Incidental Mutation 'R0466:Sema6a'
ID |
41667 |
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 |
038666-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R0466 (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: 99.2%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.1%
|
Validation Efficiency |
97% (63/65) |
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: 60 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4933412E24Rik |
T |
C |
15: 59,887,321 (GRCm39) |
Y373C |
probably benign |
Het |
Abca12 |
T |
G |
1: 71,341,822 (GRCm39) |
Q1046H |
probably damaging |
Het |
Adgrv1 |
A |
G |
13: 81,714,415 (GRCm39) |
F956S |
probably benign |
Het |
Alk |
A |
G |
17: 72,212,152 (GRCm39) |
V797A |
possibly damaging |
Het |
Ascl2 |
A |
G |
7: 142,522,217 (GRCm39) |
L77P |
probably benign |
Het |
Aspm |
A |
T |
1: 139,405,639 (GRCm39) |
I1509F |
probably damaging |
Het |
AY358078 |
A |
T |
14: 52,043,089 (GRCm39) |
Y259F |
unknown |
Het |
Cbs |
G |
A |
17: 31,835,126 (GRCm39) |
A450V |
probably benign |
Het |
Cdh11 |
T |
A |
8: 103,396,690 (GRCm39) |
Q213L |
possibly damaging |
Het |
Cdh26 |
C |
T |
2: 178,123,425 (GRCm39) |
R675C |
possibly damaging |
Het |
Cfap126 |
T |
C |
1: 170,953,769 (GRCm39) |
I113T |
probably damaging |
Het |
Clk4 |
A |
G |
11: 51,158,155 (GRCm39) |
D53G |
possibly damaging |
Het |
Dab1 |
T |
C |
4: 104,577,747 (GRCm39) |
L272P |
probably benign |
Het |
Dmtf1 |
A |
T |
5: 9,182,454 (GRCm39) |
|
probably null |
Het |
Dph5 |
A |
C |
3: 115,722,359 (GRCm39) |
D279A |
probably benign |
Het |
Fbxw19 |
T |
A |
9: 109,307,717 (GRCm39) |
T461S |
probably benign |
Het |
G3bp1 |
T |
C |
11: 55,389,452 (GRCm39) |
F383L |
probably damaging |
Het |
Gcg |
T |
C |
2: 62,307,282 (GRCm39) |
D93G |
probably damaging |
Het |
Gmps |
A |
G |
3: 63,901,365 (GRCm39) |
T395A |
probably damaging |
Het |
H2-Ob |
A |
G |
17: 34,461,633 (GRCm39) |
D124G |
probably damaging |
Het |
Itga8 |
G |
T |
2: 12,237,697 (GRCm39) |
A341E |
probably damaging |
Het |
Itih3 |
A |
G |
14: 30,634,831 (GRCm39) |
|
probably null |
Het |
Kcnh4 |
C |
T |
11: 100,637,758 (GRCm39) |
G633E |
probably benign |
Het |
Kif2c |
C |
T |
4: 117,029,489 (GRCm39) |
R215Q |
possibly damaging |
Het |
Letm1 |
A |
C |
5: 33,919,074 (GRCm39) |
|
probably benign |
Het |
Lypd8l |
T |
C |
11: 58,503,331 (GRCm39) |
|
probably benign |
Het |
Mmp3 |
A |
G |
9: 7,450,165 (GRCm39) |
D299G |
probably damaging |
Het |
Myh8 |
G |
T |
11: 67,189,405 (GRCm39) |
A1194S |
probably benign |
Het |
Naip2 |
A |
C |
13: 100,298,290 (GRCm39) |
I582S |
probably benign |
Het |
Nfib |
A |
C |
4: 82,416,775 (GRCm39) |
Y87D |
probably damaging |
Het |
Nlrp4a |
T |
C |
7: 26,162,045 (GRCm39) |
|
probably benign |
Het |
Nsmce1 |
A |
T |
7: 125,071,408 (GRCm39) |
|
probably benign |
Het |
Odad2 |
T |
A |
18: 7,286,758 (GRCm39) |
I158F |
probably benign |
Het |
Or7g12 |
T |
G |
9: 18,899,551 (GRCm39) |
V89G |
probably benign |
Het |
Or7g27 |
A |
T |
9: 19,250,475 (GRCm39) |
T240S |
probably damaging |
Het |
Patj |
C |
A |
4: 98,576,393 (GRCm39) |
Q1193K |
probably damaging |
Het |
Pcdhb5 |
G |
A |
18: 37,455,596 (GRCm39) |
V659M |
probably damaging |
Het |
Pkd1l3 |
C |
G |
8: 110,350,281 (GRCm39) |
D375E |
possibly damaging |
Het |
Pmis2 |
T |
C |
7: 30,370,817 (GRCm39) |
I46V |
probably benign |
Het |
Ppp2r5e |
A |
G |
12: 75,509,216 (GRCm39) |
|
probably benign |
Het |
Prom2 |
A |
G |
2: 127,370,709 (GRCm39) |
F825S |
probably damaging |
Het |
Rab11fip2 |
G |
A |
19: 59,894,675 (GRCm39) |
A524V |
possibly damaging |
Het |
Rb1cc1 |
A |
C |
1: 6,333,491 (GRCm39) |
|
probably null |
Het |
Rwdd3 |
G |
C |
3: 120,952,668 (GRCm39) |
Q180E |
possibly damaging |
Het |
Sgcg |
A |
T |
14: 61,459,135 (GRCm39) |
C265S |
probably damaging |
Het |
Slc16a3 |
T |
C |
11: 120,848,878 (GRCm39) |
S445P |
possibly damaging |
Het |
Slc22a3 |
G |
A |
17: 12,677,380 (GRCm39) |
Q263* |
probably null |
Het |
Sorcs3 |
A |
G |
19: 48,736,758 (GRCm39) |
T694A |
probably benign |
Het |
Tbc1d15 |
T |
C |
10: 115,055,077 (GRCm39) |
K322E |
probably damaging |
Het |
Tecta |
G |
T |
9: 42,284,369 (GRCm39) |
F905L |
probably benign |
Het |
Tmeff1 |
A |
G |
4: 48,636,853 (GRCm39) |
I184V |
possibly damaging |
Het |
Ttf1 |
A |
G |
2: 28,955,419 (GRCm39) |
H261R |
possibly damaging |
Het |
Ttll6 |
T |
A |
11: 96,036,417 (GRCm39) |
L349M |
probably damaging |
Het |
Ubac2 |
G |
A |
14: 122,211,031 (GRCm39) |
V134M |
probably damaging |
Het |
Ubxn4 |
G |
A |
1: 128,190,641 (GRCm39) |
E256K |
probably benign |
Het |
Vmn2r25 |
T |
G |
6: 123,829,008 (GRCm39) |
I89L |
probably benign |
Het |
Vmn2r6 |
A |
C |
3: 64,463,723 (GRCm39) |
F370L |
probably damaging |
Het |
Vps13b |
T |
A |
15: 35,445,748 (GRCm39) |
Y412* |
probably null |
Het |
Zfp142 |
A |
G |
1: 74,624,570 (GRCm39) |
S85P |
possibly damaging |
Het |
Zfp516 |
G |
A |
18: 82,975,579 (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 |
|
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 |
|
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 |
PCR Primer
(F):5'- ACTGACTACCTGGTCCAGGCAAAG -3'
(R):5'- GATTGCGTCATTAAGCAGAGGCAAC -3'
Sequencing Primer
(F):5'- GTCCAGGCAAAGGAATGTTTTAATC -3'
(R):5'- CAGAGGCAACTTCTTCTAAGGTC -3'
|
Posted On |
2013-05-23 |