Incidental Mutation 'IGL01722:Sema4a'
| ID |
105150 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Sema4a
|
| Ensembl Gene |
ENSMUSG00000028064 |
| Gene Name |
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A |
| Synonyms |
SemB, SemB, Semab |
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.902)
|
| Stock # |
IGL01722
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
3 |
| Chromosomal Location |
88343266-88368489 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 88345491 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Glutamic Acid
at position 531
(K531E)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000128887
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029700]
[ENSMUST00000107531]
[ENSMUST00000165898]
[ENSMUST00000166237]
[ENSMUST00000169222]
|
| AlphaFold |
Q62178 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000029700
AA Change: K531E
PolyPhen 2
Score 0.139 (Sensitivity: 0.92; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000029700
Gene: ENSMUSG00000028064
AA Change: K531E
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Sema
|
64 |
478 |
1.96e-166 |
SMART |
|
PSI
|
496 |
547 |
9.33e-13 |
SMART |
|
transmembrane domain
|
680 |
702 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000107531
AA Change: K399E
PolyPhen 2
Score 0.139 (Sensitivity: 0.92; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000103155
Gene: ENSMUSG00000028064
AA Change: K399E
| Domain | Start | End | E-Value | Type |
|---|
|
Sema
|
2 |
346 |
2.06e-101 |
SMART |
|
PSI
|
364 |
415 |
9.33e-13 |
SMART |
|
transmembrane domain
|
548 |
570 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000135539
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149145
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000156108
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000165898
AA Change: K531E
PolyPhen 2
Score 0.139 (Sensitivity: 0.92; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000128510
Gene: ENSMUSG00000028064
AA Change: K531E
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Sema
|
64 |
478 |
1.96e-166 |
SMART |
|
PSI
|
496 |
547 |
9.33e-13 |
SMART |
|
transmembrane domain
|
680 |
702 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000166237
AA Change: K531E
PolyPhen 2
Score 0.139 (Sensitivity: 0.92; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000125909
Gene: ENSMUSG00000028064
AA Change: K531E
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Sema
|
64 |
478 |
1.96e-166 |
SMART |
|
PSI
|
496 |
547 |
9.33e-13 |
SMART |
|
transmembrane domain
|
680 |
702 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000169222
AA Change: K531E
PolyPhen 2
Score 0.139 (Sensitivity: 0.92; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000128887
Gene: ENSMUSG00000028064
AA Change: K531E
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Sema
|
64 |
478 |
1.96e-166 |
SMART |
|
PSI
|
496 |
547 |
9.33e-13 |
SMART |
|
transmembrane domain
|
680 |
702 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000183768
|
| Coding Region Coverage |
|
| Validation Efficiency |
|
| 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 family of soluble and transmembrane proteins. Semaphorins are involved in numerous functions, including axon guidance, morphogenesis, carcinogenesis, and immunomodulation. The encoded protein is a single-pass type I membrane protein containing an immunoglobulin-like C2-type domain, a PSI domain and a sema domain. It inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons. It is an activator of T-cell-mediated immunity and suppresses vascular endothelial growth factor (VEGF)-mediated endothelial cell migration and proliferation in vitro and angiogenesis in vivo. Mutations in this gene are associated with retinal degenerative diseases including retinitis pigmentosa type 35 (RP35) and cone-rod dystrophy type 10 (CORD10). Multiple alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]
PHENOTYPE: Homozygotes for a knock-out allele show no obvious brain defects but exhibit impaired T cell priming and defective Th1 responses. Homozygotes for a gene trap allele show severe retinal degeneration with reduced retinal vessels, depigmentation and dysfunction of both rod and cone photoreceptors. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 29 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acvr1c |
T |
A |
2: 58,173,561 (GRCm39) |
|
probably benign |
Het |
| Alb |
G |
A |
5: 90,618,698 (GRCm39) |
|
probably null |
Het |
| Ankrd9 |
A |
G |
12: 110,943,797 (GRCm39) |
V46A |
probably damaging |
Het |
| Apol11a |
A |
T |
15: 77,401,307 (GRCm39) |
M265L |
probably benign |
Het |
| Ccdc158 |
T |
C |
5: 92,810,598 (GRCm39) |
N97D |
possibly damaging |
Het |
| Cobl |
T |
G |
11: 12,203,987 (GRCm39) |
H823P |
probably benign |
Het |
| Dnaja2 |
A |
T |
8: 86,279,908 (GRCm39) |
H90Q |
probably benign |
Het |
| Dpagt1 |
T |
C |
9: 44,238,899 (GRCm39) |
F73S |
possibly damaging |
Het |
| Dph3 |
C |
T |
14: 31,807,417 (GRCm39) |
E20K |
possibly damaging |
Het |
| Fbxl13 |
G |
T |
5: 21,695,412 (GRCm39) |
T660K |
possibly damaging |
Het |
| Gask1a |
G |
A |
9: 121,794,149 (GRCm39) |
S101N |
possibly damaging |
Het |
| Glt6d1 |
T |
C |
2: 25,684,431 (GRCm39) |
T192A |
probably benign |
Het |
| Mroh7 |
C |
T |
4: 106,560,358 (GRCm39) |
V649I |
probably benign |
Het |
| Mta3 |
T |
C |
17: 84,063,072 (GRCm39) |
Y4H |
possibly damaging |
Het |
| Myh14 |
A |
G |
7: 44,292,956 (GRCm39) |
L369P |
probably damaging |
Het |
| Or2y1 |
G |
T |
11: 49,385,793 (GRCm39) |
L144F |
probably damaging |
Het |
| Or4c52 |
T |
C |
2: 89,845,351 (GRCm39) |
C26R |
probably benign |
Het |
| Paxx |
T |
C |
2: 25,350,277 (GRCm39) |
D110G |
probably damaging |
Het |
| Pcyox1 |
T |
G |
6: 86,365,735 (GRCm39) |
D493A |
probably damaging |
Het |
| Plk2 |
A |
G |
13: 110,535,976 (GRCm39) |
E560G |
probably benign |
Het |
| Rnf6 |
A |
G |
5: 146,147,036 (GRCm39) |
F661L |
probably benign |
Het |
| Svs5 |
T |
C |
2: 164,079,446 (GRCm39) |
K154E |
possibly damaging |
Het |
| Tbx4 |
A |
T |
11: 85,802,769 (GRCm39) |
Q242L |
probably damaging |
Het |
| Tgm3 |
A |
T |
2: 129,886,488 (GRCm39) |
I570F |
probably damaging |
Het |
| Thrap3 |
A |
T |
4: 126,059,322 (GRCm39) |
M908K |
possibly damaging |
Het |
| Trmo |
A |
G |
4: 46,386,092 (GRCm39) |
|
probably null |
Het |
| Usp8 |
T |
A |
2: 126,600,072 (GRCm39) |
L997Q |
probably damaging |
Het |
| Vmn1r202 |
T |
C |
13: 22,685,890 (GRCm39) |
R176G |
probably benign |
Het |
| Vps52 |
T |
A |
17: 34,180,589 (GRCm39) |
Y308* |
probably null |
Het |
|
| Other mutations in Sema4a |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00913:Sema4a
|
APN |
3 |
88,357,117 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01769:Sema4a
|
APN |
3 |
88,357,063 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
IGL02076:Sema4a
|
APN |
3 |
88,357,829 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02202:Sema4a
|
APN |
3 |
88,357,050 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0145:Sema4a
|
UTSW |
3 |
88,358,729 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0386:Sema4a
|
UTSW |
3 |
88,344,107 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R0837:Sema4a
|
UTSW |
3 |
88,360,405 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R0863:Sema4a
|
UTSW |
3 |
88,355,456 (GRCm39) |
unclassified |
probably benign |
|
|
R1567:Sema4a
|
UTSW |
3 |
88,359,353 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1675:Sema4a
|
UTSW |
3 |
88,362,073 (GRCm39) |
missense |
possibly damaging |
0.66 |
|
R1739:Sema4a
|
UTSW |
3 |
88,344,145 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R1801:Sema4a
|
UTSW |
3 |
88,344,056 (GRCm39) |
missense |
probably benign |
0.04 |
|
R1961:Sema4a
|
UTSW |
3 |
88,345,483 (GRCm39) |
splice site |
probably benign |
|
|
R2029:Sema4a
|
UTSW |
3 |
88,358,668 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4934:Sema4a
|
UTSW |
3 |
88,345,568 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5006:Sema4a
|
UTSW |
3 |
88,344,091 (GRCm39) |
missense |
probably benign |
|
|
R5309:Sema4a
|
UTSW |
3 |
88,344,343 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5312:Sema4a
|
UTSW |
3 |
88,344,343 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5338:Sema4a
|
UTSW |
3 |
88,358,804 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5481:Sema4a
|
UTSW |
3 |
88,360,347 (GRCm39) |
nonsense |
probably null |
|
|
R5510:Sema4a
|
UTSW |
3 |
88,357,293 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6046:Sema4a
|
UTSW |
3 |
88,348,008 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7242:Sema4a
|
UTSW |
3 |
88,357,416 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8403:Sema4a
|
UTSW |
3 |
88,359,341 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8798:Sema4a
|
UTSW |
3 |
88,344,004 (GRCm39) |
missense |
possibly damaging |
0.76 |
|
R9328:Sema4a
|
UTSW |
3 |
88,345,613 (GRCm39) |
nonsense |
probably null |
|
|
R9638:Sema4a
|
UTSW |
3 |
88,357,066 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9728:Sema4a
|
UTSW |
3 |
88,348,187 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
Z1176:Sema4a
|
UTSW |
3 |
88,344,500 (GRCm39) |
missense |
probably damaging |
0.97 |
|
| Posted On |
2014-01-21 |
Incidental Mutation