Incidental Mutation 'R0095:Sema3d'
| ID |
17962 |
| 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 |
038381-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.188)
|
| Stock # |
R0095 (G1)
|
| Quality Score |
|
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
12433352-12638915 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 12613314 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Histidine
at position 464
(Y464H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000142453
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030868]
[ENSMUST00000197927]
|
| AlphaFold |
Q8BH34 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000030868
AA Change: Y464H
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: Y464H
| 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 damaging
Transcript: ENSMUST00000197927
AA Change: Y464H
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
AA Change: Y464H
| 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 |
0.5076 |
| Coding Region Coverage |
- 1x: 88.6%
- 3x: 85.1%
- 10x: 74.3%
- 20x: 56.3%
|
| Validation Efficiency |
88% (50/57) |
| 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: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adhfe1 |
T |
C |
1: 9,630,402 (GRCm39) |
I317T |
possibly damaging |
Het |
| Aldh3a2 |
C |
T |
11: 61,141,774 (GRCm39) |
G21D |
probably damaging |
Het |
| Alms1 |
C |
A |
6: 85,597,235 (GRCm39) |
T1156N |
possibly damaging |
Het |
| Anxa8 |
G |
A |
14: 33,808,028 (GRCm39) |
A6T |
probably benign |
Het |
| Arhgef4 |
C |
T |
1: 34,771,451 (GRCm39) |
Q86* |
probably null |
Het |
| Atp4a |
T |
A |
7: 30,420,160 (GRCm39) |
I769N |
probably damaging |
Het |
| Cacnb2 |
G |
T |
2: 14,963,586 (GRCm39) |
V61F |
probably damaging |
Het |
| Clcf1 |
T |
G |
19: 4,265,842 (GRCm39) |
|
probably benign |
Het |
| Cmah |
G |
T |
13: 24,620,668 (GRCm39) |
A301S |
probably benign |
Het |
| Col6a4 |
A |
G |
9: 105,952,555 (GRCm39) |
W448R |
probably benign |
Het |
| Csmd1 |
A |
T |
8: 16,283,065 (GRCm39) |
D630E |
probably damaging |
Het |
| Dock10 |
A |
T |
1: 80,501,788 (GRCm39) |
Y1434N |
probably benign |
Het |
| Etl4 |
A |
G |
2: 20,748,679 (GRCm39) |
D137G |
probably damaging |
Het |
| Fer |
A |
T |
17: 64,248,321 (GRCm39) |
E361V |
possibly damaging |
Het |
| Foxp2 |
C |
A |
6: 15,196,976 (GRCm39) |
A6E |
probably damaging |
Het |
| Gpr3 |
T |
A |
4: 132,938,597 (GRCm39) |
D25V |
probably benign |
Het |
| Gstm7 |
A |
T |
3: 107,837,879 (GRCm39) |
|
probably benign |
Het |
| Gys1 |
T |
C |
7: 45,094,073 (GRCm39) |
V332A |
possibly damaging |
Het |
| Igsf10 |
A |
T |
3: 59,238,617 (GRCm39) |
Y521* |
probably null |
Het |
| Itk |
T |
C |
11: 46,233,279 (GRCm39) |
D266G |
probably damaging |
Het |
| Kdm1a |
C |
T |
4: 136,278,205 (GRCm39) |
R839H |
probably benign |
Het |
| Lypla1 |
T |
C |
1: 4,900,550 (GRCm39) |
|
probably benign |
Het |
| Mmp1a |
G |
A |
9: 7,465,621 (GRCm39) |
G186D |
possibly damaging |
Het |
| Myl3 |
A |
C |
9: 110,596,997 (GRCm39) |
D119A |
probably damaging |
Het |
| Necab1 |
T |
A |
4: 14,960,027 (GRCm39) |
N307Y |
possibly damaging |
Het |
| Or5p81 |
A |
C |
7: 108,267,252 (GRCm39) |
I210L |
probably benign |
Het |
| Plekha5 |
T |
C |
6: 140,474,323 (GRCm39) |
F84L |
probably damaging |
Het |
| Plxnb2 |
A |
G |
15: 89,049,534 (GRCm39) |
S562P |
probably benign |
Het |
| Rfx8 |
C |
T |
1: 39,724,696 (GRCm39) |
V222M |
possibly damaging |
Het |
| Rpap3 |
A |
G |
15: 97,578,417 (GRCm39) |
|
probably benign |
Het |
| Rpl6 |
T |
G |
5: 121,343,902 (GRCm39) |
V115G |
possibly damaging |
Het |
| Sec16a |
A |
T |
2: 26,315,772 (GRCm39) |
|
probably null |
Het |
| Sgo2a |
T |
A |
1: 58,054,714 (GRCm39) |
N299K |
probably benign |
Het |
| Tecrl |
T |
C |
5: 83,442,417 (GRCm39) |
|
probably benign |
Het |
| Thsd7a |
T |
C |
6: 12,320,969 (GRCm39) |
T1569A |
probably damaging |
Het |
| U2surp |
T |
C |
9: 95,382,737 (GRCm39) |
|
probably null |
Het |
| Unc45a |
T |
C |
7: 79,979,291 (GRCm39) |
D567G |
probably damaging |
Het |
| Zfp532 |
A |
G |
18: 65,757,855 (GRCm39) |
Y596C |
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 |
|
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 |
|
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 |
|
|
| Posted On |
2013-03-25 |
Incidental Mutation