Incidental Mutation 'R4491:Sema6a'
| ID |
330754 |
| 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 |
041747-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4491 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
47378321-47504267 bp(-) (GRCm39) |
| Type of Mutation |
utr 5 prime |
| DNA Base Change (assembly) |
G to A
at 47439524 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000121442
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000019791]
[ENSMUST00000076043]
[ENSMUST00000115449]
[ENSMUST00000126684]
[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 benign
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: 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 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: ENSMUST00000144223
|
| 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 |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.1%
- 20x: 94.8%
|
| Validation Efficiency |
98% (64/65) |
| 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: 54 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 0610040J01Rik |
C |
A |
5: 64,055,812 (GRCm39) |
P183T |
probably damaging |
Het |
| Bcan |
G |
A |
3: 87,897,540 (GRCm39) |
R682* |
probably null |
Het |
| Bzw1 |
T |
A |
1: 58,443,418 (GRCm39) |
L410Q |
probably damaging |
Het |
| Cdh5 |
A |
T |
8: 104,839,672 (GRCm39) |
I48F |
probably damaging |
Het |
| Cdhr5 |
T |
C |
7: 140,853,970 (GRCm39) |
N173D |
possibly damaging |
Het |
| Cfap74 |
T |
C |
4: 155,513,628 (GRCm39) |
M480T |
probably benign |
Het |
| Col6a5 |
C |
T |
9: 105,817,211 (GRCm39) |
A367T |
unknown |
Het |
| Cpsf1 |
A |
C |
15: 76,481,922 (GRCm39) |
Y1064D |
possibly damaging |
Het |
| Defb6 |
A |
T |
8: 19,278,090 (GRCm39) |
H54L |
probably benign |
Het |
| Dmtf1 |
A |
G |
5: 9,190,379 (GRCm39) |
|
probably benign |
Het |
| Dnah12 |
T |
C |
14: 26,455,758 (GRCm39) |
L827S |
possibly damaging |
Het |
| Dnai4 |
T |
C |
4: 102,923,596 (GRCm39) |
E411G |
probably benign |
Het |
| Dsc3 |
T |
C |
18: 20,134,922 (GRCm39) |
T21A |
probably benign |
Het |
| Epb41l1 |
G |
T |
2: 156,364,088 (GRCm39) |
D866Y |
probably benign |
Het |
| Epha1 |
T |
C |
6: 42,337,600 (GRCm39) |
M860V |
probably damaging |
Het |
| Far2 |
T |
C |
6: 148,074,907 (GRCm39) |
L380P |
possibly damaging |
Het |
| Fgd5 |
A |
G |
6: 91,966,280 (GRCm39) |
I680V |
possibly damaging |
Het |
| Fnbp4 |
T |
C |
2: 90,583,312 (GRCm39) |
|
probably null |
Het |
| Focad |
G |
A |
4: 88,278,142 (GRCm39) |
|
probably null |
Het |
| Gm14180 |
T |
A |
11: 99,621,139 (GRCm39) |
|
probably benign |
Het |
| Hbb-bh2 |
T |
C |
7: 103,489,622 (GRCm39) |
T5A |
probably benign |
Het |
| Ighv7-2 |
A |
G |
12: 113,876,100 (GRCm39) |
F2L |
probably benign |
Het |
| Igsf5 |
A |
G |
16: 96,165,281 (GRCm39) |
T19A |
probably benign |
Het |
| Kcnd3 |
C |
T |
3: 105,566,082 (GRCm39) |
A421V |
probably damaging |
Het |
| Klb |
A |
G |
5: 65,533,137 (GRCm39) |
N482S |
probably benign |
Het |
| Lipo2 |
A |
C |
19: 33,699,100 (GRCm39) |
L310R |
probably damaging |
Het |
| Mc3r |
A |
G |
2: 172,091,123 (GRCm39) |
H115R |
possibly damaging |
Het |
| Meioc |
A |
G |
11: 102,565,746 (GRCm39) |
D398G |
possibly damaging |
Het |
| Or10ag60 |
G |
A |
2: 87,437,736 (GRCm39) |
M1I |
probably null |
Het |
| Or56a5 |
A |
T |
7: 104,792,983 (GRCm39) |
C172* |
probably null |
Het |
| Or7a37 |
T |
C |
10: 78,806,151 (GRCm39) |
S223P |
probably damaging |
Het |
| Pds5a |
T |
C |
5: 65,792,780 (GRCm39) |
T718A |
probably benign |
Het |
| Pdzd2 |
C |
T |
15: 12,385,723 (GRCm39) |
D1016N |
possibly damaging |
Het |
| Pla2g2c |
T |
C |
4: 138,461,719 (GRCm39) |
|
probably null |
Het |
| Plch1 |
T |
C |
3: 63,648,160 (GRCm39) |
I404V |
probably damaging |
Het |
| Pou2af3 |
A |
G |
9: 51,181,955 (GRCm39) |
F206L |
probably benign |
Het |
| Ppp2r5c |
A |
T |
12: 110,546,956 (GRCm39) |
D522V |
possibly damaging |
Het |
| Prex2 |
T |
A |
1: 11,232,487 (GRCm39) |
S851R |
probably benign |
Het |
| Rapgef1 |
C |
T |
2: 29,609,668 (GRCm39) |
P702S |
possibly damaging |
Het |
| Rasal3 |
T |
A |
17: 32,610,359 (GRCm39) |
D976V |
probably damaging |
Het |
| Rasef |
A |
C |
4: 73,652,740 (GRCm39) |
L587R |
probably damaging |
Het |
| Rptn |
A |
T |
3: 93,303,818 (GRCm39) |
R384* |
probably null |
Het |
| Sycp2 |
G |
T |
2: 178,016,778 (GRCm39) |
T608K |
probably damaging |
Het |
| Syde1 |
C |
T |
10: 78,426,062 (GRCm39) |
R35H |
probably benign |
Het |
| Taf1 |
G |
T |
X: 100,586,665 (GRCm39) |
M313I |
possibly damaging |
Het |
| Taf15 |
A |
T |
11: 83,375,520 (GRCm39) |
T31S |
probably benign |
Het |
| Tktl2 |
T |
C |
8: 66,964,664 (GRCm39) |
V74A |
probably damaging |
Het |
| Tle4 |
A |
G |
19: 14,432,229 (GRCm39) |
V489A |
probably damaging |
Het |
| Tmem30a |
T |
C |
9: 79,684,567 (GRCm39) |
H95R |
probably damaging |
Het |
| Trmt9b |
G |
A |
8: 36,972,760 (GRCm39) |
C70Y |
probably damaging |
Het |
| Vmn1r75 |
C |
A |
7: 11,614,909 (GRCm39) |
Q214K |
probably damaging |
Het |
| Vps13c |
C |
T |
9: 67,817,475 (GRCm39) |
T1049M |
probably benign |
Het |
| Zfp37 |
T |
C |
4: 62,110,365 (GRCm39) |
Q274R |
probably benign |
Het |
| Zfp648 |
T |
G |
1: 154,080,873 (GRCm39) |
L344R |
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 |
|
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'- CCTTGTCACACATGCAGTTG -3'
(R):5'- ATTCACTGTGGACAAGGCAG -3'
Sequencing Primer
(F):5'- AAAATGACTGGGTCTCTCCG -3'
(R):5'- CAGGGAACAGAAGCCTTTTGTC -3'
|
| Posted On |
2015-07-21 |
Incidental Mutation