Incidental Mutation 'R7242:Sema4a'
| ID |
563267 |
| 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 |
045349-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.902)
|
| Stock # |
R7242 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
88343266-88368489 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 88357416 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Valine
at position 230
(D230V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000029700
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029700]
[ENSMUST00000107531]
[ENSMUST00000123753]
[ENSMUST00000125526]
[ENSMUST00000127436]
[ENSMUST00000141471]
[ENSMUST00000147200]
[ENSMUST00000165898]
[ENSMUST00000166237]
[ENSMUST00000169222]
[ENSMUST00000184487]
[ENSMUST00000184876]
[ENSMUST00000185137]
|
| AlphaFold |
Q62178 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000029700
AA Change: D230V
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000029700
Gene: ENSMUSG00000028064
AA Change: D230V
| 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: D98V
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000103155
Gene: ENSMUSG00000028064
AA Change: D98V
| 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 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 damaging
Transcript: ENSMUST00000127436
AA Change: D230V
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000118706
Gene: ENSMUSG00000028064
AA Change: D230V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
64 |
234 |
5.5e-53 |
PFAM |
|
| 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: 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 damaging
Transcript: ENSMUST00000165898
AA Change: D230V
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000128510
Gene: ENSMUSG00000028064
AA Change: D230V
| 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: D230V
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000125909
Gene: ENSMUSG00000028064
AA Change: D230V
| 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: D230V
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000128887
Gene: ENSMUSG00000028064
AA Change: D230V
| 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: 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: ENSMUST00000185137
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.8%
|
| Validation Efficiency |
100% (73/73) |
| 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: 74 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700001J03Rik |
A |
T |
5: 146,121,677 (GRCm39) |
I74N |
probably damaging |
Het |
| Abca6 |
A |
T |
11: 110,132,479 (GRCm39) |
V272D |
possibly damaging |
Het |
| Acot11 |
A |
T |
4: 106,619,690 (GRCm39) |
S163R |
probably benign |
Het |
| Adcy5 |
T |
C |
16: 34,977,205 (GRCm39) |
L246P |
probably damaging |
Het |
| Adgra1 |
A |
T |
7: 139,427,573 (GRCm39) |
|
probably null |
Het |
| Adgra2 |
A |
G |
8: 27,612,055 (GRCm39) |
T1335A |
probably damaging |
Het |
| Aoc1l2 |
A |
T |
6: 48,908,062 (GRCm39) |
Y354F |
probably damaging |
Het |
| Armt1 |
T |
C |
10: 4,403,475 (GRCm39) |
S187P |
probably damaging |
Het |
| Azin1 |
T |
C |
15: 38,501,749 (GRCm39) |
M1V |
probably null |
Het |
| B430305J03Rik |
C |
T |
3: 61,271,256 (GRCm39) |
C163Y |
unknown |
Het |
| Cables1 |
T |
C |
18: 11,973,064 (GRCm39) |
S68P |
possibly damaging |
Het |
| Cacna1d |
A |
G |
14: 29,900,663 (GRCm39) |
F341L |
probably benign |
Het |
| Ccdc90b |
T |
A |
7: 92,221,776 (GRCm39) |
H118Q |
probably damaging |
Het |
| Ccn5 |
T |
C |
2: 163,670,772 (GRCm39) |
F93S |
probably benign |
Het |
| Celf1 |
T |
A |
2: 90,833,602 (GRCm39) |
C119* |
probably null |
Het |
| Cfap57 |
C |
T |
4: 118,450,293 (GRCm39) |
V610M |
possibly damaging |
Het |
| Chrm4 |
T |
A |
2: 91,757,595 (GRCm39) |
M1K |
probably null |
Het |
| Chrnd |
C |
T |
1: 87,125,201 (GRCm39) |
T418I |
probably damaging |
Het |
| Coch |
G |
T |
12: 51,640,344 (GRCm39) |
|
probably benign |
Het |
| Cop1 |
A |
G |
1: 159,112,118 (GRCm39) |
T345A |
probably benign |
Het |
| Cops6 |
A |
G |
5: 138,161,842 (GRCm39) |
T96A |
probably benign |
Het |
| Corin |
T |
C |
5: 72,462,398 (GRCm39) |
I945V |
probably benign |
Het |
| Cyp2c67 |
G |
T |
19: 39,605,783 (GRCm39) |
T371N |
probably benign |
Het |
| Dap |
T |
A |
15: 31,273,454 (GRCm39) |
*103R |
probably null |
Het |
| Defb35 |
T |
A |
8: 22,430,773 (GRCm39) |
V49E |
unknown |
Het |
| Dmtf1 |
T |
A |
5: 9,199,016 (GRCm39) |
D39V |
possibly damaging |
Het |
| Dmtn |
T |
C |
14: 70,855,460 (GRCm39) |
T10A |
probably damaging |
Het |
| Dnajc1 |
C |
T |
2: 18,298,783 (GRCm39) |
E264K |
probably benign |
Het |
| Dtx3l |
A |
T |
16: 35,753,771 (GRCm39) |
N278K |
possibly damaging |
Het |
| Fam161a |
T |
A |
11: 22,970,037 (GRCm39) |
S72T |
possibly damaging |
Het |
| Fnbp4 |
T |
A |
2: 90,576,140 (GRCm39) |
S114T |
unknown |
Het |
| Focad |
T |
G |
4: 88,228,143 (GRCm39) |
I784S |
unknown |
Het |
| Fzd8 |
A |
T |
18: 9,214,171 (GRCm39) |
T418S |
probably damaging |
Het |
| Gclc |
A |
G |
9: 77,692,653 (GRCm39) |
Y264C |
probably benign |
Het |
| Ggn |
G |
A |
7: 28,872,459 (GRCm39) |
C649Y |
possibly damaging |
Het |
| Gys1 |
A |
G |
7: 45,089,092 (GRCm39) |
|
probably null |
Het |
| Hsd3b1 |
T |
C |
3: 98,760,526 (GRCm39) |
Y155C |
probably damaging |
Het |
| Htatip2 |
A |
G |
7: 49,422,354 (GRCm39) |
K191E |
probably benign |
Het |
| Ik |
A |
T |
18: 36,881,275 (GRCm39) |
S79C |
probably null |
Het |
| Kin |
G |
A |
2: 10,096,604 (GRCm39) |
R151Q |
probably benign |
Het |
| Kpna2rt |
G |
A |
17: 90,217,563 (GRCm39) |
T61I |
probably benign |
Het |
| Mast4 |
A |
G |
13: 102,874,986 (GRCm39) |
S1461P |
probably damaging |
Het |
| Melk |
T |
A |
4: 44,360,885 (GRCm39) |
V555E |
probably damaging |
Het |
| Met |
G |
A |
6: 17,491,316 (GRCm39) |
C26Y |
probably damaging |
Het |
| Mfsd6 |
A |
T |
1: 52,748,633 (GRCm39) |
F77L |
probably damaging |
Het |
| Mib1 |
T |
A |
18: 10,741,011 (GRCm39) |
D86E |
probably damaging |
Het |
| Myl10 |
G |
C |
5: 136,726,825 (GRCm39) |
V70L |
probably benign |
Het |
| Or12e8 |
G |
A |
2: 87,188,426 (GRCm39) |
V213I |
probably benign |
Het |
| Or56b1b |
T |
G |
7: 108,164,919 (GRCm39) |
S28R |
probably benign |
Het |
| Or7a36 |
A |
T |
10: 78,820,331 (GRCm39) |
K236* |
probably null |
Het |
| Or8g21 |
A |
G |
9: 38,906,437 (GRCm39) |
I98T |
probably benign |
Het |
| Patj |
A |
T |
4: 98,480,170 (GRCm39) |
I1296L |
probably benign |
Het |
| Pcdh1 |
C |
T |
18: 38,336,270 (GRCm39) |
V122M |
probably benign |
Het |
| Pcdhac2 |
A |
T |
18: 37,277,946 (GRCm39) |
I309F |
possibly damaging |
Het |
| Phf8-ps |
A |
G |
17: 33,286,101 (GRCm39) |
Y234H |
probably damaging |
Het |
| Phtf1 |
A |
G |
3: 103,906,012 (GRCm39) |
S565G |
probably damaging |
Het |
| Plekha2 |
A |
C |
8: 25,578,411 (GRCm39) |
F30V |
probably damaging |
Het |
| Ptbp1 |
A |
G |
10: 79,692,222 (GRCm39) |
M20V |
unknown |
Het |
| Pth2r |
A |
G |
1: 65,427,779 (GRCm39) |
D484G |
probably benign |
Het |
| Rapgef2 |
G |
A |
3: 78,995,210 (GRCm39) |
Q665* |
probably null |
Het |
| Scamp1 |
G |
A |
13: 94,369,648 (GRCm39) |
T59I |
probably benign |
Het |
| Snw1 |
C |
T |
12: 87,515,415 (GRCm39) |
G45R |
possibly damaging |
Het |
| Sox30 |
T |
A |
11: 45,875,347 (GRCm39) |
|
probably null |
Het |
| Sspo |
T |
A |
6: 48,450,886 (GRCm39) |
I2665K |
probably benign |
Het |
| Stx5a |
T |
A |
19: 8,732,641 (GRCm39) |
W437R |
unknown |
Het |
| Tln1 |
A |
G |
4: 43,542,602 (GRCm39) |
V1402A |
probably benign |
Het |
| Tpm1 |
A |
G |
9: 66,935,383 (GRCm39) |
L244P |
probably benign |
Het |
| Try5 |
T |
A |
6: 41,290,388 (GRCm39) |
E32V |
probably benign |
Het |
| Ttn |
T |
C |
2: 76,552,073 (GRCm39) |
N31188S |
probably benign |
Het |
| Tulp1 |
T |
C |
17: 28,582,379 (GRCm39) |
|
probably null |
Het |
| Usp13 |
T |
G |
3: 32,919,892 (GRCm39) |
|
probably null |
Het |
| Vax2 |
A |
G |
6: 83,688,298 (GRCm39) |
E7G |
possibly damaging |
Het |
| Vmn2r45 |
A |
T |
7: 8,488,612 (GRCm39) |
Y139* |
probably null |
Het |
| Zfp423 |
T |
C |
8: 88,631,155 (GRCm39) |
D21G |
probably benign |
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 |
|
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 |
|
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'- TCAAGGCCTTGTTGCGAGTG -3'
(R):5'- CACAAGTTTGGGCCCCTTTC -3'
Sequencing Primer
(F):5'- TTGGCTTCCAAGTGGCCAG -3'
(R):5'- CGAATTAAAGTACTCCAGCTGGCTG -3'
|
| Posted On |
2019-06-26 |
Incidental Mutation