |
| Clip1 |
A |
G |
5: 123,761,281 (GRCm39) |
M873T |
possibly damaging |
Het |
| Cspg4 |
G |
C |
9: 56,797,762 (GRCm39) |
G1409R |
probably damaging |
Het |
| Dnah17 |
A |
T |
11: 117,987,362 (GRCm39) |
L1320* |
probably null |
Het |
| Dock4 |
T |
C |
12: 40,829,641 (GRCm39) |
|
probably benign |
Het |
| Eml4 |
T |
C |
17: 83,717,622 (GRCm39) |
S65P |
probably benign |
Het |
| Fblim1 |
A |
T |
4: 141,312,175 (GRCm39) |
D183E |
probably damaging |
Het |
| Foxn1 |
T |
C |
11: 78,256,763 (GRCm39) |
|
probably benign |
Het |
| Gm973 |
A |
T |
1: 59,601,930 (GRCm39) |
T515S |
possibly damaging |
Het |
| Hdac7 |
G |
A |
15: 97,704,386 (GRCm39) |
Q495* |
probably null |
Het |
| Hipk3 |
T |
C |
2: 104,301,518 (GRCm39) |
I225V |
probably benign |
Het |
| Hrc |
A |
T |
7: 44,985,638 (GRCm39) |
D263V |
probably damaging |
Het |
| Hs6st3 |
T |
C |
14: 119,375,888 (GRCm39) |
I21T |
probably benign |
Het |
| Il15ra |
A |
G |
2: 11,728,334 (GRCm39) |
T133A |
possibly damaging |
Het |
| Krt78 |
T |
C |
15: 101,854,603 (GRCm39) |
*1069W |
probably null |
Het |
| Lama3 |
T |
A |
18: 12,586,920 (GRCm39) |
M761K |
probably damaging |
Het |
| Lonp1 |
T |
C |
17: 56,922,068 (GRCm39) |
T771A |
possibly damaging |
Het |
| Macf1 |
T |
C |
4: 123,383,005 (GRCm39) |
T1320A |
probably damaging |
Het |
| Mark3 |
A |
T |
12: 111,581,875 (GRCm39) |
I115L |
probably damaging |
Het |
| Mcph1 |
T |
G |
8: 18,739,081 (GRCm39) |
|
probably benign |
Het |
| Med23 |
T |
A |
10: 24,786,664 (GRCm39) |
N923K |
probably benign |
Het |
| Msrb2 |
T |
G |
2: 19,398,032 (GRCm39) |
Y97D |
probably damaging |
Het |
| Muc6 |
C |
T |
7: 141,234,368 (GRCm39) |
G708S |
probably damaging |
Het |
| Mylk |
T |
C |
16: 34,700,673 (GRCm39) |
|
probably null |
Het |
| Nfrkb |
T |
A |
9: 31,325,980 (GRCm39) |
V1141E |
possibly damaging |
Het |
| Obscn |
T |
C |
11: 58,958,555 (GRCm39) |
E3675G |
probably damaging |
Het |
| Or11h7 |
T |
A |
14: 50,890,821 (GRCm39) |
N42K |
probably damaging |
Het |
| Or2l5 |
G |
A |
16: 19,333,586 (GRCm39) |
P267S |
probably damaging |
Het |
| Or2t6 |
A |
T |
14: 14,175,446 (GRCm38) |
V212E |
probably damaging |
Het |
| Or51aa2 |
A |
T |
7: 103,188,201 (GRCm39) |
F80Y |
probably damaging |
Het |
| Or52z14 |
A |
G |
7: 103,253,219 (GRCm39) |
|
probably null |
Het |
| Or5ac21 |
T |
C |
16: 59,124,091 (GRCm39) |
S193P |
probably damaging |
Het |
| Or8k21 |
C |
G |
2: 86,145,498 (GRCm39) |
G44A |
probably damaging |
Het |
| Pan2 |
T |
C |
10: 128,156,282 (GRCm39) |
V1171A |
probably damaging |
Het |
| Pdgfc |
C |
T |
3: 81,116,552 (GRCm39) |
T302I |
probably damaging |
Het |
| Pkhd1l1 |
G |
T |
15: 44,393,109 (GRCm39) |
V1815F |
probably damaging |
Het |
| Pnpt1 |
A |
G |
11: 29,091,256 (GRCm39) |
I337V |
probably benign |
Het |
| Psma8 |
T |
G |
18: 14,864,033 (GRCm39) |
|
probably null |
Het |
| Rbl2 |
T |
C |
8: 91,812,090 (GRCm39) |
S220P |
probably benign |
Het |
| Rere |
T |
A |
4: 150,700,190 (GRCm39) |
D1091E |
probably damaging |
Het |
| Rpa1 |
A |
G |
11: 75,197,002 (GRCm39) |
C540R |
probably damaging |
Het |
| Sgk2 |
A |
G |
2: 162,846,080 (GRCm39) |
N207S |
probably benign |
Het |
| Sirpb1a |
T |
C |
3: 15,444,141 (GRCm39) |
I370V |
probably benign |
Het |
| Slc22a19 |
A |
G |
19: 7,661,224 (GRCm39) |
|
probably benign |
Het |
| Slc26a1 |
T |
A |
5: 108,820,338 (GRCm39) |
D287V |
probably damaging |
Het |
| Slc36a4 |
T |
A |
9: 15,645,506 (GRCm39) |
V311D |
probably damaging |
Het |
| Slco1b2 |
A |
T |
6: 141,628,951 (GRCm39) |
Y551F |
probably damaging |
Het |
| Slco2a1 |
T |
A |
9: 102,956,653 (GRCm39) |
Y488* |
probably null |
Het |
| Stab2 |
A |
C |
10: 86,732,360 (GRCm39) |
|
probably null |
Het |
| Strn |
T |
C |
17: 78,999,928 (GRCm39) |
|
probably null |
Het |
| Tbxas1 |
A |
G |
6: 38,925,575 (GRCm39) |
|
probably benign |
Het |
| Thumpd3 |
A |
G |
6: 113,032,838 (GRCm39) |
N192S |
possibly damaging |
Het |
| Tns3 |
T |
A |
11: 8,385,738 (GRCm39) |
I1386F |
probably benign |
Het |
| Treml4 |
T |
A |
17: 48,579,821 (GRCm39) |
V219E |
probably damaging |
Het |
| Triobp |
T |
C |
15: 78,850,908 (GRCm39) |
V354A |
probably benign |
Het |
| Tspan8 |
A |
G |
10: 115,680,035 (GRCm39) |
I217V |
probably benign |
Het |
| Tub |
G |
A |
7: 108,627,042 (GRCm39) |
G314R |
possibly damaging |
Het |
| Ube3b |
C |
T |
5: 114,537,926 (GRCm39) |
T339M |
possibly damaging |
Het |
| Vmn2r43 |
A |
G |
7: 8,258,550 (GRCm39) |
I221T |
possibly damaging |
Het |
| Vmn2r5 |
C |
T |
3: 64,411,642 (GRCm39) |
E309K |
probably damaging |
Het |
| Zfp110 |
C |
T |
7: 12,582,429 (GRCm39) |
T359I |
probably benign |
Het |
| Zfp322a |
A |
T |
13: 23,541,074 (GRCm39) |
C223S |
probably damaging |
Het |
| Zfp512b |
G |
A |
2: 181,228,878 (GRCm39) |
R696* |
probably null |
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 |
12,613,285 (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'- ACCATCTTCAACTATGGCTGAC -3'
(R):5'- TCTGCTCACAGTACTGGTCC -3'
Sequencing Primer
(F):5'- GGCTGACAATGTTATAGTTGATGAC -3'
(R):5'- CAGTACTGGTCCAGGCTGAAGTTC -3'
|
| Posted On |
2014-08-25 |
Incidental Mutation