Incidental Mutation 'R8725:Sema3d'
| ID |
673170 |
| 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 |
068574-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.188)
|
| Stock # |
R8725 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
5 |
| Chromosomal Location |
12433352-12638915 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 12555822 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Tyrosine
at position 183
(C183Y)
|
| 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: C183Y
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: C183Y
| 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: C183Y
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
AA Change: C183Y
| 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: 100.0%
- 10x: 99.8%
- 20x: 99.5%
|
| 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: 69 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acod1 |
T |
A |
14: 103,287,075 (GRCm39) |
W69R |
probably damaging |
Het |
| Adamtsl4 |
C |
T |
3: 95,584,426 (GRCm39) |
R990Q |
possibly damaging |
Het |
| Ahdc1 |
T |
A |
4: 132,792,743 (GRCm39) |
V1328E |
possibly damaging |
Het |
| Bpifb2 |
A |
G |
2: 153,731,356 (GRCm39) |
H244R |
possibly damaging |
Het |
| Camk1 |
C |
A |
6: 113,315,109 (GRCm39) |
V199L |
probably damaging |
Het |
| Ccdc18 |
A |
T |
5: 108,328,283 (GRCm39) |
K661I |
possibly damaging |
Het |
| Cdh16 |
C |
T |
8: 105,344,874 (GRCm39) |
V444I |
probably benign |
Het |
| Cep295 |
A |
T |
9: 15,243,715 (GRCm39) |
Y1580* |
probably null |
Het |
| Cntnap5c |
A |
T |
17: 58,362,663 (GRCm39) |
N339Y |
probably damaging |
Het |
| Col6a3 |
C |
G |
1: 90,695,328 (GRCm39) |
|
probably benign |
Het |
| Deup1 |
T |
A |
9: 15,503,721 (GRCm39) |
D280V |
probably damaging |
Het |
| Dlat |
G |
T |
9: 50,560,967 (GRCm39) |
A360E |
probably damaging |
Het |
| Evpl |
T |
A |
11: 116,113,019 (GRCm39) |
D1557V |
probably benign |
Het |
| Ext1 |
A |
G |
15: 53,208,065 (GRCm39) |
V232A |
possibly damaging |
Het |
| Gdpd5 |
T |
C |
7: 99,105,726 (GRCm39) |
I514T |
possibly damaging |
Het |
| Gm14443 |
A |
T |
2: 175,010,693 (GRCm39) |
C584* |
probably null |
Het |
| Gm2696 |
T |
A |
10: 77,672,034 (GRCm39) |
C78S |
unknown |
Het |
| Gm4131 |
T |
C |
14: 62,701,300 (GRCm39) |
D276G |
possibly damaging |
Het |
| Gm5114 |
C |
T |
7: 39,060,657 (GRCm39) |
G64D |
probably benign |
Het |
| Gsx2 |
G |
T |
5: 75,236,755 (GRCm39) |
A112S |
probably benign |
Het |
| Hebp1 |
G |
T |
6: 135,114,919 (GRCm39) |
R181S |
probably damaging |
Het |
| Hectd4 |
G |
A |
5: 121,488,557 (GRCm39) |
G3616D |
probably damaging |
Het |
| Hemgn |
T |
G |
4: 46,394,638 (GRCm39) |
T491P |
probably benign |
Het |
| Idh2 |
TCCCAGGGCC |
TCC |
7: 79,748,079 (GRCm39) |
|
probably null |
Het |
| Itsn1 |
T |
C |
16: 91,636,721 (GRCm39) |
S723P |
unknown |
Het |
| Kat6a |
G |
A |
8: 23,398,293 (GRCm39) |
G287D |
probably damaging |
Het |
| Ktn1 |
T |
G |
14: 47,907,757 (GRCm39) |
|
probably benign |
Het |
| Lrrc56 |
C |
A |
7: 140,778,246 (GRCm39) |
D79E |
possibly damaging |
Het |
| Lrrn1 |
C |
T |
6: 107,544,303 (GRCm39) |
Q34* |
probably null |
Het |
| Mlxipl |
A |
G |
5: 135,157,483 (GRCm39) |
M340V |
probably benign |
Het |
| Mroh6 |
T |
C |
15: 75,756,563 (GRCm39) |
T604A |
possibly damaging |
Het |
| Or13a26 |
G |
T |
7: 140,284,607 (GRCm39) |
V148L |
probably benign |
Het |
| Or1n1 |
T |
A |
2: 36,749,610 (GRCm39) |
Y250F |
probably damaging |
Het |
| Or4c122 |
A |
T |
2: 89,079,658 (GRCm39) |
S115T |
probably benign |
Het |
| Palb2 |
A |
C |
7: 121,710,884 (GRCm39) |
V1022G |
unknown |
Het |
| Pank1 |
T |
G |
19: 34,855,989 (GRCm39) |
H163P |
possibly damaging |
Het |
| Pcdha12 |
A |
G |
18: 37,154,736 (GRCm39) |
Q485R |
probably benign |
Het |
| Pcdhb15 |
T |
A |
18: 37,608,734 (GRCm39) |
S655R |
probably damaging |
Het |
| Pcdhgb1 |
T |
A |
18: 37,814,467 (GRCm39) |
C319* |
probably null |
Het |
| Pipox |
A |
T |
11: 77,774,804 (GRCm39) |
L93* |
probably null |
Het |
| Pkd1l1 |
A |
C |
11: 8,911,482 (GRCm39) |
V265G |
|
Het |
| Pld3 |
G |
A |
7: 27,239,079 (GRCm39) |
Q149* |
probably null |
Het |
| Pramel34 |
A |
T |
5: 93,784,316 (GRCm39) |
Y383N |
probably damaging |
Het |
| Prpf3 |
T |
A |
3: 95,748,021 (GRCm39) |
T415S |
possibly damaging |
Het |
| Rasgef1b |
G |
A |
5: 99,447,895 (GRCm39) |
T105I |
unknown |
Het |
| Rere |
G |
T |
4: 150,701,792 (GRCm39) |
E24* |
probably null |
Het |
| Rftn1 |
G |
T |
17: 50,354,408 (GRCm39) |
A318D |
probably damaging |
Het |
| Ric3 |
A |
T |
7: 108,637,924 (GRCm39) |
D277E |
probably benign |
Het |
| Rnf44 |
A |
T |
13: 54,831,826 (GRCm39) |
M82K |
probably damaging |
Het |
| Rsph14 |
T |
C |
10: 74,795,516 (GRCm39) |
N223S |
probably benign |
Het |
| Rusc2 |
A |
G |
4: 43,415,396 (GRCm39) |
E234G |
probably damaging |
Het |
| Scfd2 |
T |
C |
5: 74,642,900 (GRCm39) |
N349S |
probably benign |
Het |
| Setd2 |
T |
C |
9: 110,402,912 (GRCm39) |
I74T |
|
Het |
| Slc39a12 |
T |
C |
2: 14,454,670 (GRCm39) |
S563P |
probably damaging |
Het |
| Slc9a8 |
A |
T |
2: 167,315,454 (GRCm39) |
D526V |
probably damaging |
Het |
| Smpdl3b |
G |
T |
4: 132,461,060 (GRCm39) |
T339N |
probably damaging |
Het |
| Speer1e |
A |
T |
5: 11,236,408 (GRCm39) |
Q147L |
probably benign |
Het |
| Spi1 |
G |
A |
2: 90,945,516 (GRCm39) |
G199D |
probably damaging |
Het |
| Stx2 |
T |
C |
5: 129,070,564 (GRCm39) |
T118A |
probably damaging |
Het |
| Synj2 |
C |
A |
17: 6,088,015 (GRCm39) |
S1355R |
possibly damaging |
Het |
| Taf15 |
A |
G |
11: 83,389,964 (GRCm39) |
T245A |
probably benign |
Het |
| Tnrc6b |
C |
T |
15: 80,760,653 (GRCm39) |
A120V |
probably damaging |
Het |
| Usp19 |
G |
T |
9: 108,370,934 (GRCm39) |
G198W |
probably damaging |
Het |
| Wdtc1 |
G |
T |
4: 133,041,114 (GRCm39) |
H46N |
probably damaging |
Het |
| Zbtb1 |
C |
A |
12: 76,432,646 (GRCm39) |
R211S |
probably damaging |
Het |
| Zc3h8 |
A |
G |
2: 128,775,207 (GRCm39) |
V151A |
probably benign |
Het |
| Zfp219 |
T |
C |
14: 52,244,899 (GRCm39) |
T499A |
possibly damaging |
Het |
| Zfp689 |
A |
G |
7: 127,047,940 (GRCm39) |
F31L |
probably damaging |
Het |
| Zfp879 |
C |
T |
11: 50,729,321 (GRCm39) |
D26N |
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 |
|
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 |
|
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'- TGCAGATGCTGTGTGCTCAG -3'
(R):5'- ACATGCAGGAATGCTGTCACC -3'
Sequencing Primer
(F):5'- CTGTGTGCTCAGTTCATTTTTATAGC -3'
(R):5'- GTTCATATAGTGAGGCTGGTACCAAC -3'
|
| Posted On |
2021-04-30 |
Incidental Mutation