Incidental Mutation 'R5312:Sema4a'
| ID |
405631 |
| 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 |
042895-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.902)
|
| Stock # |
R5312 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
88343266-88368489 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 88344343 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Phenylalanine
at position 636
(S636F)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000128887
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029700]
[ENSMUST00000107531]
[ENSMUST00000165898]
[ENSMUST00000166237]
[ENSMUST00000169222]
|
| AlphaFold |
Q62178 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000029700
AA Change: S636F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000029700
Gene: ENSMUSG00000028064
AA Change: S636F
| 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 damaging
Transcript: ENSMUST00000107531
AA Change: S504F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000103155
Gene: ENSMUSG00000028064
AA Change: S504F
| 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 damaging
Transcript: ENSMUST00000165898
AA Change: S636F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000128510
Gene: ENSMUSG00000028064
AA Change: S636F
| 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 damaging
Transcript: ENSMUST00000166237
AA Change: S636F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000125909
Gene: ENSMUSG00000028064
AA Change: S636F
| 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 damaging
Transcript: ENSMUST00000169222
AA Change: S636F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000128887
Gene: ENSMUSG00000028064
AA Change: S636F
| 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
|
| Meta Mutation Damage Score |
0.2595 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.2%
|
| Validation Efficiency |
100% (60/60) |
| 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: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca15 |
T |
C |
7: 119,944,592 (GRCm39) |
V409A |
probably damaging |
Het |
| Abtb1 |
A |
G |
6: 88,815,240 (GRCm39) |
F297L |
probably damaging |
Het |
| Adam22 |
C |
A |
5: 8,140,182 (GRCm39) |
G202W |
probably damaging |
Het |
| Adgrg3 |
G |
A |
8: 95,766,492 (GRCm39) |
V388I |
probably benign |
Het |
| Adnp |
T |
C |
2: 168,026,108 (GRCm39) |
T396A |
probably benign |
Het |
| Ank2 |
T |
C |
3: 126,753,417 (GRCm39) |
Q288R |
probably damaging |
Het |
| Bdp1 |
T |
C |
13: 100,234,109 (GRCm39) |
|
probably null |
Het |
| Cdc45 |
C |
T |
16: 18,614,647 (GRCm39) |
R205H |
probably damaging |
Het |
| Ceacam23 |
T |
G |
7: 17,643,067 (GRCm39) |
H492Q |
probably damaging |
Het |
| Cfap210 |
T |
C |
2: 69,617,602 (GRCm39) |
T60A |
possibly damaging |
Het |
| Cntnap5c |
A |
T |
17: 58,666,249 (GRCm39) |
E1093V |
probably benign |
Het |
| Cplx3 |
A |
T |
9: 57,518,360 (GRCm39) |
L343Q |
probably damaging |
Het |
| Dmrta1 |
A |
C |
4: 89,580,284 (GRCm39) |
N415H |
probably damaging |
Het |
| Dnaaf5 |
T |
A |
5: 139,138,617 (GRCm39) |
V266E |
probably damaging |
Het |
| Dot1l |
A |
G |
10: 80,620,471 (GRCm39) |
Q511R |
possibly damaging |
Het |
| Ehmt1 |
A |
G |
2: 24,774,207 (GRCm39) |
V201A |
probably damaging |
Het |
| Fancg |
A |
G |
4: 43,003,019 (GRCm39) |
F613L |
probably benign |
Het |
| Fbxo10 |
A |
T |
4: 45,042,036 (GRCm39) |
I731N |
possibly damaging |
Het |
| Fchsd1 |
C |
T |
18: 38,092,926 (GRCm39) |
|
probably benign |
Het |
| Ighv1-74 |
A |
G |
12: 115,766,501 (GRCm39) |
S39P |
probably damaging |
Het |
| Kbtbd11 |
A |
G |
8: 15,078,589 (GRCm39) |
D396G |
possibly damaging |
Het |
| Klc1 |
A |
G |
12: 111,762,055 (GRCm39) |
K575R |
possibly damaging |
Het |
| Mki67 |
A |
T |
7: 135,302,559 (GRCm39) |
V825E |
probably damaging |
Het |
| Mus81 |
T |
C |
19: 5,533,522 (GRCm39) |
K489R |
possibly damaging |
Het |
| Myog |
A |
G |
1: 134,218,064 (GRCm39) |
K91E |
probably damaging |
Het |
| Nfil3 |
A |
T |
13: 53,121,656 (GRCm39) |
V416E |
probably damaging |
Het |
| Nup160 |
G |
T |
2: 90,563,176 (GRCm39) |
E1314* |
probably null |
Het |
| Nwd2 |
C |
T |
5: 63,963,415 (GRCm39) |
Q1000* |
probably null |
Het |
| Or4g17 |
T |
C |
2: 111,210,179 (GRCm39) |
V278A |
possibly damaging |
Het |
| Or4k35 |
T |
G |
2: 111,100,655 (GRCm39) |
D19A |
probably benign |
Het |
| Or6c66b |
A |
C |
10: 129,377,134 (GRCm39) |
M243L |
probably benign |
Het |
| Or6c75 |
T |
A |
10: 129,337,383 (GRCm39) |
V210E |
probably damaging |
Het |
| Ppp4r4 |
T |
A |
12: 103,573,147 (GRCm39) |
|
probably null |
Het |
| Pramel16 |
A |
T |
4: 143,675,665 (GRCm39) |
I387N |
possibly damaging |
Het |
| Psg27 |
C |
A |
7: 18,290,958 (GRCm39) |
R415L |
probably benign |
Het |
| Ptprr |
T |
A |
10: 116,024,324 (GRCm39) |
S212T |
probably benign |
Het |
| Ramp3 |
T |
C |
11: 6,624,888 (GRCm39) |
F61L |
probably damaging |
Het |
| Rap1gds1 |
A |
G |
3: 138,664,389 (GRCm39) |
L322P |
probably damaging |
Het |
| Rnf5 |
A |
G |
17: 34,820,562 (GRCm39) |
F175S |
probably benign |
Het |
| Sfrp2 |
A |
G |
3: 83,676,708 (GRCm39) |
D193G |
probably damaging |
Het |
| Slc26a5 |
T |
C |
5: 22,052,258 (GRCm39) |
S24G |
probably damaging |
Het |
| Slco1a8 |
A |
T |
6: 141,918,058 (GRCm39) |
F606Y |
probably benign |
Het |
| Spg21 |
A |
G |
9: 65,376,084 (GRCm39) |
I31V |
probably benign |
Het |
| Tmem45a2 |
T |
C |
16: 56,859,370 (GRCm39) |
D287G |
possibly damaging |
Het |
| Utrn |
A |
T |
10: 12,603,513 (GRCm39) |
D627E |
probably damaging |
Het |
| Vmn2r103 |
A |
T |
17: 20,013,296 (GRCm39) |
N139I |
probably benign |
Het |
| Vps35l |
T |
C |
7: 118,412,799 (GRCm39) |
I629T |
probably damaging |
Het |
| Washc5 |
A |
T |
15: 59,217,377 (GRCm39) |
|
probably null |
Het |
| Zfp667 |
T |
C |
7: 6,308,466 (GRCm39) |
I378T |
probably benign |
Het |
| Zfp949 |
A |
C |
9: 88,449,236 (GRCm39) |
T14P |
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 |
|
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 |
|
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'- TCAGTGGAGCCTTTTCCCTG -3'
(R):5'- TTAAAGAAGTCCTGACAGTCCC -3'
Sequencing Primer
(F):5'- ACTCCCAGGAGCACGATG -3'
(R):5'- TCCATCCTGGAGCTGCC -3'
|
| Posted On |
2016-07-22 |
Incidental Mutation