Incidental Mutation 'R0863:Sema4a'
| ID |
82181 |
| Institutional Source |
Beutler Lab
|
| 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 |
| MMRRC Submission |
039037-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.913)
|
| Stock # |
R0863 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
88343266-88368489 bp(-) (GRCm39) |
| Type of Mutation |
unclassified |
| DNA Base Change (assembly) |
C to T
at 88355456 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000138858
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029700]
[ENSMUST00000107531]
[ENSMUST00000125526]
[ENSMUST00000127436]
[ENSMUST00000141471]
[ENSMUST00000169222]
[ENSMUST00000165898]
[ENSMUST00000166237]
[ENSMUST00000184487]
[ENSMUST00000184876]
[ENSMUST00000147200]
[ENSMUST00000185137]
|
| AlphaFold |
Q62178 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000029700
|
| SMART Domains |
Protein: ENSMUSP00000029700
Gene: ENSMUSG00000028064
| 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
|
| SMART Domains |
Protein: ENSMUSP00000103155
Gene: ENSMUSG00000028064
| 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 |
probably benign
Transcript: ENSMUST00000125526
|
| SMART Domains |
Protein: ENSMUSP00000119028
Gene: ENSMUSG00000028064
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
113 |
8.2e-9 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000127436
|
| SMART Domains |
Protein: ENSMUSP00000118706
Gene: ENSMUSG00000028064
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
234 |
5.5e-53 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000135539
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000135732
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000141471
|
| SMART Domains |
Protein: ENSMUSP00000114330
Gene: ENSMUSG00000028064
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000169222
|
| SMART Domains |
Protein: ENSMUSP00000128887
Gene: ENSMUSG00000028064
| 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: ENSMUST00000165898
|
| SMART Domains |
Protein: ENSMUSP00000128510
Gene: ENSMUSG00000028064
| 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: ENSMUST00000149145
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000166237
|
| SMART Domains |
Protein: ENSMUSP00000125909
Gene: ENSMUSG00000028064
| 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: ENSMUST00000184972
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000184487
|
| SMART Domains |
Protein: ENSMUSP00000139126
Gene: ENSMUSG00000028064
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
168 |
1.5e-30 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000184876
|
| SMART Domains |
Protein: ENSMUSP00000139159
Gene: ENSMUSG00000028064
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
179 |
7.7e-31 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000147200
|
| SMART Domains |
Protein: ENSMUSP00000123061
Gene: ENSMUSG00000028064
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
203 |
3.5e-45 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000185137
|
| Coding Region Coverage |
- 1x: 99.5%
- 3x: 98.9%
- 10x: 97.4%
- 20x: 94.8%
|
| Validation Efficiency |
94% (59/63) |
| 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: 59 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2310016G11Rik |
A |
G |
7: 44,327,232 (GRCm39) |
|
noncoding transcript |
Het |
| 4930433I11Rik |
A |
T |
7: 40,642,480 (GRCm39) |
T141S |
probably benign |
Het |
| Abca14 |
A |
T |
7: 119,815,453 (GRCm39) |
T234S |
probably benign |
Het |
| Acap1 |
C |
A |
11: 69,777,882 (GRCm39) |
V119L |
probably damaging |
Het |
| Actr2 |
C |
T |
11: 20,030,760 (GRCm39) |
V163I |
probably benign |
Het |
| Adcy4 |
T |
C |
14: 56,021,056 (GRCm39) |
Y27C |
probably damaging |
Het |
| Arnt2 |
T |
A |
7: 83,914,792 (GRCm39) |
K524M |
probably damaging |
Het |
| Brca1 |
T |
C |
11: 101,415,596 (GRCm39) |
Y846C |
probably benign |
Het |
| Capn7 |
T |
A |
14: 31,091,714 (GRCm39) |
C704S |
possibly damaging |
Het |
| Cep350 |
T |
A |
1: 155,737,981 (GRCm39) |
I2621L |
probably benign |
Het |
| Col11a1 |
G |
A |
3: 113,932,414 (GRCm39) |
R113H |
unknown |
Het |
| Ctnnbl1 |
C |
T |
2: 157,641,337 (GRCm39) |
|
probably benign |
Het |
| Cul9 |
T |
C |
17: 46,848,748 (GRCm39) |
|
probably null |
Het |
| Erc2 |
A |
C |
14: 27,747,105 (GRCm39) |
N345T |
probably benign |
Het |
| Fank1 |
A |
G |
7: 133,482,352 (GRCm39) |
R73G |
possibly damaging |
Het |
| Fes |
A |
T |
7: 80,030,634 (GRCm39) |
W552R |
probably damaging |
Het |
| Fsd2 |
A |
G |
7: 81,191,913 (GRCm39) |
V488A |
possibly damaging |
Het |
| Gfm1 |
T |
C |
3: 67,381,928 (GRCm39) |
S705P |
probably damaging |
Het |
| Gm9493 |
A |
T |
19: 23,597,173 (GRCm39) |
Q23L |
probably benign |
Het |
| Gucy1b2 |
T |
C |
14: 62,656,511 (GRCm39) |
D282G |
probably benign |
Het |
| H2-Ab1 |
T |
C |
17: 34,486,328 (GRCm39) |
I129T |
probably damaging |
Het |
| H2-M10.3 |
T |
A |
17: 36,677,582 (GRCm39) |
Y232F |
probably damaging |
Het |
| Iqca1 |
C |
A |
1: 90,070,453 (GRCm39) |
G133V |
probably null |
Het |
| Lonp1 |
T |
C |
17: 56,925,331 (GRCm39) |
K487R |
probably damaging |
Het |
| Ltbp1 |
A |
G |
17: 75,559,381 (GRCm39) |
Y290C |
probably damaging |
Het |
| Ms4a10 |
C |
T |
19: 10,945,957 (GRCm39) |
G58D |
probably damaging |
Het |
| Muc5b |
A |
G |
7: 141,421,454 (GRCm39) |
S4315G |
probably benign |
Het |
| Nlrp1b |
T |
A |
11: 71,072,173 (GRCm39) |
T557S |
probably benign |
Het |
| Nlrp3 |
A |
G |
11: 59,456,676 (GRCm39) |
D946G |
probably benign |
Het |
| Obscn |
T |
C |
11: 58,886,241 (GRCm39) |
|
probably benign |
Het |
| Oga |
C |
T |
19: 45,771,425 (GRCm39) |
A49T |
probably benign |
Het |
| Or10ab5 |
A |
G |
7: 108,244,865 (GRCm39) |
I306T |
probably benign |
Het |
| Or5p50 |
T |
C |
7: 107,422,581 (GRCm39) |
S32G |
probably benign |
Het |
| Or7e173 |
A |
T |
9: 19,938,509 (GRCm39) |
S242T |
probably damaging |
Het |
| Pask |
A |
T |
1: 93,242,061 (GRCm39) |
F1219I |
probably damaging |
Het |
| Pcdhb2 |
G |
A |
18: 37,428,710 (GRCm39) |
V228I |
possibly damaging |
Het |
| Phf1 |
T |
C |
17: 27,156,114 (GRCm39) |
|
probably benign |
Het |
| Plec |
G |
A |
15: 76,058,280 (GRCm39) |
Q3751* |
probably null |
Het |
| Plscr1l1 |
A |
T |
9: 92,233,140 (GRCm39) |
I88L |
possibly damaging |
Het |
| Ppp1r12c |
G |
T |
7: 4,489,365 (GRCm39) |
Q240K |
probably damaging |
Het |
| Ralgapa1 |
A |
T |
12: 55,809,466 (GRCm39) |
Y436* |
probably null |
Het |
| Ralgapa1 |
C |
A |
12: 55,829,562 (GRCm39) |
|
probably benign |
Het |
| Scel |
T |
A |
14: 103,823,916 (GRCm39) |
S381R |
possibly damaging |
Het |
| Sltm |
A |
G |
9: 70,469,190 (GRCm39) |
T150A |
probably benign |
Het |
| Spag1 |
G |
T |
15: 36,192,193 (GRCm39) |
K217N |
probably damaging |
Het |
| Ssh1 |
C |
T |
5: 114,104,792 (GRCm39) |
R9H |
probably damaging |
Het |
| St3gal4 |
C |
A |
9: 34,964,744 (GRCm39) |
V155F |
probably damaging |
Het |
| Stxbp5 |
C |
T |
10: 9,684,784 (GRCm39) |
E539K |
possibly damaging |
Het |
| Tbc1d7 |
G |
T |
13: 43,308,161 (GRCm39) |
|
probably benign |
Het |
| Thnsl2 |
A |
T |
6: 71,111,208 (GRCm39) |
L220* |
probably null |
Het |
| Tinf2 |
G |
A |
14: 55,917,566 (GRCm39) |
P308S |
probably benign |
Het |
| Tnf |
T |
C |
17: 35,420,120 (GRCm39) |
|
probably benign |
Het |
| Ttc21b |
T |
C |
2: 66,073,117 (GRCm39) |
I190V |
probably benign |
Het |
| Ttn |
T |
C |
2: 76,537,391 (GRCm39) |
T34846A |
probably benign |
Het |
| Ube4a |
A |
G |
9: 44,861,114 (GRCm39) |
V232A |
possibly damaging |
Het |
| Uri1 |
A |
T |
7: 37,669,100 (GRCm39) |
D122E |
probably damaging |
Het |
| Vmn2r94 |
T |
G |
17: 18,477,973 (GRCm39) |
Q146P |
probably damaging |
Het |
| Zan |
T |
A |
5: 137,456,901 (GRCm39) |
E1278D |
unknown |
Het |
| Zfhx4 |
T |
A |
3: 5,310,375 (GRCm39) |
S919R |
possibly damaging |
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 |
|
IGL01722:Sema4a
|
APN |
3 |
88,345,491 (GRCm39) |
missense |
probably benign |
0.14 |
|
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 |
|
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 |
|
| Predicted Primers |
PCR Primer
(F):5'- GAAGCTGCCCAAAACTATGCTTGTG -3'
(R):5'- GGCCTACCTATGCCCCAATTAATCC -3'
Sequencing Primer
(F):5'- CAGACATTTGTGGCATATGAGC -3'
(R):5'- CATATTTCAGATCCTGCGATGG -3'
|
| Posted On |
2013-11-08 |
Incidental Mutation