Incidental Mutation 'R8442:Sema3d'
| ID |
654242 |
| 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 |
067779-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.188)
|
| Stock # |
R8442 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
5 |
| Chromosomal Location |
12433352-12638915 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 12592608 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 346
(T346A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000030868
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030868]
[ENSMUST00000197927]
|
| AlphaFold |
Q8BH34 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000030868
AA Change: T346A
PolyPhen 2
Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: T346A
| 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 |
probably damaging
Transcript: ENSMUST00000197927
AA Change: T346A
PolyPhen 2
Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
AA Change: T346A
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 98.8%
|
| 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: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Apof |
T |
C |
10: 128,104,891 (GRCm39) |
L15P |
probably damaging |
Het |
| BC048671 |
T |
C |
6: 90,282,095 (GRCm39) |
F84S |
probably benign |
Het |
| Bsn |
G |
A |
9: 107,988,651 (GRCm39) |
A2367V |
probably benign |
Het |
| C2cd4a |
C |
T |
9: 67,739,039 (GRCm39) |
M1I |
probably null |
Het |
| Cd72 |
T |
A |
4: 43,450,109 (GRCm39) |
K266N |
possibly damaging |
Het |
| Col12a1 |
A |
G |
9: 79,542,781 (GRCm39) |
F2328S |
probably damaging |
Het |
| Cubn |
T |
C |
2: 13,318,855 (GRCm39) |
Y2948C |
probably damaging |
Het |
| Dagla |
A |
G |
19: 10,240,456 (GRCm39) |
|
probably null |
Het |
| Dagla |
A |
G |
19: 10,248,883 (GRCm39) |
F24L |
probably damaging |
Het |
| Dnah14 |
A |
G |
1: 181,568,849 (GRCm39) |
T2860A |
probably damaging |
Het |
| Efcab2 |
A |
T |
1: 178,265,001 (GRCm39) |
K22N |
probably benign |
Het |
| Flt1 |
C |
T |
5: 147,512,983 (GRCm39) |
R1118Q |
probably damaging |
Het |
| Foxl1 |
T |
A |
8: 121,855,224 (GRCm39) |
L175Q |
possibly damaging |
Het |
| Gm572 |
G |
T |
4: 148,743,450 (GRCm39) |
R140L |
possibly damaging |
Het |
| Gucy2g |
T |
C |
19: 55,205,833 (GRCm39) |
R676G |
probably benign |
Het |
| Hmcn2 |
C |
A |
2: 31,281,088 (GRCm39) |
L1867I |
probably benign |
Het |
| Hspb8 |
T |
C |
5: 116,560,504 (GRCm39) |
Y12C |
probably damaging |
Het |
| Igf2bp2 |
A |
C |
16: 21,883,841 (GRCm39) |
|
probably null |
Het |
| Igkv9-129 |
T |
A |
6: 67,816,784 (GRCm39) |
M3K |
probably damaging |
Het |
| Il5 |
C |
T |
11: 53,612,651 (GRCm39) |
P54S |
probably damaging |
Het |
| Kif18a |
T |
C |
2: 109,125,318 (GRCm39) |
I245T |
possibly damaging |
Het |
| Kif2b |
T |
A |
11: 91,467,140 (GRCm39) |
N381I |
possibly damaging |
Het |
| Lrrc49 |
A |
G |
9: 60,500,908 (GRCm39) |
F679S |
probably benign |
Het |
| Med24 |
A |
G |
11: 98,598,383 (GRCm39) |
F742L |
probably benign |
Het |
| Msh3 |
T |
C |
13: 92,349,020 (GRCm39) |
T1071A |
probably benign |
Het |
| Neb |
T |
C |
2: 52,177,220 (GRCm39) |
T1374A |
probably damaging |
Het |
| Or4d6 |
A |
T |
19: 12,086,091 (GRCm39) |
I47N |
probably damaging |
Het |
| Or5p75-ps1 |
A |
C |
7: 108,107,851 (GRCm39) |
Q196P |
unknown |
Het |
| P3h2 |
A |
G |
16: 25,805,955 (GRCm39) |
I296T |
probably benign |
Het |
| Pcdhb21 |
A |
T |
18: 37,646,841 (GRCm39) |
|
probably benign |
Het |
| Prkab2 |
G |
T |
3: 97,566,002 (GRCm39) |
G25C |
probably damaging |
Het |
| Ptprm |
C |
A |
17: 67,251,312 (GRCm39) |
A522S |
possibly damaging |
Het |
| Scarf2 |
A |
G |
16: 17,624,231 (GRCm39) |
D512G |
probably benign |
Het |
| Septin7 |
T |
C |
9: 25,163,938 (GRCm39) |
S2P |
unknown |
Het |
| Sfrp5 |
A |
G |
19: 42,187,236 (GRCm39) |
V278A |
probably benign |
Het |
| Taar1 |
T |
A |
10: 23,796,522 (GRCm39) |
C73* |
probably null |
Het |
| Tek |
T |
A |
4: 94,715,922 (GRCm39) |
L448Q |
probably benign |
Het |
| Tmem132a |
A |
C |
19: 10,835,833 (GRCm39) |
L899R |
probably damaging |
Het |
| Txndc5 |
T |
C |
13: 38,711,845 (GRCm39) |
|
probably benign |
Het |
| Uck1 |
C |
A |
2: 32,150,153 (GRCm39) |
|
probably benign |
Het |
| Uggt1 |
A |
G |
1: 36,212,568 (GRCm39) |
S925P |
probably damaging |
Het |
| Unc13d |
A |
T |
11: 115,958,657 (GRCm39) |
D786E |
probably damaging |
Het |
| Vmn1r26 |
T |
C |
6: 57,985,728 (GRCm39) |
T154A |
possibly 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 |
|
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 |
|
|
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'- GAAGACTGCCAACTGAGTCATTTC -3'
(R):5'- CAAACTTTATATGCCCCAGTACAG -3'
Sequencing Primer
(F):5'- CATAACTGGTAAGAAAGCTTTTACCC -3'
(R):5'- GACGTTTGGTATAGCATTGG -3'
|
| Posted On |
2020-10-20 |
Incidental Mutation