Incidental Mutation 'R5779:Sema6a'
| ID |
446905 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sema6a
|
| Ensembl Gene |
ENSMUSG00000019647 |
| Gene Name |
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A |
| Synonyms |
VIa, Semaq, Sema6A-1, sema, A730020P05Rik |
| MMRRC Submission |
043377-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5779 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
47378321-47504267 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 47381893 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Cysteine
at position 885
(R885C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000121442
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000019791]
[ENSMUST00000076043]
[ENSMUST00000115449]
[ENSMUST00000135790]
[ENSMUST00000156422]
|
| AlphaFold |
O35464 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000019791
AA Change: R885C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647
AA Change: R885C
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
18 |
N/A |
INTRINSIC |
|
Sema
|
56 |
487 |
1.06e-185 |
SMART |
|
PSI
|
514 |
569 |
9.57e-1 |
SMART |
|
transmembrane domain
|
648 |
670 |
N/A |
INTRINSIC |
|
low complexity region
|
932 |
951 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000076043
AA Change: R830C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647
AA Change: R830C
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
18 |
N/A |
INTRINSIC |
|
Sema
|
56 |
487 |
1.06e-185 |
SMART |
|
PSI
|
514 |
569 |
9.57e-1 |
SMART |
|
transmembrane domain
|
593 |
615 |
N/A |
INTRINSIC |
|
low complexity region
|
877 |
896 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000115449
AA Change: R859C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
AA Change: R859C
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
18 |
N/A |
INTRINSIC |
|
Sema
|
56 |
461 |
1.24e-168 |
SMART |
|
PSI
|
488 |
543 |
9.57e-1 |
SMART |
|
transmembrane domain
|
622 |
644 |
N/A |
INTRINSIC |
|
low complexity region
|
906 |
925 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000123228
|
| SMART Domains |
Protein: ENSMUSP00000120249
Gene: ENSMUSG00000019647
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:PSI
|
2 |
45 |
4e-26 |
BLAST |
|
PDB:3OKY|B
|
2 |
47 |
2e-26 |
PDB |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000135790
AA Change: R902C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
AA Change: R902C
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
18 |
N/A |
INTRINSIC |
|
Sema
|
56 |
487 |
1.06e-185 |
SMART |
|
PSI
|
514 |
569 |
9.57e-1 |
SMART |
|
transmembrane domain
|
665 |
687 |
N/A |
INTRINSIC |
|
low complexity region
|
949 |
968 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000156422
AA Change: R885C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647
AA Change: R885C
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
18 |
N/A |
INTRINSIC |
|
Sema
|
56 |
487 |
1.06e-185 |
SMART |
|
PSI
|
514 |
569 |
9.57e-1 |
SMART |
|
transmembrane domain
|
648 |
670 |
N/A |
INTRINSIC |
|
low complexity region
|
932 |
951 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.6467 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.8%
|
| Validation Efficiency |
88% (52/59) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The transmembrane semaphorin SEMA6A is expressed in developing neural tissue and is required for proper development of the thalamocortical projection (Leighton et al., 2001 [PubMed 11242070]).[supplied by OMIM, Feb 2011]
PHENOTYPE: Mice homozygous for a gene trapped allele exhibit defects in lamina-specific neurite stratification of specific retinal neuron subtypes and disruption of the dendritic plexus organization of On but not Off starburst amacrine cells. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca6 |
T |
C |
11: 110,075,496 (GRCm39) |
M1332V |
probably benign |
Het |
| Acsbg3 |
A |
T |
17: 57,188,061 (GRCm39) |
N190Y |
probably benign |
Het |
| Afg3l2 |
T |
C |
18: 67,573,513 (GRCm39) |
K132R |
probably null |
Het |
| Antkmt |
A |
G |
17: 26,009,631 (GRCm39) |
V194A |
probably benign |
Het |
| Arap3 |
T |
C |
18: 38,117,418 (GRCm39) |
D886G |
probably damaging |
Het |
| B3gntl1 |
G |
T |
11: 121,542,502 (GRCm39) |
|
probably null |
Het |
| Cdk12 |
T |
A |
11: 98,109,900 (GRCm39) |
S640R |
probably benign |
Het |
| Ceacam12 |
C |
A |
7: 17,803,079 (GRCm39) |
P162T |
probably benign |
Het |
| Chrna5 |
C |
A |
9: 54,905,388 (GRCm39) |
H67N |
probably benign |
Het |
| Copb1 |
T |
A |
7: 113,818,807 (GRCm39) |
D837V |
probably damaging |
Het |
| Dcaf5 |
C |
T |
12: 80,385,606 (GRCm39) |
R840H |
probably benign |
Het |
| Ect2l |
T |
A |
10: 18,039,186 (GRCm39) |
Q324L |
probably benign |
Het |
| Eef1e1 |
T |
C |
13: 38,830,249 (GRCm39) |
N141S |
probably damaging |
Het |
| Eif2ak4 |
A |
C |
2: 118,243,444 (GRCm39) |
N208T |
possibly damaging |
Het |
| Ext1 |
A |
G |
15: 53,207,949 (GRCm39) |
Y271H |
probably damaging |
Het |
| Fbxo5 |
G |
A |
10: 5,750,303 (GRCm39) |
R323C |
possibly damaging |
Het |
| Fpr-rs3 |
C |
A |
17: 20,844,488 (GRCm39) |
A218S |
possibly damaging |
Het |
| Gm20499 |
G |
A |
5: 114,955,082 (GRCm39) |
|
probably benign |
Het |
| Gm57859 |
A |
G |
11: 113,578,818 (GRCm39) |
D71G |
probably benign |
Het |
| Gucy1b2 |
C |
A |
14: 62,651,750 (GRCm39) |
L400F |
possibly damaging |
Het |
| Hgd |
T |
A |
16: 37,413,733 (GRCm39) |
L24H |
probably benign |
Het |
| Hmx3 |
C |
A |
7: 131,146,057 (GRCm39) |
S255* |
probably null |
Het |
| Ifrd1 |
A |
T |
12: 40,253,369 (GRCm39) |
F448I |
probably damaging |
Het |
| Igfn1 |
T |
A |
1: 135,894,578 (GRCm39) |
E1996V |
probably benign |
Het |
| Itpr1 |
G |
A |
6: 108,329,104 (GRCm39) |
G173R |
probably damaging |
Het |
| Kbtbd8 |
T |
C |
6: 95,095,515 (GRCm39) |
S26P |
probably benign |
Het |
| Kctd17 |
A |
T |
15: 78,321,333 (GRCm39) |
|
probably benign |
Het |
| Matr3 |
T |
C |
18: 35,717,575 (GRCm39) |
S258P |
possibly damaging |
Het |
| Mpp4 |
G |
A |
1: 59,190,825 (GRCm39) |
A90V |
probably benign |
Het |
| Mrpl20 |
G |
A |
4: 155,891,378 (GRCm39) |
R34Q |
probably damaging |
Het |
| Neb |
A |
T |
2: 52,135,313 (GRCm39) |
S3266T |
probably damaging |
Het |
| Nipal3 |
A |
G |
4: 135,179,650 (GRCm39) |
|
probably benign |
Het |
| Npas2 |
A |
T |
1: 39,326,652 (GRCm39) |
T46S |
possibly damaging |
Het |
| Nsd3 |
G |
T |
8: 26,172,685 (GRCm39) |
E815* |
probably null |
Het |
| Nup98 |
C |
A |
7: 101,801,568 (GRCm39) |
V786L |
probably benign |
Het |
| Or4k2 |
A |
T |
14: 50,424,203 (GRCm39) |
M157K |
possibly damaging |
Het |
| Pcdhb3 |
T |
C |
18: 37,434,520 (GRCm39) |
V162A |
probably benign |
Het |
| Pcgf2 |
G |
A |
11: 97,581,117 (GRCm39) |
P58L |
probably damaging |
Het |
| Penk |
A |
G |
4: 4,134,318 (GRCm39) |
F110L |
probably damaging |
Het |
| Relch |
T |
G |
1: 105,615,072 (GRCm39) |
N246K |
probably damaging |
Het |
| Scfd1 |
A |
G |
12: 51,478,312 (GRCm39) |
N508S |
probably benign |
Het |
| Scn2a |
T |
C |
2: 65,594,827 (GRCm39) |
V1892A |
probably benign |
Het |
| Sik2 |
T |
C |
9: 50,807,145 (GRCm39) |
H755R |
probably benign |
Het |
| Slc36a3 |
A |
T |
11: 55,026,094 (GRCm39) |
Y241* |
probably null |
Het |
| Smg5 |
T |
C |
3: 88,258,925 (GRCm39) |
|
probably benign |
Het |
| Spag9 |
A |
G |
11: 94,005,079 (GRCm39) |
T1049A |
probably benign |
Het |
| Tas2r103 |
T |
C |
6: 133,013,908 (GRCm39) |
M53V |
probably benign |
Het |
| Tpr |
C |
T |
1: 150,299,292 (GRCm39) |
A1090V |
probably damaging |
Het |
| Traf5 |
T |
A |
1: 191,729,633 (GRCm39) |
R473W |
probably damaging |
Het |
| Ush2a |
T |
C |
1: 188,175,707 (GRCm39) |
|
probably null |
Het |
| Vit |
A |
G |
17: 78,853,855 (GRCm39) |
T34A |
probably benign |
Het |
|
| Other mutations in Sema6a |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00336:Sema6a
|
APN |
18 |
47,423,042 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL01351:Sema6a
|
APN |
18 |
47,414,369 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
IGL01594:Sema6a
|
APN |
18 |
47,381,884 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01953:Sema6a
|
APN |
18 |
47,423,187 (GRCm39) |
nonsense |
probably null |
|
|
IGL02077:Sema6a
|
APN |
18 |
47,416,465 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
IGL02632:Sema6a
|
APN |
18 |
47,423,222 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02957:Sema6a
|
APN |
18 |
47,382,291 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03013:Sema6a
|
APN |
18 |
47,381,461 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL03279:Sema6a
|
APN |
18 |
47,433,157 (GRCm39) |
nonsense |
probably null |
|
|
saphire
|
UTSW |
18 |
47,439,496 (GRCm39) |
nonsense |
probably null |
|
|
IGL02988:Sema6a
|
UTSW |
18 |
47,431,281 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0114:Sema6a
|
UTSW |
18 |
47,423,244 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0311:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0312:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0347:Sema6a
|
UTSW |
18 |
47,424,196 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0350:Sema6a
|
UTSW |
18 |
47,403,785 (GRCm39) |
missense |
probably benign |
|
|
R0366:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0368:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0391:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0403:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0466:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0515:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0517:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0542:Sema6a
|
UTSW |
18 |
47,381,643 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0557:Sema6a
|
UTSW |
18 |
47,382,567 (GRCm39) |
missense |
probably benign |
0.01 |
|
R0569:Sema6a
|
UTSW |
18 |
47,403,872 (GRCm39) |
splice site |
probably null |
|
|
R0650:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0689:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0694:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0726:Sema6a
|
UTSW |
18 |
47,425,048 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0741:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0821:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0824:Sema6a
|
UTSW |
18 |
47,423,112 (GRCm39) |
splice site |
probably null |
|
|
R0924:Sema6a
|
UTSW |
18 |
47,381,559 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1108:Sema6a
|
UTSW |
18 |
47,439,498 (GRCm39) |
missense |
probably benign |
0.02 |
|
R1255:Sema6a
|
UTSW |
18 |
47,382,366 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1422:Sema6a
|
UTSW |
18 |
47,439,498 (GRCm39) |
missense |
probably benign |
0.02 |
|
R1531:Sema6a
|
UTSW |
18 |
47,382,066 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1707:Sema6a
|
UTSW |
18 |
47,416,512 (GRCm39) |
missense |
probably benign |
0.04 |
|
R1746:Sema6a
|
UTSW |
18 |
47,439,416 (GRCm39) |
splice site |
probably benign |
|
|
R1807:Sema6a
|
UTSW |
18 |
47,409,491 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R1974:Sema6a
|
UTSW |
18 |
47,403,696 (GRCm39) |
missense |
probably benign |
0.04 |
|
R1987:Sema6a
|
UTSW |
18 |
47,433,209 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2044:Sema6a
|
UTSW |
18 |
47,439,496 (GRCm39) |
nonsense |
probably null |
|
|
R3719:Sema6a
|
UTSW |
18 |
47,382,144 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4491:Sema6a
|
UTSW |
18 |
47,439,524 (GRCm39) |
utr 5 prime |
probably benign |
|
|
R4552:Sema6a
|
UTSW |
18 |
47,424,990 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4707:Sema6a
|
UTSW |
18 |
47,381,779 (GRCm39) |
missense |
probably benign |
0.43 |
|
R4710:Sema6a
|
UTSW |
18 |
47,403,750 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4713:Sema6a
|
UTSW |
18 |
47,382,363 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
R4963:Sema6a
|
UTSW |
18 |
47,431,318 (GRCm39) |
missense |
possibly damaging |
0.48 |
|
R5088:Sema6a
|
UTSW |
18 |
47,382,196 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5133:Sema6a
|
UTSW |
18 |
47,433,195 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5135:Sema6a
|
UTSW |
18 |
47,424,239 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5141:Sema6a
|
UTSW |
18 |
47,381,455 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5277:Sema6a
|
UTSW |
18 |
47,409,611 (GRCm39) |
intron |
probably benign |
|
|
R5551:Sema6a
|
UTSW |
18 |
47,381,595 (GRCm39) |
missense |
possibly damaging |
0.76 |
|
R5618:Sema6a
|
UTSW |
18 |
47,415,015 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5717:Sema6a
|
UTSW |
18 |
47,382,330 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5729:Sema6a
|
UTSW |
18 |
47,414,410 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5917:Sema6a
|
UTSW |
18 |
47,414,405 (GRCm39) |
missense |
probably benign |
0.05 |
|
R6054:Sema6a
|
UTSW |
18 |
47,416,470 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R6142:Sema6a
|
UTSW |
18 |
47,414,266 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6209:Sema6a
|
UTSW |
18 |
47,431,369 (GRCm39) |
splice site |
probably null |
|
|
R6307:Sema6a
|
UTSW |
18 |
47,382,231 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6734:Sema6a
|
UTSW |
18 |
47,412,236 (GRCm39) |
missense |
probably benign |
0.31 |
|
R7014:Sema6a
|
UTSW |
18 |
47,431,284 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7033:Sema6a
|
UTSW |
18 |
47,381,637 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R7574:Sema6a
|
UTSW |
18 |
47,424,231 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8054:Sema6a
|
UTSW |
18 |
47,424,972 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8250:Sema6a
|
UTSW |
18 |
47,423,182 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8408:Sema6a
|
UTSW |
18 |
47,381,958 (GRCm39) |
missense |
probably benign |
0.34 |
|
R8411:Sema6a
|
UTSW |
18 |
47,382,022 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8900:Sema6a
|
UTSW |
18 |
47,424,182 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9140:Sema6a
|
UTSW |
18 |
47,415,009 (GRCm39) |
missense |
probably benign |
|
|
R9158:Sema6a
|
UTSW |
18 |
47,431,330 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R9488:Sema6a
|
UTSW |
18 |
47,437,216 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9565:Sema6a
|
UTSW |
18 |
47,382,594 (GRCm39) |
missense |
probably null |
1.00 |
|
R9652:Sema6a
|
UTSW |
18 |
47,382,252 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9732:Sema6a
|
UTSW |
18 |
47,381,925 (GRCm39) |
missense |
probably damaging |
0.96 |
|
X0065:Sema6a
|
UTSW |
18 |
47,416,386 (GRCm39) |
missense |
possibly damaging |
0.78 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGCTGTGCACCTGGATAGAG -3'
(R):5'- GTACGTAGATCAGCCCAAAATG -3'
Sequencing Primer
(F):5'- CAAAGCTCTGGTTCCTGGAGAG -3'
(R):5'- TCAGCCCAAAATGAGCGAG -3'
|
| Posted On |
2016-12-15 |
Incidental Mutation