Incidental Mutation 'R5481:Sema4a'
| ID |
434306 |
| 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 |
043042-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.913)
|
| Stock # |
R5481 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
88343266-88368489 bp(-) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
A to T
at 88360347 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Stop codon
at position 77
(Y77*)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000139159
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029700]
[ENSMUST00000107531]
[ENSMUST00000123753]
[ENSMUST00000125526]
[ENSMUST00000127436]
[ENSMUST00000147200]
[ENSMUST00000165898]
[ENSMUST00000166237]
[ENSMUST00000169222]
[ENSMUST00000184487]
[ENSMUST00000184876]
[ENSMUST00000185137]
[ENSMUST00000141471]
|
| AlphaFold |
Q62178 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000029700
AA Change: Y77*
|
| SMART Domains |
Protein: ENSMUSP00000029700
Gene: ENSMUSG00000028064
AA Change: Y77*
| 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: ENSMUST00000123753
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000125526
AA Change: Y77*
|
| SMART Domains |
Protein: ENSMUSP00000119028
Gene: ENSMUSG00000028064
AA Change: Y77*
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
113 |
8.2e-9 |
PFAM |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000127436
AA Change: Y77*
|
| SMART Domains |
Protein: ENSMUSP00000118706
Gene: ENSMUSG00000028064
AA Change: Y77*
| 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 null
Transcript: ENSMUST00000147200
AA Change: Y77*
|
| SMART Domains |
Protein: ENSMUSP00000123061
Gene: ENSMUSG00000028064
AA Change: Y77*
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
203 |
3.5e-45 |
PFAM |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000165898
AA Change: Y77*
|
| SMART Domains |
Protein: ENSMUSP00000128510
Gene: ENSMUSG00000028064
AA Change: Y77*
| 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 null
Transcript: ENSMUST00000166237
AA Change: Y77*
|
| SMART Domains |
Protein: ENSMUSP00000125909
Gene: ENSMUSG00000028064
AA Change: Y77*
| 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 null
Transcript: ENSMUST00000169222
AA Change: Y77*
|
| SMART Domains |
Protein: ENSMUSP00000128887
Gene: ENSMUSG00000028064
AA Change: Y77*
| 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 null
Transcript: ENSMUST00000184487
AA Change: Y77*
|
| SMART Domains |
Protein: ENSMUSP00000139126
Gene: ENSMUSG00000028064
AA Change: Y77*
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
168 |
1.5e-30 |
PFAM |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000184876
AA Change: Y77*
|
| SMART Domains |
Protein: ENSMUSP00000139159
Gene: ENSMUSG00000028064
AA Change: Y77*
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
179 |
7.7e-31 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000184972
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146921
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149145
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000185137
|
| 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 |
|
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 97.6%
- 10x: 95.1%
- 20x: 90.0%
|
| 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: 62 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930522H14Rik |
A |
G |
4: 109,362,759 (GRCm39) |
S187P |
probably damaging |
Het |
| Aass |
C |
A |
6: 23,113,475 (GRCm39) |
V282L |
probably benign |
Het |
| Adh6a |
G |
T |
3: 138,031,719 (GRCm39) |
V204F |
probably damaging |
Het |
| Adrm1b |
A |
G |
3: 92,336,658 (GRCm39) |
S15P |
possibly damaging |
Het |
| Aspm |
A |
G |
1: 139,384,799 (GRCm39) |
K148E |
possibly damaging |
Het |
| Atp12a |
A |
T |
14: 56,610,846 (GRCm39) |
D330V |
possibly damaging |
Het |
| Barhl1 |
A |
G |
2: 28,805,352 (GRCm39) |
Y114H |
probably damaging |
Het |
| BC106179 |
T |
A |
16: 23,042,918 (GRCm39) |
|
probably benign |
Het |
| Cabin1 |
A |
G |
10: 75,570,900 (GRCm39) |
L792P |
probably benign |
Het |
| Calcoco2 |
A |
G |
11: 95,998,369 (GRCm39) |
V18A |
probably damaging |
Het |
| Chpf2 |
A |
T |
5: 24,794,340 (GRCm39) |
H170L |
probably damaging |
Het |
| Chrna1 |
T |
A |
2: 73,397,270 (GRCm39) |
I340F |
possibly damaging |
Het |
| Ckap5 |
A |
T |
2: 91,402,792 (GRCm39) |
I690F |
possibly damaging |
Het |
| Col10a1 |
A |
G |
10: 34,271,660 (GRCm39) |
H544R |
probably benign |
Het |
| Cyp2b19 |
A |
C |
7: 26,466,246 (GRCm39) |
T350P |
probably damaging |
Het |
| Dgkq |
A |
G |
5: 108,796,676 (GRCm39) |
|
probably null |
Het |
| Dnah1 |
A |
G |
14: 31,030,828 (GRCm39) |
V443A |
possibly damaging |
Het |
| Erbb3 |
T |
C |
10: 128,408,349 (GRCm39) |
D855G |
probably damaging |
Het |
| Fam3c |
T |
C |
6: 22,321,357 (GRCm39) |
D138G |
probably benign |
Het |
| Fen1 |
A |
G |
19: 10,178,022 (GRCm39) |
C141R |
probably damaging |
Het |
| Flnc |
G |
A |
6: 29,441,216 (GRCm39) |
G390D |
probably damaging |
Het |
| Fnip1 |
C |
A |
11: 54,393,470 (GRCm39) |
D635E |
probably benign |
Het |
| Fry |
A |
T |
5: 150,183,784 (GRCm39) |
L17F |
probably benign |
Het |
| Fsip2 |
T |
C |
2: 82,810,230 (GRCm39) |
I2183T |
probably benign |
Het |
| Gfpt1 |
T |
A |
6: 87,027,951 (GRCm39) |
I19N |
probably damaging |
Het |
| Hus1b |
T |
C |
13: 31,130,942 (GRCm39) |
D239G |
probably benign |
Het |
| Kif1a |
T |
C |
1: 92,987,966 (GRCm39) |
K546R |
probably benign |
Het |
| Kmt2d |
A |
G |
15: 98,759,886 (GRCm39) |
V1124A |
unknown |
Het |
| Krtap16-1 |
A |
G |
11: 99,876,153 (GRCm39) |
I417T |
probably damaging |
Het |
| Manba |
A |
T |
3: 135,230,317 (GRCm39) |
N297Y |
possibly damaging |
Het |
| Mblac1 |
A |
G |
5: 138,193,078 (GRCm39) |
D140G |
probably damaging |
Het |
| Mlh1 |
T |
C |
9: 111,058,905 (GRCm39) |
|
probably null |
Het |
| Morc1 |
T |
A |
16: 48,381,848 (GRCm39) |
|
probably null |
Het |
| Morc3 |
C |
A |
16: 93,659,543 (GRCm39) |
P449Q |
probably damaging |
Het |
| Mtr |
T |
C |
13: 12,203,041 (GRCm39) |
|
probably null |
Het |
| Mylk |
T |
A |
16: 34,741,974 (GRCm39) |
C829S |
probably benign |
Het |
| Myo1d |
A |
G |
11: 80,553,921 (GRCm39) |
I520T |
possibly damaging |
Het |
| Ncam2 |
C |
T |
16: 81,231,766 (GRCm39) |
R77* |
probably null |
Het |
| Nos1 |
A |
T |
5: 118,005,819 (GRCm39) |
I180F |
probably benign |
Het |
| Ntsr1 |
C |
T |
2: 180,183,313 (GRCm39) |
T341M |
possibly damaging |
Het |
| Or8b51 |
A |
T |
9: 38,568,916 (GRCm39) |
F257L |
probably benign |
Het |
| P2rx7 |
A |
G |
5: 122,818,883 (GRCm39) |
D435G |
possibly damaging |
Het |
| Peli2 |
C |
A |
14: 48,490,090 (GRCm39) |
N136K |
probably damaging |
Het |
| Pigt |
C |
A |
2: 164,348,342 (GRCm39) |
P429H |
probably damaging |
Het |
| Pik3r2 |
T |
C |
8: 71,222,408 (GRCm39) |
I515V |
probably benign |
Het |
| Pkhd1l1 |
A |
G |
15: 44,422,042 (GRCm39) |
Y3104C |
probably damaging |
Het |
| Ppp1r16a |
A |
C |
15: 76,575,221 (GRCm39) |
E43A |
probably damaging |
Het |
| Ptpn18 |
T |
C |
1: 34,510,744 (GRCm39) |
L260P |
possibly damaging |
Het |
| Scaf11 |
A |
T |
15: 96,318,498 (GRCm39) |
S355R |
probably damaging |
Het |
| Serpinb9b |
T |
C |
13: 33,222,076 (GRCm39) |
V230A |
possibly damaging |
Het |
| Sfswap |
T |
A |
5: 129,591,882 (GRCm39) |
S300T |
probably damaging |
Het |
| Slc22a30 |
T |
C |
19: 8,314,201 (GRCm39) |
N495S |
probably benign |
Het |
| Srcap |
G |
A |
7: 127,131,369 (GRCm39) |
G836D |
probably damaging |
Het |
| Stard4 |
A |
C |
18: 33,338,298 (GRCm39) |
C137W |
probably benign |
Het |
| Stat6 |
A |
G |
10: 127,483,695 (GRCm39) |
|
probably null |
Het |
| Steap3 |
T |
C |
1: 120,169,454 (GRCm39) |
D243G |
probably benign |
Het |
| Taf1c |
A |
G |
8: 120,325,979 (GRCm39) |
S628P |
probably damaging |
Het |
| Unkl |
C |
T |
17: 25,420,146 (GRCm39) |
Q13* |
probably null |
Het |
| Usp38 |
A |
G |
8: 81,719,952 (GRCm39) |
S426P |
possibly damaging |
Het |
| Vmn2r8 |
T |
C |
5: 108,949,636 (GRCm39) |
T404A |
probably benign |
Het |
| Washc1 |
T |
C |
17: 66,425,860 (GRCm39) |
V425A |
probably benign |
Het |
| Zfyve9 |
A |
G |
4: 108,501,546 (GRCm39) |
I590T |
probably 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 |
|
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 |
|
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'- GTCACTGCTGACTCAGAGTG -3'
(R):5'- CCCTGCTGTTGAAGGATGAAGG -3'
Sequencing Primer
(F):5'- CTGACTCAGAGTGGCAGGTG -3'
(R):5'- CCTGCTGTTGAAGGATGAAGGAAATG -3'
|
| Posted On |
2016-10-06 |
Incidental Mutation