Incidental Mutation 'R9158:Sema6a'
ID |
695540 |
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 |
068942-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R9158 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
18 |
Chromosomal Location |
47378321-47504267 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 47431330 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Isoleucine
at position 123
(V123I)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000019791
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000019791]
[ENSMUST00000076043]
[ENSMUST00000115449]
[ENSMUST00000126684]
[ENSMUST00000135790]
[ENSMUST00000156422]
|
AlphaFold |
O35464 |
PDB Structure |
Mouse Semaphorin 6A extracellular domain [X-RAY DIFFRACTION]
Plexin A2 / Semaphorin 6A complex [X-RAY DIFFRACTION]
Mouse Semaphorin 6A, extracellular domains 1-2 [X-RAY DIFFRACTION]
Plexin A2 in complex with Semaphorin 6A [X-RAY DIFFRACTION]
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000019791
AA Change: V123I
PolyPhen 2
Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000019791 Gene: ENSMUSG00000019647 AA Change: V123I
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: V123I
PolyPhen 2
Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000075420 Gene: ENSMUSG00000019647 AA Change: V123I
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: V123I
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000111109 Gene: ENSMUSG00000019647 AA Change: V123I
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 damaging
Transcript: ENSMUST00000126684
AA Change: V123I
PolyPhen 2
Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000118655 Gene: ENSMUSG00000019647 AA Change: V123I
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
18 |
N/A |
INTRINSIC |
Pfam:Sema
|
56 |
216 |
2.5e-51 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000135790
AA Change: V123I
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000120011 Gene: ENSMUSG00000019647 AA Change: V123I
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: V123I
PolyPhen 2
Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000121442 Gene: ENSMUSG00000019647 AA Change: V123I
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 |
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.5%
|
Validation Efficiency |
100% (62/62) |
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: 61 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adam25 |
G |
A |
8: 41,208,645 (GRCm39) |
C637Y |
probably damaging |
Het |
Ahdc1 |
A |
G |
4: 132,792,505 (GRCm39) |
T1249A |
possibly damaging |
Het |
Alkbh3 |
A |
G |
2: 93,835,082 (GRCm39) |
S88P |
probably damaging |
Het |
Ankrd17 |
C |
A |
5: 90,416,575 (GRCm39) |
A1086S |
probably damaging |
Het |
Ankzf1 |
T |
A |
1: 75,173,020 (GRCm39) |
V372E |
probably damaging |
Het |
Apbb1ip |
T |
C |
2: 22,764,951 (GRCm39) |
V544A |
probably benign |
Het |
Atp13a2 |
T |
C |
4: 140,724,112 (GRCm39) |
|
probably null |
Het |
Cacna2d1 |
A |
G |
5: 16,140,039 (GRCm39) |
T10A |
probably benign |
Het |
Cadps |
T |
C |
14: 12,546,356 (GRCm38) |
N500S |
probably benign |
Het |
Casp16 |
A |
G |
17: 23,769,948 (GRCm39) |
|
probably benign |
Het |
Cdh22 |
T |
A |
2: 165,012,627 (GRCm39) |
I153F |
probably damaging |
Het |
Clip2 |
T |
C |
5: 134,521,251 (GRCm39) |
E964G |
probably benign |
Het |
Cracdl |
A |
T |
1: 37,670,442 (GRCm39) |
M166K |
probably damaging |
Het |
Cryga |
T |
C |
1: 65,142,198 (GRCm39) |
D65G |
probably benign |
Het |
Dap3 |
A |
G |
3: 88,832,637 (GRCm39) |
Y357H |
probably damaging |
Het |
Eef2 |
C |
T |
10: 81,014,693 (GRCm39) |
|
probably benign |
Het |
Gja4 |
A |
G |
4: 127,206,466 (GRCm39) |
L99P |
probably damaging |
Het |
Glb1l3 |
A |
T |
9: 26,765,005 (GRCm39) |
Y135* |
probably null |
Het |
Gm5114 |
T |
G |
7: 39,060,486 (GRCm39) |
D121A |
probably damaging |
Het |
Gm6525 |
A |
G |
3: 84,082,255 (GRCm39) |
K59E |
probably benign |
Het |
Herc1 |
C |
T |
9: 66,376,400 (GRCm39) |
L3407F |
probably benign |
Het |
Hmgcr |
G |
A |
13: 96,792,170 (GRCm39) |
R589* |
probably null |
Het |
Iglv3 |
A |
C |
16: 19,060,012 (GRCm39) |
D105E |
probably damaging |
Het |
Il1r1 |
G |
A |
1: 40,332,391 (GRCm39) |
W60* |
probably null |
Het |
Il31ra |
C |
T |
13: 112,670,394 (GRCm39) |
W331* |
probably null |
Het |
Inca1 |
C |
T |
11: 70,581,376 (GRCm39) |
C16Y |
probably damaging |
Het |
Inpp4a |
A |
G |
1: 37,442,552 (GRCm39) |
T628A |
possibly damaging |
Het |
Kdm2a |
C |
G |
19: 4,374,715 (GRCm39) |
R805S |
possibly damaging |
Het |
Kel |
T |
A |
6: 41,664,905 (GRCm39) |
I620L |
probably benign |
Het |
Kmt2d |
C |
T |
15: 98,741,020 (GRCm39) |
G4638R |
unknown |
Het |
Lilrb4b |
T |
A |
10: 51,357,829 (GRCm39) |
N174K |
possibly damaging |
Het |
Ltbp2 |
G |
A |
12: 84,837,864 (GRCm39) |
P1192L |
probably benign |
Het |
Ltf |
T |
A |
9: 110,868,003 (GRCm39) |
V615E |
probably damaging |
Het |
Map7d1 |
G |
T |
4: 126,130,478 (GRCm39) |
Q443K |
possibly damaging |
Het |
Mapk9 |
A |
G |
11: 49,745,095 (GRCm39) |
D3G |
probably benign |
Het |
Nktr |
T |
G |
9: 121,582,154 (GRCm39) |
S1424A |
unknown |
Het |
Npas1 |
A |
G |
7: 16,195,333 (GRCm39) |
S332P |
possibly damaging |
Het |
Or13a25 |
T |
C |
7: 140,247,547 (GRCm39) |
S109P |
possibly damaging |
Het |
Or52n2c |
T |
C |
7: 104,574,086 (GRCm39) |
Y295C |
probably damaging |
Het |
Or5ak4 |
A |
G |
2: 85,161,348 (GRCm39) |
I298T |
probably benign |
Het |
Or6d12 |
T |
C |
6: 116,492,791 (GRCm39) |
F18L |
possibly damaging |
Het |
Or8b12b |
C |
A |
9: 37,684,800 (GRCm39) |
P282T |
probably damaging |
Het |
Pcdh8 |
A |
G |
14: 80,005,182 (GRCm39) |
W948R |
probably damaging |
Het |
Pde3a |
A |
G |
6: 141,195,614 (GRCm39) |
E100G |
probably benign |
Het |
Phrf1 |
T |
A |
7: 140,836,466 (GRCm39) |
V246D |
unknown |
Het |
Pitpnb |
A |
T |
5: 111,530,876 (GRCm39) |
N223I |
probably damaging |
Het |
Pkd1l3 |
A |
T |
8: 110,394,207 (GRCm39) |
R2065* |
probably null |
Het |
Prepl |
T |
C |
17: 85,383,379 (GRCm39) |
D355G |
possibly damaging |
Het |
Runx2 |
A |
G |
17: 45,046,508 (GRCm39) |
V5A |
probably benign |
Het |
Sema4g |
T |
A |
19: 44,986,846 (GRCm39) |
V433D |
possibly damaging |
Het |
Senp6 |
A |
G |
9: 79,994,732 (GRCm39) |
K24E |
probably benign |
Het |
Slc22a8 |
T |
A |
19: 8,583,427 (GRCm39) |
S211T |
probably damaging |
Het |
Slc34a2 |
A |
G |
5: 53,221,217 (GRCm39) |
D221G |
possibly damaging |
Het |
Tmprss11g |
A |
T |
5: 86,637,166 (GRCm39) |
L323Q |
probably damaging |
Het |
Tpcn1 |
T |
C |
5: 120,687,988 (GRCm39) |
|
probably benign |
Het |
Trim65 |
G |
A |
11: 116,018,050 (GRCm39) |
T311I |
probably benign |
Het |
Tub |
T |
C |
7: 108,625,962 (GRCm39) |
F284L |
possibly damaging |
Het |
Ube2j1 |
G |
A |
4: 33,036,711 (GRCm39) |
V12I |
probably benign |
Het |
Vmn2r101 |
A |
T |
17: 19,809,161 (GRCm39) |
N97Y |
probably benign |
Het |
Vmn2r49 |
C |
A |
7: 9,722,835 (GRCm39) |
W146C |
probably damaging |
Het |
Zfp628 |
T |
C |
7: 4,922,153 (GRCm39) |
L125P |
probably damaging |
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 |
R5779:Sema6a
|
UTSW |
18 |
47,381,893 (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 |
|
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'- CCCATGTGGTGTAGCGTTAC -3'
(R):5'- AACCCAGCTGTGTATTGCTCC -3'
Sequencing Primer
(F):5'- GTTACCCCGCTTCAGTTGCTG -3'
(R):5'- CAGTCATCCTGAGAAGGCTTCTAAG -3'
|
Posted On |
2022-01-20 |