Incidental Mutation 'R1567:Sema4a'
ID |
175329 |
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 |
039606-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.902)
|
Stock # |
R1567 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
3 |
Chromosomal Location |
88343266-88368489 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 88359353 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Cysteine to Serine
at position 113
(C113S)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000139159
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029700]
[ENSMUST00000107531]
[ENSMUST00000123753]
[ENSMUST00000125526]
[ENSMUST00000127436]
[ENSMUST00000169222]
[ENSMUST00000166237]
[ENSMUST00000184876]
[ENSMUST00000184487]
[ENSMUST00000147200]
[ENSMUST00000165898]
[ENSMUST00000141471]
[ENSMUST00000185137]
|
AlphaFold |
Q62178 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000029700
AA Change: C113S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000029700 Gene: ENSMUSG00000028064 AA Change: C113S
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: C14S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000103155 Gene: ENSMUSG00000028064 AA Change: C14S
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 damaging
Transcript: ENSMUST00000125526
AA Change: C113S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000119028 Gene: ENSMUSG00000028064 AA Change: C113S
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: C113S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000118706 Gene: ENSMUSG00000028064 AA Change: C113S
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 |
probably damaging
Transcript: ENSMUST00000169222
AA Change: C113S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000128887 Gene: ENSMUSG00000028064 AA Change: C113S
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: C113S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000125909 Gene: ENSMUSG00000028064 AA Change: C113S
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: ENSMUST00000184876
AA Change: C113S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000139159 Gene: ENSMUSG00000028064 AA Change: C113S
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
Pfam:Sema
|
64 |
179 |
7.7e-31 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000184487
AA Change: C113S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000139126 Gene: ENSMUSG00000028064 AA Change: C113S
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
32 |
N/A |
INTRINSIC |
Pfam:Sema
|
64 |
168 |
1.5e-30 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000147200
AA Change: C113S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000123061 Gene: ENSMUSG00000028064 AA Change: C113S
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: C113S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000128510 Gene: ENSMUSG00000028064 AA Change: C113S
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: ENSMUST00000146921
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000184972
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149145
|
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: ENSMUST00000185137
|
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.2%
- 10x: 95.8%
- 20x: 91.0%
|
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: 65 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca16 |
G |
A |
7: 120,030,352 (GRCm39) |
V155I |
probably benign |
Het |
Actrt2 |
T |
C |
4: 154,751,371 (GRCm39) |
Q255R |
possibly damaging |
Het |
Adar |
A |
T |
3: 89,643,088 (GRCm39) |
H323L |
probably benign |
Het |
Adgrg5 |
T |
A |
8: 95,664,326 (GRCm39) |
V312E |
probably damaging |
Het |
Anapc1 |
T |
C |
2: 128,459,636 (GRCm39) |
T1808A |
probably damaging |
Het |
Aox3 |
C |
A |
1: 58,233,852 (GRCm39) |
A1285E |
probably damaging |
Het |
Arhgap40 |
T |
A |
2: 158,388,719 (GRCm39) |
L551Q |
probably damaging |
Het |
Blk |
A |
G |
14: 63,618,178 (GRCm39) |
S243P |
probably damaging |
Het |
Cfap206 |
G |
T |
4: 34,716,490 (GRCm39) |
A325E |
probably benign |
Het |
Cimap1b |
C |
A |
15: 89,261,981 (GRCm39) |
R137L |
probably benign |
Het |
Cnn3 |
A |
T |
3: 121,243,607 (GRCm39) |
K23* |
probably null |
Het |
Cog8 |
G |
A |
8: 107,780,740 (GRCm39) |
R173* |
probably null |
Het |
Col11a1 |
G |
A |
3: 113,932,261 (GRCm39) |
R880H |
unknown |
Het |
Cyp2c40 |
T |
C |
19: 39,792,215 (GRCm39) |
Q243R |
probably null |
Het |
Dcbld1 |
A |
G |
10: 52,195,752 (GRCm39) |
E391G |
probably damaging |
Het |
Dchs1 |
C |
A |
7: 105,421,068 (GRCm39) |
A451S |
probably benign |
Het |
Ddx43 |
A |
G |
9: 78,323,991 (GRCm39) |
K441E |
probably damaging |
Het |
Depdc1a |
A |
T |
3: 159,228,177 (GRCm39) |
I310F |
possibly damaging |
Het |
Dnah17 |
C |
T |
11: 118,016,811 (GRCm39) |
V247M |
probably damaging |
Het |
Dtd1 |
G |
T |
2: 144,588,945 (GRCm39) |
G201V |
probably damaging |
Het |
Eif1ad3 |
A |
T |
12: 87,843,754 (GRCm39) |
I134F |
unknown |
Het |
Enoph1 |
G |
A |
5: 100,208,884 (GRCm39) |
G80S |
probably benign |
Het |
Fam76a |
A |
T |
4: 132,645,039 (GRCm39) |
Y48* |
probably null |
Het |
Fut9 |
T |
G |
4: 25,620,344 (GRCm39) |
T157P |
probably damaging |
Het |
Gm57859 |
T |
A |
11: 113,578,728 (GRCm39) |
V41D |
probably damaging |
Het |
Gtpbp1 |
T |
C |
15: 79,596,391 (GRCm39) |
I310T |
probably damaging |
Het |
Hk3 |
T |
A |
13: 55,154,418 (GRCm39) |
I753F |
probably damaging |
Het |
Hnrnpl |
G |
T |
7: 28,519,608 (GRCm39) |
A419S |
possibly damaging |
Het |
Ighv5-6 |
T |
C |
12: 113,589,528 (GRCm39) |
|
probably benign |
Het |
Itpkb |
A |
G |
1: 180,249,423 (GRCm39) |
T933A |
probably benign |
Het |
Kcnn2 |
T |
G |
18: 45,803,401 (GRCm39) |
|
probably null |
Het |
Klra3 |
G |
C |
6: 130,310,107 (GRCm39) |
R138G |
probably benign |
Het |
Lmcd1 |
C |
T |
6: 112,287,526 (GRCm39) |
R71C |
probably damaging |
Het |
Mrgprb1 |
A |
T |
7: 48,097,201 (GRCm39) |
V237E |
probably damaging |
Het |
Mybl1 |
T |
A |
1: 9,755,976 (GRCm39) |
E191V |
probably damaging |
Het |
Nbas |
T |
A |
12: 13,335,279 (GRCm39) |
F158I |
possibly damaging |
Het |
Nbr1 |
C |
G |
11: 101,466,037 (GRCm39) |
L748V |
probably damaging |
Het |
Nlrp10 |
G |
A |
7: 108,526,257 (GRCm39) |
T27M |
probably benign |
Het |
Notch3 |
G |
A |
17: 32,377,554 (GRCm39) |
T174I |
possibly damaging |
Het |
Nup85 |
T |
A |
11: 115,459,224 (GRCm39) |
I109K |
possibly damaging |
Het |
Or10h28 |
A |
G |
17: 33,488,450 (GRCm39) |
I251V |
probably benign |
Het |
Or2b28 |
A |
T |
13: 21,531,595 (GRCm39) |
I166L |
probably benign |
Het |
Or2n1e |
A |
G |
17: 38,586,459 (GRCm39) |
I266V |
possibly damaging |
Het |
Or4c12b |
T |
C |
2: 89,647,528 (GRCm39) |
L280P |
probably damaging |
Het |
Or4k48 |
G |
T |
2: 111,476,271 (GRCm39) |
Q24K |
possibly damaging |
Het |
Or5b105 |
T |
C |
19: 13,080,006 (GRCm39) |
T221A |
probably benign |
Het |
Phf2 |
T |
C |
13: 48,985,589 (GRCm39) |
K64E |
unknown |
Het |
Polr2a |
T |
C |
11: 69,636,857 (GRCm39) |
T365A |
probably benign |
Het |
Prkcd |
A |
G |
14: 30,329,405 (GRCm39) |
C12R |
probably benign |
Het |
Ptprq |
T |
C |
10: 107,401,748 (GRCm39) |
I1915V |
probably benign |
Het |
Rcbtb2 |
G |
A |
14: 73,399,902 (GRCm39) |
V112I |
probably benign |
Het |
Rxfp3 |
A |
G |
15: 11,036,187 (GRCm39) |
V395A |
probably benign |
Het |
Ryr2 |
C |
A |
13: 11,774,563 (GRCm39) |
G1198C |
possibly damaging |
Het |
Scn1a |
T |
A |
2: 66,103,675 (GRCm39) |
I1851F |
probably damaging |
Het |
Selenop |
A |
G |
15: 3,309,180 (GRCm39) |
*377W |
probably null |
Het |
Sf3b1 |
C |
G |
1: 55,058,554 (GRCm39) |
E12Q |
possibly damaging |
Het |
Speg |
T |
C |
1: 75,404,691 (GRCm39) |
S2575P |
probably benign |
Het |
Stk24 |
T |
A |
14: 121,545,468 (GRCm39) |
I97L |
probably benign |
Het |
Tap2 |
A |
G |
17: 34,433,065 (GRCm39) |
K449R |
probably benign |
Het |
Tecpr2 |
T |
A |
12: 110,908,030 (GRCm39) |
|
probably null |
Het |
Ttn |
T |
A |
2: 76,727,955 (GRCm39) |
|
probably benign |
Het |
Uggt2 |
A |
G |
14: 119,246,505 (GRCm39) |
F1204L |
possibly damaging |
Het |
Ugt2b36 |
T |
C |
5: 87,240,258 (GRCm39) |
I42M |
probably damaging |
Het |
Zdhhc8 |
A |
G |
16: 18,044,984 (GRCm39) |
L274P |
probably benign |
Het |
Zfp974 |
C |
A |
7: 27,610,148 (GRCm39) |
D526Y |
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 |
|
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'- AACTTGACAGAACATGACCCACTGG -3'
(R):5'- GTTTATAACCACTGCTGCGAATGCC -3'
Sequencing Primer
(F):5'- GGATAATCACAGGAACAGGTCCTC -3'
(R):5'- ggccaagcctaattttgaactc -3'
|
Posted On |
2014-04-24 |