Incidental Mutation 'R0157:Sema3d'
| ID |
22905 |
| 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 |
038437-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.188)
|
| Stock # |
R0157 (G1)
|
| Quality Score |
218 |
|
Status
|
Validated
(trace)
|
| Chromosome |
5 |
| Chromosomal Location |
12433352-12638915 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 12558104 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Valine
at position 212
(D212V)
|
| 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: D212V
PolyPhen 2
Score 0.872 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: D212V
| 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: ENSMUST00000196093
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000196618
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000197927
AA Change: D212V
PolyPhen 2
Score 0.946 (Sensitivity: 0.80; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
AA Change: D212V
| 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 |
0.8343 |
| Coding Region Coverage |
- 1x: 98.9%
- 3x: 97.9%
- 10x: 95.0%
- 20x: 88.5%
|
| Validation Efficiency |
64% (47/73) |
| 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: 71 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adap2 |
T |
A |
11: 80,056,527 (GRCm39) |
I180N |
probably damaging |
Het |
| Alk |
T |
A |
17: 72,256,840 (GRCm39) |
N673I |
probably benign |
Het |
| Ankrd7 |
T |
C |
6: 18,866,539 (GRCm39) |
S20P |
probably damaging |
Het |
| Arhgef26 |
T |
G |
3: 62,288,392 (GRCm39) |
D487E |
probably damaging |
Het |
| Arhgef4 |
A |
G |
1: 34,845,475 (GRCm39) |
D1500G |
probably damaging |
Het |
| Arhgef7 |
A |
G |
8: 11,835,812 (GRCm39) |
I39V |
probably damaging |
Het |
| Asap2 |
T |
A |
12: 21,256,326 (GRCm39) |
I208N |
probably damaging |
Het |
| Atad5 |
T |
C |
11: 79,980,643 (GRCm39) |
V16A |
possibly damaging |
Het |
| Atp2b1 |
T |
C |
10: 98,835,809 (GRCm39) |
I518T |
probably damaging |
Het |
| B130006D01Rik |
T |
C |
11: 95,617,211 (GRCm39) |
|
probably benign |
Het |
| BC028528 |
A |
G |
3: 95,792,280 (GRCm39) |
|
probably null |
Het |
| Bpifb6 |
T |
A |
2: 153,745,886 (GRCm39) |
L74Q |
probably benign |
Het |
| Bptf |
T |
C |
11: 106,965,484 (GRCm39) |
T1122A |
possibly damaging |
Het |
| Cacna2d4 |
T |
A |
6: 119,289,385 (GRCm39) |
D806E |
probably benign |
Het |
| Cdhr3 |
T |
C |
12: 33,111,649 (GRCm39) |
Q287R |
possibly damaging |
Het |
| Cdk12 |
A |
G |
11: 98,140,602 (GRCm39) |
|
probably benign |
Het |
| Cenpf |
T |
A |
1: 189,384,556 (GRCm39) |
T2575S |
probably benign |
Het |
| Chd7 |
T |
A |
4: 8,833,759 (GRCm39) |
I1171N |
probably damaging |
Het |
| Chd9 |
T |
C |
8: 91,735,464 (GRCm39) |
|
probably null |
Het |
| Ckmt1 |
A |
G |
2: 121,193,522 (GRCm39) |
T361A |
possibly damaging |
Het |
| Clec4d |
G |
T |
6: 123,244,095 (GRCm39) |
R68L |
probably benign |
Het |
| Csmd2 |
G |
T |
4: 128,415,704 (GRCm39) |
V2678F |
probably benign |
Het |
| Cul7 |
T |
A |
17: 46,964,761 (GRCm39) |
V131E |
possibly damaging |
Het |
| Dab2 |
T |
C |
15: 6,459,308 (GRCm39) |
S407P |
probably benign |
Het |
| Dnah17 |
C |
T |
11: 118,017,997 (GRCm39) |
G166D |
probably benign |
Het |
| F13b |
G |
A |
1: 139,431,585 (GRCm39) |
V52I |
probably benign |
Het |
| Gjd4 |
T |
C |
18: 9,280,549 (GRCm39) |
I176M |
probably benign |
Het |
| Hoxc11 |
A |
G |
15: 102,863,436 (GRCm39) |
Y159C |
probably damaging |
Het |
| Hydin |
T |
C |
8: 111,026,642 (GRCm39) |
I120T |
possibly damaging |
Het |
| Il20rb |
A |
G |
9: 100,355,132 (GRCm39) |
Y104H |
probably damaging |
Het |
| Krtap21-1 |
A |
G |
16: 89,200,430 (GRCm39) |
C71R |
unknown |
Het |
| Lamc1 |
T |
C |
1: 153,138,353 (GRCm39) |
D167G |
probably benign |
Het |
| Lin7c |
C |
A |
2: 109,725,514 (GRCm39) |
A73E |
probably damaging |
Het |
| Meiosin |
T |
C |
7: 18,840,945 (GRCm39) |
H63R |
possibly damaging |
Het |
| Mms22l |
C |
A |
4: 24,588,224 (GRCm39) |
A952E |
probably damaging |
Het |
| Myh3 |
A |
G |
11: 66,973,735 (GRCm39) |
N136S |
probably benign |
Het |
| Ndufb10 |
T |
C |
17: 24,943,218 (GRCm39) |
T31A |
probably benign |
Het |
| Nlrp2 |
T |
C |
7: 5,311,769 (GRCm39) |
Y37C |
possibly damaging |
Het |
| Or2t44 |
T |
C |
11: 58,677,885 (GRCm39) |
F275S |
probably damaging |
Het |
| Or2y14 |
T |
C |
11: 49,404,600 (GRCm39) |
I45T |
probably damaging |
Het |
| Orc3 |
C |
A |
4: 34,607,130 (GRCm39) |
|
probably null |
Het |
| Pard3b |
A |
C |
1: 62,250,792 (GRCm39) |
M512L |
probably damaging |
Het |
| Pcdh10 |
A |
G |
3: 45,334,136 (GRCm39) |
D150G |
probably damaging |
Het |
| Pcolce |
A |
T |
5: 137,608,741 (GRCm39) |
|
probably null |
Het |
| Pdcl |
A |
C |
2: 37,242,189 (GRCm39) |
I187S |
probably damaging |
Het |
| Pkn1 |
T |
C |
8: 84,419,449 (GRCm39) |
I51M |
probably damaging |
Het |
| Pla2g4e |
T |
A |
2: 120,000,662 (GRCm39) |
T692S |
probably benign |
Het |
| Plcb2 |
C |
A |
2: 118,549,022 (GRCm39) |
V380F |
probably damaging |
Het |
| Pmpcb |
A |
T |
5: 21,947,950 (GRCm39) |
I218F |
probably damaging |
Het |
| Pms1 |
A |
T |
1: 53,234,196 (GRCm39) |
Y773* |
probably null |
Het |
| Polr2e |
C |
T |
10: 79,872,615 (GRCm39) |
G184R |
probably damaging |
Het |
| Polr3a |
T |
C |
14: 24,529,254 (GRCm39) |
I369V |
probably damaging |
Het |
| Pramel21 |
C |
T |
4: 143,342,366 (GRCm39) |
P158S |
probably damaging |
Het |
| Prpf4b |
T |
C |
13: 35,068,014 (GRCm39) |
|
probably benign |
Het |
| Pzp |
G |
A |
6: 128,500,939 (GRCm39) |
Q140* |
probably null |
Het |
| Qrich2 |
T |
A |
11: 116,332,221 (GRCm39) |
E2325V |
probably damaging |
Het |
| R3hdm2 |
T |
G |
10: 127,307,858 (GRCm39) |
L373R |
probably damaging |
Het |
| Sidt2 |
A |
G |
9: 45,850,565 (GRCm39) |
I850T |
probably damaging |
Het |
| Slc22a29 |
C |
T |
19: 8,140,106 (GRCm39) |
R433H |
possibly damaging |
Het |
| Slitrk6 |
A |
T |
14: 110,987,364 (GRCm39) |
L781H |
probably damaging |
Het |
| Sox21 |
G |
A |
14: 118,473,354 (GRCm39) |
|
probably benign |
Het |
| Steap3 |
A |
G |
1: 120,155,379 (GRCm39) |
*527R |
probably null |
Het |
| Svep1 |
T |
C |
4: 58,069,830 (GRCm39) |
E2652G |
possibly damaging |
Het |
| Taar2 |
T |
A |
10: 23,817,389 (GRCm39) |
F310I |
probably damaging |
Het |
| Tasor2 |
C |
A |
13: 3,625,550 (GRCm39) |
V1467L |
probably benign |
Het |
| Tecta |
A |
G |
9: 42,286,307 (GRCm39) |
V783A |
probably benign |
Het |
| Vmn1r173 |
T |
A |
7: 23,401,822 (GRCm39) |
I19N |
probably damaging |
Het |
| Vwa5b1 |
T |
A |
4: 138,332,190 (GRCm39) |
M276L |
probably benign |
Het |
| Yeats2 |
A |
C |
16: 20,040,427 (GRCm39) |
*142C |
probably null |
Het |
| Zfp26 |
G |
T |
9: 20,349,166 (GRCm39) |
T466K |
probably benign |
Het |
| Zfp426 |
T |
C |
9: 20,382,432 (GRCm39) |
N171S |
probably benign |
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 |
|
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 |
|
|
| Predicted Primers |
PCR Primer
(F):5'- AGCAAATACGGATTTCACTATCCAGCTT -3'
(R):5'- AGCTGAAACGCTGGCTCTATATCTGAT -3'
Sequencing Primer
(F):5'- GGATTTCACTATCCAGCTTTTTAGG -3'
(R):5'- cacacacacacacacacac -3'
|
| Posted On |
2013-04-16 |
Incidental Mutation