Incidental Mutation 'R4713:Sema6a'
| ID |
353406 |
| 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 |
041601-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4713 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
47378321-47504267 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 47382363 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Leucine
at position 728
(H728L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000121442
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000019791]
[ENSMUST00000076043]
[ENSMUST00000115449]
[ENSMUST00000135790]
[ENSMUST00000156422]
|
| AlphaFold |
O35464 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000019791
AA Change: H728L
PolyPhen 2
Score 0.787 (Sensitivity: 0.85; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647
AA Change: H728L
| 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 |
possibly damaging
Transcript: ENSMUST00000076043
AA Change: H673L
PolyPhen 2
Score 0.697 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647
AA Change: H673L
| 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 |
possibly damaging
Transcript: ENSMUST00000115449
AA Change: H702L
PolyPhen 2
Score 0.787 (Sensitivity: 0.85; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
AA Change: H702L
| 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 |
possibly damaging
Transcript: ENSMUST00000135790
AA Change: H745L
PolyPhen 2
Score 0.679 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
AA Change: H745L
| 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 |
possibly damaging
Transcript: ENSMUST00000156422
AA Change: H728L
PolyPhen 2
Score 0.787 (Sensitivity: 0.85; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647
AA Change: H728L
| 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: 99.1%
- 3x: 98.5%
- 10x: 96.7%
- 20x: 94.0%
|
| Validation Efficiency |
|
| 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: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgrb3 |
G |
T |
1: 25,586,613 (GRCm39) |
T360K |
probably damaging |
Het |
| AW551984 |
T |
C |
9: 39,508,449 (GRCm39) |
K356E |
probably benign |
Het |
| Bpifb2 |
T |
A |
2: 153,723,113 (GRCm39) |
V123E |
probably damaging |
Het |
| Cacna1a |
T |
G |
8: 85,276,143 (GRCm39) |
F532V |
probably damaging |
Het |
| Cct8 |
C |
A |
16: 87,284,576 (GRCm39) |
E204* |
probably null |
Het |
| Cd163 |
T |
A |
6: 124,294,577 (GRCm39) |
|
probably null |
Het |
| Cep152 |
C |
A |
2: 125,429,868 (GRCm39) |
A685S |
possibly damaging |
Het |
| Chdh |
A |
G |
14: 29,758,798 (GRCm39) |
D581G |
probably benign |
Het |
| Cnpy3 |
A |
C |
17: 47,058,391 (GRCm39) |
Y77* |
probably null |
Het |
| Col5a3 |
T |
C |
9: 20,704,870 (GRCm39) |
E762G |
unknown |
Het |
| Creb3 |
A |
G |
4: 43,563,247 (GRCm39) |
T115A |
probably benign |
Het |
| Dlat |
G |
T |
9: 50,555,781 (GRCm39) |
A412E |
probably benign |
Het |
| Dnah2 |
T |
C |
11: 69,367,514 (GRCm39) |
N1789S |
probably damaging |
Het |
| Dzank1 |
C |
T |
2: 144,333,724 (GRCm39) |
E370K |
probably benign |
Het |
| Eif3m |
A |
T |
2: 104,837,184 (GRCm39) |
|
probably null |
Het |
| Gimap8 |
A |
T |
6: 48,635,920 (GRCm39) |
M562L |
probably benign |
Het |
| Gprc6a |
T |
A |
10: 51,507,553 (GRCm39) |
|
probably benign |
Het |
| Gsr |
T |
G |
8: 34,170,347 (GRCm39) |
|
probably null |
Het |
| Gstcd |
A |
G |
3: 132,688,860 (GRCm39) |
V630A |
probably damaging |
Het |
| Hip1r |
T |
C |
5: 124,128,043 (GRCm39) |
I116T |
probably benign |
Het |
| Hivep3 |
A |
G |
4: 119,989,000 (GRCm39) |
E1817G |
probably damaging |
Het |
| Inpp5f |
A |
C |
7: 128,265,449 (GRCm39) |
T135P |
probably damaging |
Het |
| Ism2 |
A |
G |
12: 87,331,801 (GRCm39) |
|
silent |
Het |
| Itga11 |
A |
G |
9: 62,673,070 (GRCm39) |
D784G |
probably damaging |
Het |
| Itpr2 |
A |
G |
6: 146,274,671 (GRCm39) |
F837S |
probably damaging |
Het |
| Itpr2 |
T |
C |
6: 146,298,456 (GRCm39) |
E10G |
probably damaging |
Het |
| Knl1 |
A |
T |
2: 118,899,618 (GRCm39) |
K440* |
probably null |
Het |
| Lonp2 |
T |
C |
8: 87,439,943 (GRCm39) |
S648P |
probably damaging |
Het |
| Lrba |
T |
C |
3: 86,267,175 (GRCm39) |
S1622P |
probably benign |
Het |
| Lrp2 |
G |
T |
2: 69,318,310 (GRCm39) |
A2047D |
probably damaging |
Het |
| Mcm3 |
G |
A |
1: 20,873,801 (GRCm39) |
T773I |
probably benign |
Het |
| Mki67 |
A |
G |
7: 135,297,198 (GRCm39) |
V2612A |
probably benign |
Het |
| Mnx1 |
C |
A |
5: 29,683,129 (GRCm39) |
G49W |
probably damaging |
Het |
| Muc5b |
T |
A |
7: 141,402,816 (GRCm39) |
Y673* |
probably null |
Het |
| Myo15a |
A |
G |
11: 60,370,756 (GRCm39) |
H1172R |
probably benign |
Het |
| Myo1g |
T |
C |
11: 6,466,080 (GRCm39) |
K363R |
probably null |
Het |
| Ncoa4 |
T |
A |
14: 31,898,598 (GRCm39) |
C473S |
probably benign |
Het |
| Nefh |
T |
C |
11: 4,889,656 (GRCm39) |
T988A |
unknown |
Het |
| Nwd2 |
T |
A |
5: 63,961,803 (GRCm39) |
D462E |
probably benign |
Het |
| Or2av9 |
T |
C |
11: 58,380,913 (GRCm39) |
T223A |
probably benign |
Het |
| Pira13 |
G |
T |
7: 3,825,680 (GRCm39) |
Y396* |
probably null |
Het |
| Plec |
T |
C |
15: 76,065,267 (GRCm39) |
E1466G |
unknown |
Het |
| Prl3d2 |
G |
T |
13: 27,306,379 (GRCm39) |
M35I |
probably benign |
Het |
| Reln |
T |
A |
5: 22,357,461 (GRCm39) |
I202F |
probably benign |
Het |
| Rhot1 |
T |
A |
11: 80,116,428 (GRCm39) |
D78E |
probably benign |
Het |
| Rsph3b |
T |
C |
17: 7,172,528 (GRCm39) |
|
probably null |
Het |
| Scn10a |
C |
T |
9: 119,438,717 (GRCm39) |
M1717I |
probably damaging |
Het |
| Slc26a3 |
G |
T |
12: 31,507,079 (GRCm39) |
A345S |
possibly damaging |
Het |
| Slc35d2 |
A |
G |
13: 64,247,097 (GRCm39) |
V261A |
possibly damaging |
Het |
| Slc49a3 |
T |
C |
5: 108,589,945 (GRCm39) |
T486A |
probably damaging |
Het |
| Ssmem1 |
A |
G |
6: 30,519,513 (GRCm39) |
D66G |
probably damaging |
Het |
| Sult2a8 |
A |
T |
7: 14,159,402 (GRCm39) |
N72K |
probably benign |
Het |
| Tbx10 |
T |
C |
19: 4,046,921 (GRCm39) |
L108P |
probably damaging |
Het |
| Tex14 |
T |
C |
11: 87,427,691 (GRCm39) |
S48P |
probably damaging |
Het |
| Tmie |
A |
G |
9: 110,696,596 (GRCm39) |
L95P |
probably damaging |
Het |
| Tom1l2 |
C |
G |
11: 60,161,259 (GRCm39) |
R84P |
probably damaging |
Het |
| Trpm3 |
T |
A |
19: 22,866,799 (GRCm39) |
D543E |
possibly damaging |
Het |
| Vipr2 |
A |
C |
12: 116,043,751 (GRCm39) |
R49S |
probably benign |
Het |
| Vps8 |
A |
T |
16: 21,261,189 (GRCm39) |
S110C |
probably damaging |
Het |
| Zfp791 |
T |
A |
8: 85,837,597 (GRCm39) |
N89I |
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 |
|
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 |
PCR Primer
(F):5'- CCTTGGTGCAGGCATTGATG -3'
(R):5'- GCCATTGCAGTCATTCTGGC -3'
Sequencing Primer
(F):5'- CAGGCATTGATGATGTTCTGGTTCC -3'
(R):5'- TTCTCGGGCATCATCGTG -3'
|
| Posted On |
2015-10-21 |
Incidental Mutation