Incidental Mutation 'R0055:Sema3a'
| ID |
58957 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sema3a
|
| Ensembl Gene |
ENSMUSG00000028883 |
| Gene Name |
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A |
| Synonyms |
Semad, collapsin-1, SemD, sema III, semaphorin III |
| MMRRC Submission |
038349-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.947)
|
| Stock # |
R0055 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
13175381-13652533 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 13450004 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Isoleucine
at position 27
(N27I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000122621
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030714]
[ENSMUST00000095012]
[ENSMUST00000125629]
[ENSMUST00000137798]
[ENSMUST00000141968]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000030714
AA Change: N27I
PolyPhen 2
Score 0.034 (Sensitivity: 0.95; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000030714
Gene: ENSMUSG00000028883
AA Change: N27I
| Domain | Start | End | E-Value | Type |
|---|
|
Sema
|
57 |
498 |
4.09e-219 |
SMART |
|
PSI
|
516 |
568 |
3.03e-12 |
SMART |
|
IG
|
583 |
669 |
3.54e-4 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000095012
AA Change: N27I
PolyPhen 2
Score 0.034 (Sensitivity: 0.95; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000092621
Gene: ENSMUSG00000028883
AA Change: N27I
| Domain | Start | End | E-Value | Type |
|---|
|
Sema
|
57 |
498 |
4.09e-219 |
SMART |
|
PSI
|
516 |
568 |
3.03e-12 |
SMART |
|
IG
|
583 |
669 |
3.54e-4 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000125629
AA Change: N27I
PolyPhen 2
Score 0.034 (Sensitivity: 0.95; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000121710
Gene: ENSMUSG00000028883
AA Change: N27I
| Domain | Start | End | E-Value | Type |
|---|
|
PDB:4GZA|G
|
20 |
72 |
1e-30 |
PDB |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000137798
AA Change: N27I
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000128153
Gene: ENSMUSG00000028883
AA Change: N27I
| Domain | Start | End | E-Value | Type |
|---|
|
Sema
|
57 |
498 |
4.09e-219 |
SMART |
|
PSI
|
516 |
568 |
3.03e-12 |
SMART |
|
IG
|
583 |
669 |
3.54e-4 |
SMART |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000141968
AA Change: N27I
PolyPhen 2
Score 0.921 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000122621
Gene: ENSMUSG00000028883
AA Change: N27I
| Domain | Start | End | E-Value | Type |
|---|
|
PDB:4GZA|G
|
20 |
62 |
3e-23 |
PDB |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000195907
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000200073
|
| Meta Mutation Damage Score |
0.2189 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.9%
- 10x: 97.6%
- 20x: 95.6%
|
| Validation Efficiency |
98% (59/60) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the semaphorin family and encodes a protein with an Ig-like C2-type (immunoglobulin-like) domain, a PSI domain and a Sema domain. This secreted protein can function as either a chemorepulsive agent, inhibiting axonal outgrowth, or as a chemoattractive agent, stimulating the growth of apical dendrites. In both cases, the protein is vital for normal neuronal pattern development. Increased expression of this protein is associated with schizophrenia and is seen in a variety of human tumor cell lines. Also, aberrant release of this protein is associated with the progression of Alzheimer's disease. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations exhibit patterning abnormalities of sensory and sympathetic neurons, abnormal embryonic bones and cartilaginous structures, cardiac defects, and high postnatal mortality. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A2ml1 |
T |
C |
6: 128,547,057 (GRCm39) |
|
probably benign |
Het |
| Atp6v1h |
A |
T |
1: 5,154,677 (GRCm39) |
T2S |
probably benign |
Het |
| Bcl11b |
G |
A |
12: 107,932,036 (GRCm39) |
P179S |
probably benign |
Het |
| Cacna1a |
C |
T |
8: 85,306,687 (GRCm39) |
|
probably benign |
Het |
| Ccdc146 |
C |
T |
5: 21,502,004 (GRCm39) |
|
probably null |
Het |
| Ccdc61 |
T |
C |
7: 18,626,461 (GRCm39) |
D128G |
probably damaging |
Het |
| Cd55 |
A |
G |
1: 130,387,313 (GRCm39) |
|
probably benign |
Het |
| Cdk7 |
C |
A |
13: 100,855,812 (GRCm39) |
E99* |
probably null |
Het |
| Cfap96 |
A |
T |
8: 46,421,198 (GRCm39) |
S108R |
probably damaging |
Het |
| Cox8a |
A |
T |
19: 7,194,874 (GRCm39) |
S2T |
probably damaging |
Het |
| Cracdl |
A |
C |
1: 37,663,337 (GRCm39) |
S854A |
probably benign |
Het |
| Dennd5a |
A |
G |
7: 109,498,998 (GRCm39) |
I955T |
possibly damaging |
Het |
| Dop1a |
A |
C |
9: 86,394,705 (GRCm39) |
E602A |
probably benign |
Het |
| Ephx4 |
T |
C |
5: 107,560,944 (GRCm39) |
L32S |
probably damaging |
Het |
| Fbxo21 |
T |
A |
5: 118,138,555 (GRCm39) |
D493E |
probably benign |
Het |
| Frmd4b |
A |
T |
6: 97,300,610 (GRCm39) |
|
probably benign |
Het |
| Fzd1 |
A |
T |
5: 4,806,037 (GRCm39) |
M515K |
possibly damaging |
Het |
| Gli2 |
A |
G |
1: 118,818,138 (GRCm39) |
|
probably benign |
Het |
| Gm12887 |
T |
A |
4: 121,473,666 (GRCm39) |
K61N |
probably damaging |
Het |
| Grin2a |
A |
T |
16: 9,487,671 (GRCm39) |
V409D |
probably damaging |
Het |
| Grin2b |
T |
C |
6: 135,900,201 (GRCm39) |
I227V |
probably benign |
Het |
| Helz2 |
T |
G |
2: 180,870,614 (GRCm39) |
D2879A |
possibly damaging |
Het |
| Itpr2 |
T |
C |
6: 146,224,631 (GRCm39) |
N1453S |
probably benign |
Het |
| Itpr3 |
C |
A |
17: 27,317,296 (GRCm39) |
S817Y |
probably damaging |
Het |
| Lin7c |
T |
A |
2: 109,726,798 (GRCm39) |
|
probably benign |
Het |
| Ly75 |
T |
C |
2: 60,152,262 (GRCm39) |
E1097G |
probably benign |
Het |
| Mcm10 |
T |
C |
2: 4,996,218 (GRCm39) |
N882D |
probably damaging |
Het |
| Mettl13 |
A |
T |
1: 162,373,750 (GRCm39) |
L167Q |
probably damaging |
Het |
| Morn2 |
A |
T |
17: 80,602,942 (GRCm39) |
M1L |
probably benign |
Het |
| Mybph |
G |
T |
1: 134,121,590 (GRCm39) |
V88L |
probably damaging |
Het |
| Nefm |
T |
A |
14: 68,358,648 (GRCm39) |
|
probably benign |
Het |
| Nf1 |
A |
G |
11: 79,362,377 (GRCm39) |
E1497G |
probably damaging |
Het |
| Or2j3 |
T |
C |
17: 38,615,702 (GRCm39) |
S217G |
possibly damaging |
Het |
| Or4k37 |
T |
A |
2: 111,158,870 (GRCm39) |
Y35* |
probably null |
Het |
| Or51ah3 |
A |
G |
7: 103,210,244 (GRCm39) |
K187E |
probably damaging |
Het |
| Or52e18 |
T |
A |
7: 104,609,703 (GRCm39) |
T79S |
possibly damaging |
Het |
| Phf8-ps |
A |
T |
17: 33,285,696 (GRCm39) |
W369R |
probably damaging |
Het |
| Plcd3 |
C |
G |
11: 102,968,411 (GRCm39) |
W382S |
probably damaging |
Het |
| Plxna1 |
T |
A |
6: 89,306,721 (GRCm39) |
I1370F |
possibly damaging |
Het |
| Qng1 |
T |
C |
13: 58,531,980 (GRCm39) |
D192G |
probably damaging |
Het |
| Rarb |
G |
A |
14: 16,509,066 (GRCm38) |
R106C |
probably damaging |
Het |
| Rps6ka5 |
G |
A |
12: 100,644,839 (GRCm39) |
T37I |
probably damaging |
Het |
| Runx1 |
G |
T |
16: 92,441,029 (GRCm39) |
|
probably benign |
Het |
| Scube1 |
A |
G |
15: 83,518,937 (GRCm39) |
V301A |
probably damaging |
Het |
| Slc15a3 |
G |
T |
19: 10,820,406 (GRCm39) |
E8* |
probably null |
Het |
| Slc22a5 |
T |
C |
11: 53,782,032 (GRCm39) |
S112G |
probably benign |
Het |
| Slc25a45 |
T |
C |
19: 5,930,495 (GRCm39) |
F3L |
probably damaging |
Het |
| Slc4a4 |
A |
C |
5: 89,304,195 (GRCm39) |
H502P |
possibly damaging |
Het |
| Slfn10-ps |
A |
G |
11: 82,921,126 (GRCm39) |
|
noncoding transcript |
Het |
| Slit2 |
C |
A |
5: 48,439,068 (GRCm39) |
C1077* |
probably null |
Het |
| Spn |
A |
G |
7: 126,735,494 (GRCm39) |
F82L |
possibly damaging |
Het |
| Tbccd1 |
A |
G |
16: 22,660,655 (GRCm39) |
W54R |
probably damaging |
Het |
| Ucp1 |
G |
T |
8: 84,017,233 (GRCm39) |
E8* |
probably null |
Het |
| Unc80 |
A |
T |
1: 66,545,782 (GRCm39) |
|
probably benign |
Het |
| Vsnl1 |
A |
T |
12: 11,436,987 (GRCm39) |
|
probably null |
Het |
| Zdhhc11 |
C |
T |
13: 74,130,805 (GRCm39) |
Q295* |
probably null |
Het |
| Zfp457 |
T |
A |
13: 67,442,098 (GRCm39) |
H63L |
probably damaging |
Het |
|
| Other mutations in Sema3a |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01022:Sema3a
|
APN |
5 |
13,523,433 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01783:Sema3a
|
APN |
5 |
13,611,767 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02423:Sema3a
|
APN |
5 |
13,615,776 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02728:Sema3a
|
APN |
5 |
13,615,881 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02739:Sema3a
|
APN |
5 |
13,501,128 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02987:Sema3a
|
APN |
5 |
13,615,863 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03106:Sema3a
|
APN |
5 |
13,649,456 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0334:Sema3a
|
UTSW |
5 |
13,607,268 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0684:Sema3a
|
UTSW |
5 |
13,606,494 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R0750:Sema3a
|
UTSW |
5 |
13,607,092 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1204:Sema3a
|
UTSW |
5 |
13,573,142 (GRCm39) |
critical splice donor site |
probably benign |
|
|
R1221:Sema3a
|
UTSW |
5 |
13,566,190 (GRCm39) |
missense |
probably benign |
|
|
R1484:Sema3a
|
UTSW |
5 |
13,523,407 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1663:Sema3a
|
UTSW |
5 |
13,607,092 (GRCm39) |
critical splice donor site |
probably null |
|
|
R2079:Sema3a
|
UTSW |
5 |
13,501,098 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R4165:Sema3a
|
UTSW |
5 |
13,523,364 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R4596:Sema3a
|
UTSW |
5 |
13,620,125 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4867:Sema3a
|
UTSW |
5 |
13,501,208 (GRCm39) |
missense |
probably benign |
0.05 |
|
R4904:Sema3a
|
UTSW |
5 |
13,631,066 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5107:Sema3a
|
UTSW |
5 |
13,627,572 (GRCm39) |
nonsense |
probably null |
|
|
R5327:Sema3a
|
UTSW |
5 |
13,649,357 (GRCm39) |
missense |
probably benign |
0.25 |
|
R5343:Sema3a
|
UTSW |
5 |
13,523,373 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5430:Sema3a
|
UTSW |
5 |
13,615,730 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5604:Sema3a
|
UTSW |
5 |
13,523,487 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5774:Sema3a
|
UTSW |
5 |
13,573,131 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6057:Sema3a
|
UTSW |
5 |
13,615,832 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6110:Sema3a
|
UTSW |
5 |
13,630,969 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6132:Sema3a
|
UTSW |
5 |
13,573,142 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6310:Sema3a
|
UTSW |
5 |
13,606,986 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6754:Sema3a
|
UTSW |
5 |
13,649,243 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R6788:Sema3a
|
UTSW |
5 |
13,647,584 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R6878:Sema3a
|
UTSW |
5 |
13,505,511 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R7411:Sema3a
|
UTSW |
5 |
13,566,230 (GRCm39) |
nonsense |
probably null |
|
|
R7501:Sema3a
|
UTSW |
5 |
13,607,008 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7514:Sema3a
|
UTSW |
5 |
13,573,093 (GRCm39) |
missense |
probably benign |
0.03 |
|
R7531:Sema3a
|
UTSW |
5 |
13,615,805 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7538:Sema3a
|
UTSW |
5 |
13,611,787 (GRCm39) |
missense |
probably benign |
0.42 |
|
R7970:Sema3a
|
UTSW |
5 |
13,649,375 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R8121:Sema3a
|
UTSW |
5 |
13,649,215 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8283:Sema3a
|
UTSW |
5 |
13,450,030 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8434:Sema3a
|
UTSW |
5 |
13,523,487 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8918:Sema3a
|
UTSW |
5 |
13,573,099 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9500:Sema3a
|
UTSW |
5 |
13,615,854 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
X0064:Sema3a
|
UTSW |
5 |
13,631,066 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGAACTTCTCTGGCCGCACAATAC -3'
(R):5'- AGGGAAACACAGTCTTTTCGCCATC -3'
Sequencing Primer
(F):5'- TGGCCGCACAATACAGGAAG -3'
(R):5'- GCGTACAACTAAGGAGATACTGTTC -3'
|
| Posted On |
2013-07-11 |
Incidental Mutation