Incidental Mutation 'R9389:Sema5b'
| ID |
710509 |
| 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 |
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R9389 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
16 |
| Chromosomal Location |
35361517-35485103 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to C
at 35466092 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamine to Proline
at position 125
(Q125P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000112536
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000050625]
[ENSMUST00000120756]
|
| AlphaFold |
Q60519 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000050625
AA Change: Q125P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000057494
Gene: ENSMUSG00000052133
AA Change: Q125P
| 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 damaging
Transcript: ENSMUST00000120756
AA Change: Q125P
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000112536
Gene: ENSMUSG00000052133
AA Change: Q125P
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.0%
|
| Validation Efficiency |
100% (55/55) |
| 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: 56 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb1b |
G |
A |
5: 8,875,614 (GRCm39) |
V596I |
probably benign |
Het |
| Agtpbp1 |
A |
T |
13: 59,613,884 (GRCm39) |
M1019K |
probably damaging |
Het |
| Arfgef3 |
A |
G |
10: 18,479,271 (GRCm39) |
V1448A |
probably damaging |
Het |
| Baz1a |
T |
A |
12: 54,963,608 (GRCm39) |
E828D |
probably damaging |
Het |
| Ces1f |
A |
T |
8: 93,996,600 (GRCm39) |
|
probably null |
Het |
| Cfap53 |
T |
A |
18: 74,432,414 (GRCm39) |
|
probably null |
Het |
| Col6a4 |
T |
C |
9: 105,877,983 (GRCm39) |
Y1998C |
probably damaging |
Het |
| Col9a2 |
A |
G |
4: 120,911,948 (GRCm39) |
T675A |
probably benign |
Het |
| Dusp6 |
G |
A |
10: 99,099,839 (GRCm39) |
V96M |
possibly damaging |
Het |
| Elmo1 |
T |
G |
13: 20,369,661 (GRCm39) |
M22R |
probably benign |
Het |
| Fem1al |
A |
G |
11: 29,775,107 (GRCm39) |
S117P |
probably damaging |
Het |
| Gm19965 |
A |
G |
1: 116,749,566 (GRCm39) |
N416D |
|
Het |
| Gpr162 |
A |
G |
6: 124,838,357 (GRCm39) |
Y98H |
probably damaging |
Het |
| Igfals |
G |
A |
17: 25,100,600 (GRCm39) |
V564I |
probably benign |
Het |
| Il4 |
C |
T |
11: 53,504,837 (GRCm39) |
R76H |
probably damaging |
Het |
| Itgb1 |
T |
A |
8: 129,433,637 (GRCm39) |
N50K |
probably benign |
Het |
| Itpr3 |
A |
T |
17: 27,314,899 (GRCm39) |
Y682F |
possibly damaging |
Het |
| Jak3 |
C |
T |
8: 72,136,696 (GRCm39) |
P668S |
probably damaging |
Het |
| Malrd1 |
A |
T |
2: 15,707,967 (GRCm39) |
N932I |
unknown |
Het |
| Mast4 |
C |
A |
13: 103,470,438 (GRCm39) |
R88L |
probably benign |
Het |
| Mfsd11 |
T |
G |
11: 116,764,161 (GRCm39) |
S381A |
probably benign |
Het |
| Mrm3 |
A |
G |
11: 76,140,856 (GRCm39) |
D288G |
probably damaging |
Het |
| Myg1 |
G |
T |
15: 102,245,372 (GRCm39) |
V198F |
probably damaging |
Het |
| Naip5 |
T |
A |
13: 100,356,338 (GRCm39) |
E1092D |
probably benign |
Het |
| Npy6r |
T |
C |
18: 44,408,759 (GRCm39) |
I60T |
probably damaging |
Het |
| Or12j3 |
T |
C |
7: 139,952,930 (GRCm39) |
T198A |
probably benign |
Het |
| Or13p3 |
A |
T |
4: 118,567,353 (GRCm39) |
M250L |
probably benign |
Het |
| Or4f57 |
G |
T |
2: 111,790,872 (GRCm39) |
P182H |
probably damaging |
Het |
| Or5aq6 |
A |
T |
2: 86,923,390 (GRCm39) |
M117K |
possibly damaging |
Het |
| Or5k14 |
C |
T |
16: 58,692,976 (GRCm39) |
C179Y |
probably damaging |
Het |
| Or6c215 |
G |
A |
10: 129,637,540 (GRCm39) |
P285S |
probably damaging |
Het |
| Ovgp1 |
CCACTGGTGTTTCTAAGACCACCACTGGCATTTCTAAGACCATCACTGGTGTTTCTAAGACCACCACTGGCATTTCTAAGACCACCACTGGCATTTCTAAGACCACCACTGGGGTTTCTAAGATCACCACTGGTGTTTCTAAGACCACCACTGGCATTTCTAAGACCA |
CCACTGGTGTTTCTAAGACCACCACTGGCATTTCTAAGACCACCACTGGCATTTCTAAGACCACCACTGGGGTTTCTAAGATCACCACTGGTGTTTCTAAGACCACCACTGGCATTTCTAAGACCA |
3: 105,893,841 (GRCm39) |
|
probably benign |
Het |
| Oxtr |
C |
A |
6: 112,466,310 (GRCm39) |
R150L |
probably damaging |
Het |
| Pappa |
A |
T |
4: 65,099,125 (GRCm39) |
Y548F |
probably damaging |
Het |
| Pip4k2a |
T |
C |
2: 18,912,890 (GRCm39) |
K73R |
probably damaging |
Het |
| Pla2g4f |
T |
A |
2: 120,132,781 (GRCm39) |
D685V |
probably damaging |
Het |
| Ppp1r35 |
T |
A |
5: 137,777,577 (GRCm39) |
L81Q |
probably damaging |
Het |
| Prss3b |
C |
T |
6: 41,010,079 (GRCm39) |
G85D |
probably benign |
Het |
| Ptprf |
C |
A |
4: 118,093,236 (GRCm39) |
A469S |
probably benign |
Het |
| Ranbp3l |
T |
A |
15: 9,057,304 (GRCm39) |
N322K |
probably damaging |
Het |
| Rev3l |
T |
A |
10: 39,698,967 (GRCm39) |
Y1155N |
possibly damaging |
Het |
| Rfesd |
T |
C |
13: 76,151,131 (GRCm39) |
Y96C |
probably damaging |
Het |
| Runx1 |
C |
T |
16: 92,410,568 (GRCm39) |
V283I |
possibly damaging |
Het |
| Skic3 |
A |
G |
13: 76,275,158 (GRCm39) |
D403G |
probably benign |
Het |
| Spef2 |
A |
T |
15: 9,725,307 (GRCm39) |
M150K |
probably damaging |
Het |
| Srcap |
T |
G |
7: 127,141,455 (GRCm39) |
L1745W |
probably damaging |
Het |
| Srgap2 |
A |
G |
1: 131,283,365 (GRCm39) |
Y239H |
probably damaging |
Het |
| Svil |
T |
A |
18: 5,090,811 (GRCm39) |
H1304Q |
possibly damaging |
Het |
| Syne1 |
T |
C |
10: 5,179,193 (GRCm39) |
D4427G |
possibly damaging |
Het |
| Tg |
T |
A |
15: 66,561,173 (GRCm39) |
M1065K |
probably benign |
Het |
| Tgm2 |
T |
C |
2: 157,959,816 (GRCm39) |
T656A |
probably benign |
Het |
| Ubr4 |
A |
G |
4: 139,153,235 (GRCm39) |
K809E |
|
Het |
| Vmn1r88 |
T |
C |
7: 12,912,546 (GRCm39) |
S301P |
probably damaging |
Het |
| Wdr27 |
A |
G |
17: 15,111,980 (GRCm39) |
V671A |
possibly damaging |
Het |
| Zbtb17 |
G |
A |
4: 141,193,131 (GRCm39) |
V550I |
possibly damaging |
Het |
| Zeb2 |
A |
T |
2: 44,887,920 (GRCm39) |
I379N |
probably damaging |
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 |
|
R0905:Sema5b
|
UTSW |
16 |
35,443,001 (GRCm39) |
missense |
probably benign |
0.33 |
|
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 |
|
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'- TCTTGGGGAATCCTTGCGAG -3'
(R):5'- GAGATACATTCTCCACCCATCCTG -3'
Sequencing Primer
(F):5'- AATCCTTGCGAGCATGGG -3'
(R):5'- ACCCATCCTGCTACGTTTGTCAG -3'
|
| Posted On |
2022-04-18 |
Incidental Mutation