Incidental Mutation 'R0312:Sema6a'
ID |
65246 |
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 |
038522-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R0312 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
18 |
Chromosomal Location |
47378321-47504267 bp(-) (GRCm39) |
Type of Mutation |
splice site (1849 bp from exon) |
DNA Base Change (assembly) |
G to A
at 47423112 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
|
Ref Sequence |
ENSEMBL: ENSMUSP00000118655
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000019791]
[ENSMUST00000076043]
[ENSMUST00000115449]
[ENSMUST00000126684]
[ENSMUST00000135790]
[ENSMUST00000156422]
|
AlphaFold |
O35464 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000019791
AA Change: A298V
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
SMART Domains |
Protein: ENSMUSP00000019791 Gene: ENSMUSG00000019647 AA Change: A298V
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: A298V
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
SMART Domains |
Protein: ENSMUSP00000075420 Gene: ENSMUSG00000019647 AA Change: A298V
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: A298V
PolyPhen 2
Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000111109 Gene: ENSMUSG00000019647 AA Change: A298V
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 null
Transcript: ENSMUST00000126684
|
SMART Domains |
Protein: ENSMUSP00000118655 Gene: ENSMUSG00000019647
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: A298V
PolyPhen 2
Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000120011 Gene: ENSMUSG00000019647 AA Change: A298V
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 |
noncoding transcript
Transcript: ENSMUST00000141224
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151382
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000156422
AA Change: A298V
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
SMART Domains |
Protein: ENSMUSP00000121442 Gene: ENSMUSG00000019647 AA Change: A298V
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 |
0.7184 |
Coding Region Coverage |
- 1x: 98.9%
- 3x: 97.9%
- 10x: 95.3%
- 20x: 90.3%
|
Validation Efficiency |
100% (60/60) |
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: 62 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abcb5 |
G |
T |
12: 118,836,572 (GRCm39) |
A1113D |
probably damaging |
Het |
Adcy1 |
G |
T |
11: 7,099,538 (GRCm39) |
A673S |
probably benign |
Het |
Apob |
T |
A |
12: 8,059,034 (GRCm39) |
H2505Q |
probably benign |
Het |
Arhgap12 |
A |
G |
18: 6,061,982 (GRCm39) |
|
probably benign |
Het |
Bcl9 |
C |
T |
3: 97,116,727 (GRCm39) |
E656K |
probably benign |
Het |
Bnc1 |
C |
T |
7: 81,627,072 (GRCm39) |
R106H |
possibly damaging |
Het |
Ccdc54 |
T |
C |
16: 50,411,165 (GRCm39) |
K34E |
possibly damaging |
Het |
Cfap65 |
G |
A |
1: 74,943,226 (GRCm39) |
R1600W |
probably damaging |
Het |
Csmd1 |
A |
T |
8: 16,034,760 (GRCm39) |
N2470K |
probably damaging |
Het |
Cspp1 |
T |
C |
1: 10,129,054 (GRCm39) |
|
probably benign |
Het |
Dgkz |
A |
T |
2: 91,768,684 (GRCm39) |
I699N |
probably damaging |
Het |
Dhx40 |
G |
A |
11: 86,662,775 (GRCm39) |
T639I |
probably damaging |
Het |
Dlg1 |
A |
G |
16: 31,609,085 (GRCm39) |
T227A |
probably benign |
Het |
Dnah10 |
G |
A |
5: 124,873,433 (GRCm39) |
|
probably benign |
Het |
Dnah3 |
T |
A |
7: 119,644,882 (GRCm39) |
K1133M |
probably damaging |
Het |
Dock5 |
G |
C |
14: 68,033,440 (GRCm39) |
F976L |
possibly damaging |
Het |
Evc |
C |
T |
5: 37,485,885 (GRCm39) |
C97Y |
possibly damaging |
Het |
Fbxw7 |
T |
C |
3: 84,874,876 (GRCm39) |
|
probably benign |
Het |
Fggy |
A |
C |
4: 95,732,422 (GRCm39) |
D112A |
probably damaging |
Het |
Fpgs |
A |
G |
2: 32,574,813 (GRCm39) |
Y435H |
probably damaging |
Het |
Fryl |
T |
A |
5: 73,230,231 (GRCm39) |
H1642L |
probably damaging |
Het |
G3bp1 |
T |
C |
11: 55,389,452 (GRCm39) |
F383L |
probably damaging |
Het |
Gda |
T |
A |
19: 21,394,369 (GRCm39) |
I237F |
probably damaging |
Het |
Glt1d1 |
A |
G |
5: 127,768,134 (GRCm39) |
N247S |
probably damaging |
Het |
Gm7647 |
T |
C |
5: 95,110,839 (GRCm39) |
S7P |
probably benign |
Het |
Gpr31b |
C |
T |
17: 13,270,498 (GRCm39) |
V224I |
probably damaging |
Het |
Hlf |
G |
A |
11: 90,278,701 (GRCm39) |
P121L |
possibly damaging |
Het |
Hsh2d |
G |
A |
8: 72,954,304 (GRCm39) |
D229N |
probably benign |
Het |
Ism1 |
G |
T |
2: 139,520,592 (GRCm39) |
M1I |
probably null |
Het |
Kansl1l |
T |
C |
1: 66,817,265 (GRCm39) |
N365S |
probably null |
Het |
Lama1 |
T |
C |
17: 68,082,846 (GRCm39) |
L1368P |
possibly damaging |
Het |
Lima1 |
A |
G |
15: 99,678,968 (GRCm39) |
V491A |
possibly damaging |
Het |
Lrch1 |
G |
T |
14: 75,185,034 (GRCm39) |
H23N |
possibly damaging |
Het |
Lrp1b |
A |
G |
2: 41,172,183 (GRCm39) |
V1488A |
probably damaging |
Het |
Lrp8 |
T |
C |
4: 107,664,052 (GRCm39) |
|
probably benign |
Het |
Lrrc8e |
A |
G |
8: 4,285,733 (GRCm39) |
S653G |
probably benign |
Het |
Mnat1 |
A |
G |
12: 73,228,558 (GRCm39) |
T141A |
possibly damaging |
Het |
Mpeg1 |
C |
A |
19: 12,439,767 (GRCm39) |
N408K |
probably damaging |
Het |
Myo7b |
T |
C |
18: 32,147,390 (GRCm39) |
E51G |
possibly damaging |
Het |
Myrf |
G |
C |
19: 10,195,526 (GRCm39) |
T428S |
probably benign |
Het |
Naa35 |
A |
G |
13: 59,757,395 (GRCm39) |
T257A |
probably benign |
Het |
Obox5 |
T |
A |
7: 15,491,485 (GRCm39) |
H8Q |
probably damaging |
Het |
Or1j4 |
A |
T |
2: 36,740,372 (GRCm39) |
I105L |
probably benign |
Het |
Or51q1c |
T |
C |
7: 103,653,232 (GRCm39) |
V250A |
probably damaging |
Het |
Or5h26 |
A |
T |
16: 58,988,202 (GRCm39) |
F101L |
probably benign |
Het |
Phldb2 |
G |
T |
16: 45,609,410 (GRCm39) |
T732N |
probably damaging |
Het |
Phyhip |
G |
T |
14: 70,704,410 (GRCm39) |
A210S |
possibly damaging |
Het |
Pik3r4 |
A |
G |
9: 105,563,409 (GRCm39) |
D1262G |
probably damaging |
Het |
Pip |
G |
A |
6: 41,826,798 (GRCm39) |
E48K |
possibly damaging |
Het |
Plk4 |
C |
T |
3: 40,767,982 (GRCm39) |
L74F |
probably damaging |
Het |
Prdm14 |
G |
A |
1: 13,189,031 (GRCm39) |
R438W |
probably damaging |
Het |
Rab19 |
G |
A |
6: 39,361,023 (GRCm39) |
R57H |
probably benign |
Het |
Rtl1 |
G |
T |
12: 109,556,661 (GRCm39) |
P1726Q |
probably damaging |
Het |
Skint6 |
A |
T |
4: 112,666,297 (GRCm39) |
V1176D |
possibly damaging |
Het |
Slc12a1 |
A |
G |
2: 125,067,948 (GRCm39) |
I1012V |
probably damaging |
Het |
Slc1a3 |
C |
T |
15: 8,665,721 (GRCm39) |
M509I |
probably benign |
Het |
Spata18 |
G |
A |
5: 73,824,224 (GRCm39) |
G35E |
probably benign |
Het |
Spata31h1 |
A |
T |
10: 82,120,203 (GRCm39) |
I4269N |
probably damaging |
Het |
Sspo |
C |
T |
6: 48,432,335 (GRCm39) |
P801L |
possibly damaging |
Het |
Ugt2b37 |
C |
T |
5: 87,398,524 (GRCm39) |
G304D |
probably damaging |
Het |
Vmn2r25 |
A |
T |
6: 123,805,539 (GRCm39) |
|
probably benign |
Het |
Xrcc6 |
C |
A |
15: 81,911,423 (GRCm39) |
|
probably null |
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 |
|
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 |
|
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 |
|
Posted On |
2013-08-08 |