Incidental Mutation 'R2276:Sema3d'
| ID |
242791 |
| 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 |
040275-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.188)
|
| Stock # |
R2276 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
12433352-12638915 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 12592549 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamine to Leucine
at position 326
(Q326L)
|
| 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: Q326L
PolyPhen 2
Score 0.635 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: Q326L
| 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: Q326L
PolyPhen 2
Score 0.635 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
AA Change: Q326L
| 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 |
0.3731 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.8%
|
| Validation Efficiency |
100% (65/65) |
| 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: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Akap11 |
T |
A |
14: 78,747,477 (GRCm39) |
I1637L |
possibly damaging |
Het |
| Ankrd27 |
T |
C |
7: 35,315,265 (GRCm39) |
|
probably benign |
Het |
| Anxa3 |
T |
C |
5: 96,978,349 (GRCm39) |
|
probably null |
Het |
| Arfgef2 |
G |
C |
2: 166,707,679 (GRCm39) |
G1025A |
probably benign |
Het |
| Arhgap21 |
T |
C |
2: 20,868,037 (GRCm39) |
I829V |
possibly damaging |
Het |
| Arhgap42 |
T |
C |
9: 9,035,512 (GRCm39) |
M277V |
probably benign |
Het |
| Cep112 |
A |
T |
11: 108,746,671 (GRCm39) |
R176S |
probably damaging |
Het |
| Chd9 |
C |
T |
8: 91,760,615 (GRCm39) |
P2120L |
probably benign |
Het |
| Cnga1 |
C |
T |
5: 72,776,404 (GRCm39) |
V20I |
possibly damaging |
Het |
| Cpped1 |
A |
C |
16: 11,712,745 (GRCm39) |
|
probably null |
Het |
| Cr2 |
T |
C |
1: 194,839,676 (GRCm39) |
R960G |
possibly damaging |
Het |
| Dbf4 |
T |
C |
5: 8,471,333 (GRCm39) |
N36S |
possibly damaging |
Het |
| Dnah6 |
G |
A |
6: 73,090,564 (GRCm39) |
S2210L |
probably benign |
Het |
| Dnajb12 |
C |
T |
10: 59,728,799 (GRCm39) |
T229I |
probably benign |
Het |
| Dnajc28 |
G |
A |
16: 91,413,755 (GRCm39) |
T187M |
probably damaging |
Het |
| Epb41l2 |
T |
C |
10: 25,364,842 (GRCm39) |
|
probably benign |
Het |
| Fam178b |
A |
G |
1: 36,671,539 (GRCm39) |
L194P |
probably damaging |
Het |
| Fam50b |
C |
T |
13: 34,930,823 (GRCm39) |
Q100* |
probably null |
Het |
| Gimap9 |
A |
G |
6: 48,654,812 (GRCm39) |
H133R |
probably benign |
Het |
| Gpbp1 |
A |
T |
13: 111,603,512 (GRCm39) |
|
probably null |
Het |
| Gpr89 |
A |
G |
3: 96,804,743 (GRCm39) |
Y38H |
probably damaging |
Het |
| Gsdmc3 |
T |
A |
15: 63,732,105 (GRCm39) |
Y307F |
probably benign |
Het |
| H4c16 |
T |
A |
6: 136,781,299 (GRCm39) |
I27F |
probably damaging |
Het |
| Hip1 |
C |
T |
5: 135,485,900 (GRCm39) |
R101K |
probably damaging |
Het |
| Hsf4 |
G |
A |
8: 105,996,628 (GRCm39) |
D18N |
probably null |
Het |
| Igfn1 |
T |
C |
1: 135,892,479 (GRCm39) |
K2214E |
probably damaging |
Het |
| Itgal |
A |
T |
7: 126,927,919 (GRCm39) |
E1038V |
probably null |
Het |
| Kank2 |
C |
A |
9: 21,681,080 (GRCm39) |
M816I |
probably damaging |
Het |
| Kctd15 |
T |
C |
7: 34,344,366 (GRCm39) |
D95G |
possibly damaging |
Het |
| Kif1a |
A |
T |
1: 92,996,199 (GRCm39) |
|
probably benign |
Het |
| Lgi4 |
T |
G |
7: 30,760,037 (GRCm39) |
L78V |
probably damaging |
Het |
| Lrrc7 |
A |
G |
3: 157,885,429 (GRCm39) |
F432L |
probably damaging |
Het |
| Madd |
A |
T |
2: 90,974,028 (GRCm39) |
C1419S |
possibly damaging |
Het |
| Nisch |
T |
C |
14: 30,898,803 (GRCm39) |
|
probably benign |
Het |
| Or2h1b |
A |
T |
17: 37,462,145 (GRCm39) |
C239* |
probably null |
Het |
| Osbpl2 |
G |
A |
2: 179,790,319 (GRCm39) |
G198S |
possibly damaging |
Het |
| Pclo |
T |
A |
5: 14,764,287 (GRCm39) |
D4253E |
unknown |
Het |
| Phactr1 |
A |
T |
13: 43,231,265 (GRCm39) |
S244C |
possibly damaging |
Het |
| Pja2 |
T |
C |
17: 64,599,865 (GRCm39) |
S478G |
probably damaging |
Het |
| Prex1 |
A |
T |
2: 166,419,875 (GRCm39) |
I79N |
probably benign |
Het |
| Ptpn4 |
T |
C |
1: 119,612,321 (GRCm39) |
D24G |
probably damaging |
Het |
| Rars2 |
T |
C |
4: 34,656,835 (GRCm39) |
S495P |
probably damaging |
Het |
| Rhebl1 |
A |
T |
15: 98,776,167 (GRCm39) |
D162E |
probably benign |
Het |
| Rhou |
T |
C |
8: 124,382,258 (GRCm39) |
V100A |
probably damaging |
Het |
| Rpn2 |
A |
G |
2: 157,152,208 (GRCm39) |
T394A |
possibly damaging |
Het |
| Ryr3 |
A |
T |
2: 112,479,664 (GRCm39) |
M4386K |
possibly damaging |
Het |
| Scmh1 |
G |
T |
4: 120,340,869 (GRCm39) |
C185F |
probably damaging |
Het |
| Sis |
T |
A |
3: 72,821,934 (GRCm39) |
K1376* |
probably null |
Het |
| Slc25a29 |
T |
C |
12: 108,792,852 (GRCm39) |
E242G |
probably benign |
Het |
| Slc26a5 |
A |
G |
5: 22,028,545 (GRCm39) |
V304A |
probably benign |
Het |
| Slc39a7 |
C |
T |
17: 34,250,241 (GRCm39) |
|
probably benign |
Het |
| Slco1a4 |
A |
G |
6: 141,761,308 (GRCm39) |
V435A |
possibly damaging |
Het |
| Syne2 |
A |
G |
12: 75,974,240 (GRCm39) |
E1146G |
possibly damaging |
Het |
| Tgm5 |
T |
A |
2: 120,879,304 (GRCm39) |
|
probably benign |
Het |
| Tgm7 |
A |
G |
2: 120,929,045 (GRCm39) |
S284P |
probably damaging |
Het |
| Tmem132d |
G |
A |
5: 127,872,987 (GRCm39) |
R541W |
probably damaging |
Het |
| Tmem170 |
C |
A |
8: 112,596,349 (GRCm39) |
V59L |
probably benign |
Het |
| Tpbgl |
G |
T |
7: 99,275,233 (GRCm39) |
A208E |
possibly damaging |
Het |
| Ttc23l |
A |
G |
15: 10,523,678 (GRCm39) |
I347T |
possibly damaging |
Het |
| Ulk1 |
T |
C |
5: 110,936,028 (GRCm39) |
E827G |
probably benign |
Het |
| Vps13a |
A |
G |
19: 16,687,790 (GRCm39) |
V886A |
possibly damaging |
Het |
| Wrn |
A |
T |
8: 33,814,584 (GRCm39) |
C44S |
probably benign |
Het |
| Zscan22 |
T |
A |
7: 12,640,750 (GRCm39) |
C331* |
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 |
12,634,965 (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 |
|
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'- ATGAAGACTGCCAACTGAGTCATTTC -3'
(R):5'- ACTTTATATGCCCCAGTACAGG -3'
Sequencing Primer
(F):5'- CTGGTAAGAAAGCTTTTACCC -3'
(R):5'- CCTACCTGGTTGTGGTAA -3'
|
| Posted On |
2014-10-16 |
Incidental Mutation