Incidental Mutation 'R2844:Sema5b'
| ID |
251473 |
| 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, Semag, SemG |
| MMRRC Submission |
040437-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R2844 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
16 |
| Chromosomal Location |
35541145-35664732 bp(+) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 35659931 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Serine
at position 656
(N656S)
|
| 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: N656S
PolyPhen 2
Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000057494
Gene: ENSMUSG00000052133
AA Change: N656S
| 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: N656S
PolyPhen 2
Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000112536
Gene: ENSMUSG00000052133
AA Change: N656S
| 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: ENSMUST00000128347
|
| SMART Domains |
Protein: ENSMUSP00000121703
Gene: ENSMUSG00000052133
| Domain | Start | End | E-Value | Type |
|---|
|
TSP1
|
1 |
32 |
8.81e-1 |
SMART |
|
TSP1
|
35 |
82 |
1.02e-1 |
SMART |
|
transmembrane domain
|
102 |
124 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128966
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139805
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149097
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149855
|
| SMART Domains |
Protein: ENSMUSP00000115969
Gene: ENSMUSG00000052133
| Domain | Start | End | E-Value | Type |
|---|
|
TSP1
|
17 |
70 |
3.34e-15 |
SMART |
|
TSP1
|
75 |
121 |
3.42e-12 |
SMART |
|
TSP1
|
206 |
258 |
1.58e-16 |
SMART |
|
TSP1
|
263 |
315 |
2.45e-13 |
SMART |
|
TSP1
|
317 |
364 |
1.02e-1 |
SMART |
|
transmembrane domain
|
384 |
406 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.3703 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.8%
|
| Validation Efficiency |
98% (42/43) |
| 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: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb1a |
A |
T |
5: 8,686,164 |
I186F |
probably benign |
Het |
| Afg3l1 |
T |
C |
8: 123,494,939 |
|
probably benign |
Het |
| Atg4a |
G |
A |
X: 140,992,840 |
E106K |
probably benign |
Het |
| C130079G13Rik |
G |
A |
3: 59,936,409 |
V175I |
probably benign |
Het |
| Ccdc50 |
A |
G |
16: 27,406,729 |
E64G |
probably damaging |
Het |
| Celsr3 |
G |
T |
9: 108,829,308 |
G997W |
probably damaging |
Het |
| Chd8 |
C |
T |
14: 52,204,495 |
E2138K |
possibly damaging |
Het |
| Col19a1 |
C |
T |
1: 24,559,681 |
G77E |
unknown |
Het |
| Fhad1 |
G |
T |
4: 141,904,968 |
Q1287K |
probably benign |
Het |
| Fzr1 |
G |
T |
10: 81,369,418 |
T159K |
probably damaging |
Het |
| Gm10608 |
CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA |
CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA |
9: 119,160,716 |
|
probably null |
Het |
| Gna13 |
T |
C |
11: 109,363,125 |
I51T |
probably damaging |
Het |
| Gorab |
A |
G |
1: 163,396,806 |
|
probably null |
Het |
| Hydin |
T |
C |
8: 110,519,114 |
V2153A |
probably benign |
Het |
| Ints6 |
A |
G |
14: 62,704,826 |
V486A |
probably damaging |
Het |
| Irx2 |
A |
G |
13: 72,631,590 |
K331R |
probably damaging |
Het |
| Lrrc6 |
A |
G |
15: 66,447,676 |
|
probably benign |
Het |
| Mark2 |
T |
C |
19: 7,286,862 |
E116G |
probably damaging |
Het |
| Med14 |
A |
T |
X: 12,683,996 |
H684Q |
probably benign |
Het |
| Olfr384 |
A |
T |
11: 73,603,383 |
T268S |
probably benign |
Het |
| Pde5a |
T |
C |
3: 122,851,708 |
L755P |
probably damaging |
Het |
| Pex14 |
A |
T |
4: 148,963,511 |
I203N |
probably benign |
Het |
| Pi4ka |
T |
C |
16: 17,350,793 |
E691G |
probably damaging |
Het |
| Plekha1 |
G |
T |
7: 130,908,365 |
W280C |
probably damaging |
Het |
| Pnoc |
A |
T |
14: 65,404,835 |
F160I |
probably damaging |
Het |
| Ppfia3 |
C |
A |
7: 45,356,428 |
R348L |
probably damaging |
Het |
| Ppil6 |
A |
T |
10: 41,501,693 |
|
probably benign |
Het |
| Psmd13 |
C |
A |
7: 140,897,740 |
|
probably benign |
Het |
| Psme4 |
T |
C |
11: 30,845,173 |
|
probably benign |
Het |
| Rfx3 |
T |
C |
19: 27,806,786 |
|
probably benign |
Het |
| Rnase11 |
A |
G |
14: 51,049,770 |
L109S |
probably damaging |
Het |
| Rngtt |
A |
G |
4: 33,368,678 |
T404A |
probably benign |
Het |
| Sbf1 |
A |
G |
15: 89,303,218 |
|
probably null |
Het |
| Ssh3 |
T |
C |
19: 4,265,296 |
Y338C |
probably damaging |
Het |
| Tgfbr3l |
A |
G |
8: 4,249,280 |
D49G |
probably damaging |
Het |
| Thbs1 |
C |
T |
2: 118,117,628 |
T423I |
probably benign |
Het |
| Ttc17 |
A |
T |
2: 94,376,074 |
Y243* |
probably null |
Het |
| Zbtb8os |
A |
T |
4: 129,341,516 |
E54D |
probably damaging |
Het |
| Zfp648 |
A |
T |
1: 154,205,135 |
K347* |
probably null |
Het |
| Zfp84 |
T |
G |
7: 29,775,333 |
|
probably null |
Het |
|
| Other mutations in Sema5b |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00901:Sema5b
|
APN |
16 |
35,651,315 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL01584:Sema5b
|
APN |
16 |
35,645,423 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL01859:Sema5b
|
APN |
16 |
35,647,109 (GRCm38) |
missense |
possibly damaging |
0.94 |
|
IGL02195:Sema5b
|
APN |
16 |
35,660,479 (GRCm38) |
critical splice acceptor site |
probably null |
|
|
IGL02346:Sema5b
|
APN |
16 |
35,649,755 (GRCm38) |
missense |
probably damaging |
1.00 |
|
IGL02850:Sema5b
|
APN |
16 |
35,660,515 (GRCm38) |
missense |
probably benign |
0.01 |
|
IGL03277:Sema5b
|
APN |
16 |
35,651,312 (GRCm38) |
missense |
probably damaging |
0.96 |
|
R0101:Sema5b
|
UTSW |
16 |
35,663,102 (GRCm38) |
splice site |
probably benign |
|
|
R0368:Sema5b
|
UTSW |
16 |
35,628,100 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R0426:Sema5b
|
UTSW |
16 |
35,646,355 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R0675:Sema5b
|
UTSW |
16 |
35,660,333 (GRCm38) |
missense |
probably benign |
0.00 |
|
R0905:Sema5b
|
UTSW |
16 |
35,622,631 (GRCm38) |
missense |
probably benign |
0.33 |
|
R1163:Sema5b
|
UTSW |
16 |
35,628,096 (GRCm38) |
missense |
probably benign |
0.19 |
|
R1195:Sema5b
|
UTSW |
16 |
35,651,660 (GRCm38) |
missense |
probably null |
0.94 |
|
R1195:Sema5b
|
UTSW |
16 |
35,651,660 (GRCm38) |
missense |
probably null |
0.94 |
|
R1666:Sema5b
|
UTSW |
16 |
35,658,482 (GRCm38) |
missense |
probably benign |
0.03 |
|
R1706:Sema5b
|
UTSW |
16 |
35,649,755 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R1733:Sema5b
|
UTSW |
16 |
35,646,367 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1775:Sema5b
|
UTSW |
16 |
35,660,324 (GRCm38) |
missense |
probably benign |
|
|
R2215:Sema5b
|
UTSW |
16 |
35,660,215 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R3086:Sema5b
|
UTSW |
16 |
35,622,723 (GRCm38) |
missense |
probably benign |
|
|
R3613:Sema5b
|
UTSW |
16 |
35,660,150 (GRCm38) |
missense |
probably benign |
|
|
R4774:Sema5b
|
UTSW |
16 |
35,663,182 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5743:Sema5b
|
UTSW |
16 |
35,658,476 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5856:Sema5b
|
UTSW |
16 |
35,646,386 (GRCm38) |
nonsense |
probably null |
|
|
R5993:Sema5b
|
UTSW |
16 |
35,646,202 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R6248:Sema5b
|
UTSW |
16 |
35,628,007 (GRCm38) |
splice site |
probably null |
|
|
R6420:Sema5b
|
UTSW |
16 |
35,663,146 (GRCm38) |
missense |
probably benign |
0.08 |
|
R6795:Sema5b
|
UTSW |
16 |
35,658,571 (GRCm38) |
nonsense |
probably null |
|
|
R6825:Sema5b
|
UTSW |
16 |
35,628,007 (GRCm38) |
splice site |
probably null |
|
|
R7066:Sema5b
|
UTSW |
16 |
35,651,312 (GRCm38) |
missense |
probably benign |
0.26 |
|
R7244:Sema5b
|
UTSW |
16 |
35,660,545 (GRCm38) |
missense |
probably benign |
|
|
R7446:Sema5b
|
UTSW |
16 |
35,647,203 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7497:Sema5b
|
UTSW |
16 |
35,661,330 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7516:Sema5b
|
UTSW |
16 |
35,651,170 (GRCm38) |
missense |
probably benign |
0.05 |
|
R7878:Sema5b
|
UTSW |
16 |
35,661,626 (GRCm38) |
missense |
probably benign |
0.00 |
|
R7922:Sema5b
|
UTSW |
16 |
35,658,256 (GRCm38) |
frame shift |
probably null |
|
|
R8397:Sema5b
|
UTSW |
16 |
35,651,321 (GRCm38) |
missense |
possibly damaging |
0.59 |
|
R8537:Sema5b
|
UTSW |
16 |
35,651,609 (GRCm38) |
missense |
possibly damaging |
0.49 |
|
R8929:Sema5b
|
UTSW |
16 |
35,647,367 (GRCm38) |
intron |
probably benign |
|
|
R9262:Sema5b
|
UTSW |
16 |
35,632,853 (GRCm38) |
missense |
possibly damaging |
0.57 |
|
R9389:Sema5b
|
UTSW |
16 |
35,645,722 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R9579:Sema5b
|
UTSW |
16 |
35,647,212 (GRCm38) |
missense |
probably benign |
0.01 |
|
R9623:Sema5b
|
UTSW |
16 |
35,622,751 (GRCm38) |
missense |
possibly damaging |
0.74 |
|
Z1088:Sema5b
|
UTSW |
16 |
35,660,590 (GRCm38) |
missense |
probably damaging |
0.99 |
|
Z1176:Sema5b
|
UTSW |
16 |
35,649,864 (GRCm38) |
missense |
probably benign |
0.01 |
|
Z1176:Sema5b
|
UTSW |
16 |
35,646,273 (GRCm38) |
missense |
probably benign |
0.05 |
|
Z1176:Sema5b
|
UTSW |
16 |
35,628,018 (GRCm38) |
missense |
probably benign |
0.01 |
|
| Predicted Primers |
PCR Primer
(F):5'- TCAGCGAAGTTGCAGCAACC -3'
(R):5'- TTGCAGGTCTTGAACTCCTTCG -3'
Sequencing Primer
(F):5'- GTTGCAGCAACCCGGCG -3'
(R):5'- TGAGGGTGGCTTCAGACC -3'
|
| Posted On |
2014-12-04 |
Incidental Mutation