Incidental Mutation 'R0905:Sema5b'
| ID |
83306 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sema5b
|
| Ensembl Gene |
ENSMUSG00000052133 |
| Gene Name |
sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B |
| Synonyms |
SemG, SemG, Semag |
| MMRRC Submission |
039063-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R0905 (G1)
|
| Quality Score |
182 |
|
Status
|
Validated
|
| Chromosome |
16 |
| Chromosomal Location |
35361517-35485103 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 35443001 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 2
(V2A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000112536
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000050625]
[ENSMUST00000120756]
|
| AlphaFold |
Q60519 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000050625
AA Change: V2A
PolyPhen 2
Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000057494
Gene: ENSMUSG00000052133
AA Change: V2A
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
Sema
|
68 |
479 |
1.68e-174 |
SMART |
|
PSI
|
497 |
544 |
9.18e-12 |
SMART |
|
TSP1
|
609 |
662 |
3.34e-15 |
SMART |
|
TSP1
|
667 |
713 |
3.42e-12 |
SMART |
|
TSP1
|
798 |
850 |
1.58e-16 |
SMART |
|
TSP1
|
855 |
907 |
2.45e-13 |
SMART |
|
TSP1
|
910 |
957 |
1.02e-1 |
SMART |
|
transmembrane domain
|
977 |
999 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000120756
AA Change: V2A
PolyPhen 2
Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000112536
Gene: ENSMUSG00000052133
AA Change: V2A
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
Sema
|
68 |
479 |
1.68e-174 |
SMART |
|
PSI
|
497 |
544 |
9.18e-12 |
SMART |
|
TSP1
|
609 |
662 |
3.34e-15 |
SMART |
|
TSP1
|
667 |
742 |
7.61e-10 |
SMART |
|
TSP1
|
827 |
879 |
1.58e-16 |
SMART |
|
TSP1
|
884 |
936 |
2.45e-13 |
SMART |
|
TSP1
|
939 |
986 |
1.02e-1 |
SMART |
|
transmembrane domain
|
1006 |
1028 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000133554
|
| Meta Mutation Damage Score |
0.1547 |
| Coding Region Coverage |
- 1x: 99.6%
- 3x: 98.9%
- 10x: 96.9%
- 20x: 92.6%
|
| Validation Efficiency |
100% (42/42) |
| 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 protein family which regulates axon growth during development of the nervous system. The encoded protein has a characteristic Sema domain near the N-terminus, through which semaphorins bind to plexin, and five thrombospondin type 1 repeats in the C-terminal region of the protein. The protein product may be cleaved and exist as a secreted molecule (PMID: 19463192). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
PHENOTYPE: Mice homozygous for a null mutation display defects in neurite arborization of multiple retinal cell types. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 39 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Arhgap21 |
G |
A |
2: 20,854,745 (GRCm39) |
T1539M |
possibly damaging |
Het |
| Birc2 |
A |
T |
9: 7,851,052 (GRCm39) |
*138R |
probably null |
Het |
| Bsn |
C |
A |
9: 107,982,834 (GRCm39) |
D3640Y |
unknown |
Het |
| Bsph1 |
A |
T |
7: 13,184,839 (GRCm39) |
M1L |
probably benign |
Het |
| Cdkl1 |
A |
T |
12: 69,803,338 (GRCm39) |
Y179* |
probably null |
Het |
| Cfap74 |
G |
A |
4: 155,503,153 (GRCm39) |
|
probably null |
Het |
| Crtc1 |
A |
T |
8: 70,843,905 (GRCm39) |
S454T |
probably damaging |
Het |
| Cspg5 |
A |
T |
9: 110,075,594 (GRCm39) |
D110V |
probably damaging |
Het |
| Cyp2w1 |
A |
T |
5: 139,342,194 (GRCm39) |
Y380F |
probably benign |
Het |
| Dbn1 |
T |
C |
13: 55,622,040 (GRCm39) |
|
probably benign |
Het |
| Epb41l4b |
T |
C |
4: 57,103,528 (GRCm39) |
K103E |
probably damaging |
Het |
| Eps8 |
C |
T |
6: 137,491,305 (GRCm39) |
V358I |
probably benign |
Het |
| Gm12253 |
G |
T |
11: 58,330,846 (GRCm39) |
|
probably benign |
Het |
| Hltf |
T |
A |
3: 20,163,033 (GRCm39) |
|
probably null |
Het |
| Hsd17b11 |
C |
T |
5: 104,157,744 (GRCm39) |
V123I |
probably benign |
Het |
| Il31ra |
T |
A |
13: 112,668,207 (GRCm39) |
E481V |
probably damaging |
Het |
| Impdh2 |
A |
G |
9: 108,438,296 (GRCm39) |
|
probably benign |
Het |
| Itih5 |
G |
A |
2: 10,253,999 (GRCm39) |
R750Q |
probably benign |
Het |
| Kndc1 |
A |
C |
7: 139,503,651 (GRCm39) |
K985T |
possibly damaging |
Het |
| Lgr6 |
C |
T |
1: 134,921,748 (GRCm39) |
A199T |
probably damaging |
Het |
| Lgsn |
A |
T |
1: 31,242,824 (GRCm39) |
Y302F |
probably damaging |
Het |
| Lrp1b |
A |
G |
2: 41,174,197 (GRCm39) |
S1541P |
probably damaging |
Het |
| Mast4 |
A |
G |
13: 102,907,292 (GRCm39) |
M528T |
probably damaging |
Het |
| Mzf1 |
C |
A |
7: 12,786,698 (GRCm39) |
R124L |
possibly damaging |
Het |
| Ndufs2 |
T |
C |
1: 171,063,922 (GRCm39) |
|
probably null |
Het |
| Nwd1 |
G |
A |
8: 73,436,077 (GRCm39) |
V1436M |
probably damaging |
Het |
| Phf12 |
C |
T |
11: 77,900,230 (GRCm39) |
R109* |
probably null |
Het |
| Pml |
A |
G |
9: 58,156,822 (GRCm39) |
|
probably null |
Het |
| Ppfia2 |
T |
C |
10: 106,655,372 (GRCm39) |
I313T |
probably benign |
Het |
| Prdm14 |
C |
T |
1: 13,195,662 (GRCm39) |
G133D |
probably benign |
Het |
| Ptgr3 |
A |
G |
18: 84,113,332 (GRCm39) |
H336R |
probably benign |
Het |
| Pygl |
A |
G |
12: 70,257,791 (GRCm39) |
|
probably benign |
Het |
| Rassf10 |
C |
T |
7: 112,554,575 (GRCm39) |
T392M |
probably damaging |
Het |
| Rpe65 |
T |
C |
3: 159,307,220 (GRCm39) |
S54P |
possibly damaging |
Het |
| Sgsm3 |
T |
C |
15: 80,895,546 (GRCm39) |
I699T |
probably damaging |
Het |
| Spn |
T |
C |
7: 126,735,503 (GRCm39) |
T335A |
probably damaging |
Het |
| Tecta |
T |
C |
9: 42,250,290 (GRCm39) |
D1834G |
probably damaging |
Het |
| Trp53bp1 |
C |
A |
2: 121,034,799 (GRCm39) |
|
probably benign |
Het |
| Ttc3 |
A |
T |
16: 94,257,648 (GRCm39) |
K1652* |
probably null |
Het |
|
| Other mutations in Sema5b |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00901:Sema5b
|
APN |
16 |
35,471,685 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01584:Sema5b
|
APN |
16 |
35,465,793 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01859:Sema5b
|
APN |
16 |
35,467,479 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
IGL02195:Sema5b
|
APN |
16 |
35,480,849 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
IGL02346:Sema5b
|
APN |
16 |
35,470,125 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02850:Sema5b
|
APN |
16 |
35,480,885 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL03277:Sema5b
|
APN |
16 |
35,471,682 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R0101:Sema5b
|
UTSW |
16 |
35,483,472 (GRCm39) |
splice site |
probably benign |
|
|
R0368:Sema5b
|
UTSW |
16 |
35,448,470 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0426:Sema5b
|
UTSW |
16 |
35,466,725 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0675:Sema5b
|
UTSW |
16 |
35,480,703 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1163:Sema5b
|
UTSW |
16 |
35,448,466 (GRCm39) |
missense |
probably benign |
0.19 |
|
R1195:Sema5b
|
UTSW |
16 |
35,472,030 (GRCm39) |
missense |
probably null |
0.94 |
|
R1195:Sema5b
|
UTSW |
16 |
35,472,030 (GRCm39) |
missense |
probably null |
0.94 |
|
R1666:Sema5b
|
UTSW |
16 |
35,478,852 (GRCm39) |
missense |
probably benign |
0.03 |
|
R1706:Sema5b
|
UTSW |
16 |
35,470,125 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1733:Sema5b
|
UTSW |
16 |
35,466,737 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1775:Sema5b
|
UTSW |
16 |
35,480,694 (GRCm39) |
missense |
probably benign |
|
|
R2215:Sema5b
|
UTSW |
16 |
35,480,585 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2844:Sema5b
|
UTSW |
16 |
35,480,301 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3086:Sema5b
|
UTSW |
16 |
35,443,093 (GRCm39) |
missense |
probably benign |
|
|
R3613:Sema5b
|
UTSW |
16 |
35,480,520 (GRCm39) |
missense |
probably benign |
|
|
R4774:Sema5b
|
UTSW |
16 |
35,483,552 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5743:Sema5b
|
UTSW |
16 |
35,478,846 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5856:Sema5b
|
UTSW |
16 |
35,466,756 (GRCm39) |
nonsense |
probably null |
|
|
R5993:Sema5b
|
UTSW |
16 |
35,466,572 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6248:Sema5b
|
UTSW |
16 |
35,448,377 (GRCm39) |
splice site |
probably null |
|
|
R6420:Sema5b
|
UTSW |
16 |
35,483,516 (GRCm39) |
missense |
probably benign |
0.08 |
|
R6795:Sema5b
|
UTSW |
16 |
35,478,941 (GRCm39) |
nonsense |
probably null |
|
|
R6825:Sema5b
|
UTSW |
16 |
35,448,377 (GRCm39) |
splice site |
probably null |
|
|
R7066:Sema5b
|
UTSW |
16 |
35,471,682 (GRCm39) |
missense |
probably benign |
0.26 |
|
R7244:Sema5b
|
UTSW |
16 |
35,480,915 (GRCm39) |
missense |
probably benign |
|
|
R7446:Sema5b
|
UTSW |
16 |
35,467,573 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7497:Sema5b
|
UTSW |
16 |
35,481,700 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7516:Sema5b
|
UTSW |
16 |
35,471,540 (GRCm39) |
missense |
probably benign |
0.05 |
|
R7878:Sema5b
|
UTSW |
16 |
35,481,996 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7922:Sema5b
|
UTSW |
16 |
35,478,626 (GRCm39) |
frame shift |
probably null |
|
|
R8397:Sema5b
|
UTSW |
16 |
35,471,691 (GRCm39) |
missense |
possibly damaging |
0.59 |
|
R8537:Sema5b
|
UTSW |
16 |
35,471,979 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R8929:Sema5b
|
UTSW |
16 |
35,467,737 (GRCm39) |
intron |
probably benign |
|
|
R9262:Sema5b
|
UTSW |
16 |
35,453,223 (GRCm39) |
missense |
possibly damaging |
0.57 |
|
R9389:Sema5b
|
UTSW |
16 |
35,466,092 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9579:Sema5b
|
UTSW |
16 |
35,467,582 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9623:Sema5b
|
UTSW |
16 |
35,443,121 (GRCm39) |
missense |
possibly damaging |
0.74 |
|
Z1088:Sema5b
|
UTSW |
16 |
35,480,960 (GRCm39) |
missense |
probably damaging |
0.99 |
|
Z1176:Sema5b
|
UTSW |
16 |
35,470,234 (GRCm39) |
missense |
probably benign |
0.01 |
|
Z1176:Sema5b
|
UTSW |
16 |
35,466,643 (GRCm39) |
missense |
probably benign |
0.05 |
|
Z1176:Sema5b
|
UTSW |
16 |
35,448,388 (GRCm39) |
missense |
probably benign |
0.01 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTCTGCACATGACTGCCCACTG -3'
(R):5'- TCTCACCTTCAAAGGCCACGATG -3'
Sequencing Primer
(F):5'- gcccactgccccagttc -3'
(R):5'- AAGGCCACGATGGGGTG -3'
|
| Posted On |
2013-11-08 |
Incidental Mutation