Incidental Mutation 'R0569:Sema6a'
| ID |
46336 |
| 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 |
038760-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R0569 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
47378321-47504267 bp(-) (GRCm39) |
| Type of Mutation |
splice site |
| DNA Base Change (assembly) |
A to T
at 47403872 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000111109
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000019791]
[ENSMUST00000076043]
[ENSMUST00000115449]
[ENSMUST00000115449]
[ENSMUST00000135790]
[ENSMUST00000156422]
|
| AlphaFold |
O35464 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000019791
|
| SMART Domains |
Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647
| 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 benign
Transcript: ENSMUST00000076043
|
| SMART Domains |
Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647
| 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 null
Transcript: ENSMUST00000115449
|
| SMART Domains |
Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
| 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: ENSMUST00000115449
|
| SMART Domains |
Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
| 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 benign
Transcript: ENSMUST00000135790
|
| SMART Domains |
Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
| 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 benign
Transcript: ENSMUST00000156422
|
| SMART Domains |
Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647
| 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 |
0.9755 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.7%
- 20x: 93.8%
|
| Validation Efficiency |
97% (56/58) |
| 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: 59 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4833420G17Rik |
A |
G |
13: 119,621,016 (GRCm39) |
I572M |
possibly damaging |
Het |
| 4930447A16Rik |
T |
C |
15: 37,425,863 (GRCm39) |
M1T |
probably null |
Het |
| 4930590J08Rik |
C |
A |
6: 91,919,559 (GRCm39) |
C739* |
probably null |
Het |
| Adcy1 |
T |
A |
11: 7,096,514 (GRCm39) |
V634E |
probably benign |
Het |
| Ankfy1 |
T |
A |
11: 72,644,434 (GRCm39) |
H710Q |
possibly damaging |
Het |
| Ankrd60 |
C |
T |
2: 173,412,859 (GRCm39) |
V90M |
probably damaging |
Het |
| Asgr2 |
A |
T |
11: 69,988,703 (GRCm39) |
Q132L |
probably benign |
Het |
| Cchcr1 |
T |
A |
17: 35,839,865 (GRCm39) |
|
probably null |
Het |
| Ces1h |
T |
C |
8: 94,078,774 (GRCm39) |
K523E |
unknown |
Het |
| Clec3a |
G |
T |
8: 115,152,476 (GRCm39) |
G161C |
probably damaging |
Het |
| Cracr2b |
G |
A |
7: 141,044,848 (GRCm39) |
|
probably benign |
Het |
| Cyp2b10 |
A |
T |
7: 25,597,160 (GRCm39) |
L17F |
probably damaging |
Het |
| Dhx29 |
T |
A |
13: 113,084,748 (GRCm39) |
N655K |
probably benign |
Het |
| Dst |
C |
A |
1: 34,332,508 (GRCm39) |
L4748I |
probably damaging |
Het |
| Eif2b5 |
G |
C |
16: 20,321,303 (GRCm39) |
L285F |
probably benign |
Het |
| Enox1 |
T |
A |
14: 77,875,117 (GRCm39) |
D441E |
probably damaging |
Het |
| Fam110a |
T |
C |
2: 151,812,404 (GRCm39) |
E122G |
probably damaging |
Het |
| Fam161b |
T |
A |
12: 84,395,413 (GRCm39) |
E510V |
probably damaging |
Het |
| Gabrd |
T |
C |
4: 155,469,880 (GRCm39) |
Y443C |
probably damaging |
Het |
| Gcn1 |
T |
G |
5: 115,733,118 (GRCm39) |
S1052A |
probably benign |
Het |
| Gnptab |
A |
G |
10: 88,264,419 (GRCm39) |
E279G |
possibly damaging |
Het |
| Hoxa6 |
T |
A |
6: 52,185,163 (GRCm39) |
|
probably null |
Het |
| Ibtk |
T |
A |
9: 85,590,234 (GRCm39) |
|
probably benign |
Het |
| Il6ra |
A |
T |
3: 89,785,149 (GRCm39) |
|
probably null |
Het |
| Iqgap3 |
C |
T |
3: 87,998,032 (GRCm39) |
|
probably benign |
Het |
| Kcnk2 |
A |
C |
1: 189,071,998 (GRCm39) |
L110R |
probably damaging |
Het |
| Knl1 |
T |
A |
2: 118,927,916 (GRCm39) |
V1919D |
possibly damaging |
Het |
| Lrp1b |
A |
T |
2: 40,779,251 (GRCm39) |
L2597Q |
probably benign |
Het |
| Magi3 |
A |
G |
3: 103,923,358 (GRCm39) |
S1120P |
probably benign |
Het |
| Map3k8 |
T |
C |
18: 4,349,162 (GRCm39) |
D52G |
probably benign |
Het |
| Mcat |
C |
T |
15: 83,433,449 (GRCm39) |
R198H |
probably benign |
Het |
| Mnd1 |
A |
G |
3: 84,012,286 (GRCm39) |
V141A |
probably benign |
Het |
| Morc1 |
T |
C |
16: 48,407,485 (GRCm39) |
L667P |
probably benign |
Het |
| Mrps6 |
A |
G |
16: 91,908,808 (GRCm39) |
K125E |
possibly damaging |
Het |
| Mst1 |
T |
C |
9: 107,959,500 (GRCm39) |
F262S |
probably damaging |
Het |
| Or5j3 |
T |
G |
2: 86,128,941 (GRCm39) |
I260M |
probably damaging |
Het |
| Or7e178 |
T |
A |
9: 20,225,875 (GRCm39) |
I114F |
probably damaging |
Het |
| Pbsn |
C |
G |
X: 76,897,046 (GRCm39) |
G15A |
possibly damaging |
Het |
| Pcnx1 |
T |
C |
12: 82,038,804 (GRCm39) |
I2023T |
probably benign |
Het |
| Pds5a |
T |
G |
5: 65,813,744 (GRCm39) |
N247T |
probably damaging |
Het |
| Peak1 |
T |
C |
9: 56,167,373 (GRCm39) |
Y185C |
probably damaging |
Het |
| Phkb |
T |
A |
8: 86,744,031 (GRCm39) |
I560N |
probably damaging |
Het |
| Plekhn1 |
T |
C |
4: 156,309,658 (GRCm39) |
I160V |
probably damaging |
Het |
| Rabgap1 |
T |
G |
2: 37,379,729 (GRCm39) |
|
probably benign |
Het |
| Rdh10 |
T |
G |
1: 16,199,517 (GRCm39) |
V241G |
probably damaging |
Het |
| Selenow |
A |
T |
7: 15,654,042 (GRCm39) |
C37S |
probably benign |
Het |
| Slc12a3 |
T |
C |
8: 95,057,153 (GRCm39) |
|
probably null |
Het |
| Slc22a21 |
T |
G |
11: 53,842,636 (GRCm39) |
M498L |
probably benign |
Het |
| Spink5 |
A |
T |
18: 44,122,486 (GRCm39) |
N317I |
probably damaging |
Het |
| Srek1 |
A |
G |
13: 103,885,370 (GRCm39) |
|
probably benign |
Het |
| Syt11 |
A |
G |
3: 88,655,230 (GRCm39) |
V357A |
probably benign |
Het |
| Tcof1 |
T |
A |
18: 60,962,107 (GRCm39) |
K707N |
possibly damaging |
Het |
| Tfip11 |
C |
T |
5: 112,475,960 (GRCm39) |
R42C |
probably damaging |
Het |
| Trim39 |
T |
C |
17: 36,574,623 (GRCm39) |
K260E |
probably benign |
Het |
| Ttn |
T |
C |
2: 76,553,663 (GRCm39) |
T22658A |
possibly damaging |
Het |
| Unc45b |
C |
T |
11: 82,827,638 (GRCm39) |
|
probably benign |
Het |
| Vmn1r236 |
A |
G |
17: 21,507,172 (GRCm39) |
I97V |
probably benign |
Het |
| Vps13c |
T |
C |
9: 67,881,001 (GRCm39) |
V657A |
probably damaging |
Het |
| Zkscan2 |
A |
G |
7: 123,097,898 (GRCm39) |
V166A |
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 |
|
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 |
PCR Primer
(F):5'- TCAATGATGGTGCCCAAGAGGTTC -3'
(R):5'- TGAGACAGTCTGTGTCCCTTCATCC -3'
Sequencing Primer
(F):5'- TCACGCTGCTAGGATTCAG -3'
(R):5'- GGTATAGAtctctctctctctctctc -3'
|
| Posted On |
2013-06-11 |
Incidental Mutation