Incidental Mutation 'R9638:Sema4a'
| ID |
725814 |
| 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 |
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.902)
|
| Stock # |
R9638 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
88343266-88368489 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 88357066 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Tyrosine
at position 302
(N302Y)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000029700
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029700]
[ENSMUST00000107531]
[ENSMUST00000125526]
[ENSMUST00000127436]
[ENSMUST00000141471]
[ENSMUST00000147200]
[ENSMUST00000165898]
[ENSMUST00000166237]
[ENSMUST00000169222]
[ENSMUST00000184487]
[ENSMUST00000184876]
[ENSMUST00000185137]
|
| AlphaFold |
Q62178 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000029700
AA Change: N302Y
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000029700
Gene: ENSMUSG00000028064
AA Change: N302Y
| 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: N170Y
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000103155
Gene: ENSMUSG00000028064
AA Change: N170Y
| 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 |
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: N302Y
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000128510
Gene: ENSMUSG00000028064
AA Change: N302Y
| 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: N302Y
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000125909
Gene: ENSMUSG00000028064
AA Change: N302Y
| 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: N302Y
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000128887
Gene: ENSMUSG00000028064
AA Change: N302Y
| 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: 99.7%
- 20x: 99.0%
|
| 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: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca1 |
T |
G |
4: 53,092,806 (GRCm39) |
E326A |
probably damaging |
Het |
| Aldh1a1 |
T |
A |
19: 20,614,100 (GRCm39) |
N423K |
probably benign |
Het |
| Aldh4a1 |
T |
A |
4: 139,371,427 (GRCm39) |
I447N |
probably damaging |
Het |
| Atg9b |
T |
C |
5: 24,596,406 (GRCm39) |
D170G |
possibly damaging |
Het |
| Bnc2 |
C |
T |
4: 84,332,492 (GRCm39) |
V75M |
probably damaging |
Het |
| Bnip3l |
G |
A |
14: 67,246,214 (GRCm39) |
P7L |
possibly damaging |
Het |
| Ccdc162 |
C |
A |
10: 41,437,159 (GRCm39) |
C1750F |
probably benign |
Het |
| Cdh10 |
T |
A |
15: 18,964,301 (GRCm39) |
N154K |
probably damaging |
Het |
| Cdh22 |
T |
C |
2: 164,988,687 (GRCm39) |
I223V |
probably damaging |
Het |
| Ces1b |
T |
A |
8: 93,806,534 (GRCm39) |
H4L |
probably benign |
Het |
| Cfap46 |
A |
T |
7: 139,209,763 (GRCm39) |
F1806I |
unknown |
Het |
| Cwh43 |
T |
A |
5: 73,565,486 (GRCm39) |
V17D |
possibly damaging |
Het |
| Ddx3y |
C |
T |
Y: 1,263,599 (GRCm39) |
G623D |
probably benign |
Het |
| Dtna |
A |
T |
18: 23,744,122 (GRCm39) |
I389L |
probably benign |
Het |
| F830016B08Rik |
A |
G |
18: 60,432,956 (GRCm39) |
D13G |
probably benign |
Het |
| Fam161b |
T |
C |
12: 84,403,187 (GRCm39) |
I148V |
probably benign |
Het |
| Fhip1a |
T |
A |
3: 85,568,391 (GRCm39) |
N1043Y |
probably damaging |
Het |
| Fli1 |
T |
C |
9: 32,388,020 (GRCm39) |
Y23C |
probably damaging |
Het |
| Gimap6 |
A |
G |
6: 48,679,424 (GRCm39) |
V204A |
probably benign |
Het |
| Ighv4-1 |
T |
G |
12: 113,911,904 (GRCm39) |
R116S |
probably damaging |
Het |
| Isx |
T |
C |
8: 75,619,566 (GRCm39) |
L239P |
probably damaging |
Het |
| Krt1 |
AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC |
AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC |
15: 101,758,813 (GRCm39) |
|
probably benign |
Het |
| Krt81 |
T |
C |
15: 101,358,856 (GRCm39) |
T299A |
probably benign |
Het |
| Lrrc30 |
A |
G |
17: 67,939,226 (GRCm39) |
L118P |
probably damaging |
Het |
| Mapk8ip3 |
T |
C |
17: 25,118,023 (GRCm39) |
T1290A |
probably benign |
Het |
| Mef2b |
ACCCTCACCC |
ACC |
8: 70,619,506 (GRCm39) |
|
probably null |
Het |
| Meltf |
G |
A |
16: 31,706,409 (GRCm39) |
E298K |
possibly damaging |
Het |
| Muc16 |
T |
A |
9: 18,550,626 (GRCm39) |
E5222D |
probably benign |
Het |
| Nin |
T |
C |
12: 70,067,618 (GRCm39) |
N2003S |
|
Het |
| Or1e23 |
A |
G |
11: 73,407,875 (GRCm39) |
I50T |
probably benign |
Het |
| Or2b4 |
G |
A |
17: 38,116,509 (GRCm39) |
V158M |
probably damaging |
Het |
| Or51f1d |
T |
C |
7: 102,701,018 (GRCm39) |
L171P |
probably damaging |
Het |
| Palld |
A |
G |
8: 62,002,788 (GRCm39) |
V826A |
unknown |
Het |
| Paxbp1 |
C |
A |
16: 90,831,881 (GRCm39) |
V336L |
probably benign |
Het |
| Paxbp1 |
T |
A |
16: 90,831,882 (GRCm39) |
E335D |
probably benign |
Het |
| Por |
C |
A |
5: 135,754,615 (GRCm39) |
Q12K |
unknown |
Het |
| Pot1a |
G |
A |
6: 25,750,106 (GRCm39) |
Q519* |
probably null |
Het |
| Psd |
GCC |
GC |
19: 46,301,841 (GRCm39) |
|
probably null |
Het |
| Ptger4 |
A |
G |
15: 5,264,693 (GRCm39) |
F321S |
probably damaging |
Het |
| Ptk7 |
A |
G |
17: 46,890,519 (GRCm39) |
Y438H |
possibly damaging |
Het |
| Rimklb |
A |
T |
6: 122,433,558 (GRCm39) |
N254K |
probably benign |
Het |
| Rpn2 |
A |
T |
2: 157,125,566 (GRCm39) |
T26S |
probably benign |
Het |
| Rtn4rl2 |
A |
T |
2: 84,710,760 (GRCm39) |
L168H |
probably damaging |
Het |
| Scel |
G |
T |
14: 103,779,409 (GRCm39) |
A127S |
possibly damaging |
Het |
| Supt3 |
A |
G |
17: 45,234,133 (GRCm39) |
T50A |
possibly damaging |
Het |
| Upf3a |
G |
A |
8: 13,848,343 (GRCm39) |
A380T |
probably benign |
Het |
| Zbtb14 |
G |
A |
17: 69,695,375 (GRCm39) |
E358K |
probably damaging |
Het |
| Zfp677 |
A |
T |
17: 21,618,056 (GRCm39) |
H371L |
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 |
|
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 |
|
|
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'- CCTACACATGAGAGACAGTCCG -3'
(R):5'- TGGCCACTTGGAAGCCAATG -3'
Sequencing Primer
(F):5'- ACATGAGAGACAGTCCGGTTCC -3'
(R):5'- CCACTTGGAAGCCAATGGGAATG -3'
|
| Posted On |
2022-09-12 |
Incidental Mutation