Incidental Mutation 'R5088:Sema6a'
ID |
387609 |
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 |
042677-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R5088 (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 47382196 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Isoleucine to Phenylalanine
at position 784
(I784F)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000121442
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000019791]
[ENSMUST00000076043]
[ENSMUST00000115449]
[ENSMUST00000135790]
[ENSMUST00000156422]
|
AlphaFold |
O35464 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000019791
AA Change: I784F
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000019791 Gene: ENSMUSG00000019647 AA Change: I784F
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: I729F
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000075420 Gene: ENSMUSG00000019647 AA Change: I729F
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: I758F
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000111109 Gene: ENSMUSG00000019647 AA Change: I758F
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 damaging
Transcript: ENSMUST00000135790
AA Change: I801F
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000120011 Gene: ENSMUSG00000019647 AA Change: I801F
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 |
probably damaging
Transcript: ENSMUST00000156422
AA Change: I784F
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000121442 Gene: ENSMUSG00000019647 AA Change: I784F
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: 99.2%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 93.9%
|
Validation Efficiency |
99% (72/73) |
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: 65 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4930522L14Rik |
A |
T |
5: 109,883,939 (GRCm39) |
C640S |
probably damaging |
Het |
4931429L15Rik |
T |
C |
9: 46,217,038 (GRCm39) |
R246G |
probably benign |
Het |
Aak1 |
T |
C |
6: 86,921,462 (GRCm39) |
|
probably null |
Het |
Abcc5 |
A |
G |
16: 20,195,412 (GRCm39) |
L695P |
probably damaging |
Het |
Alcam |
T |
A |
16: 52,109,290 (GRCm39) |
T328S |
probably damaging |
Het |
Alpk1 |
A |
G |
3: 127,478,969 (GRCm39) |
|
probably benign |
Het |
Arel1 |
A |
G |
12: 84,970,889 (GRCm39) |
L642P |
probably damaging |
Het |
Atrip |
T |
C |
9: 108,888,964 (GRCm39) |
D741G |
probably damaging |
Het |
Bmp1 |
T |
C |
14: 70,723,659 (GRCm39) |
T726A |
possibly damaging |
Het |
Bnip3 |
A |
G |
7: 138,496,337 (GRCm39) |
|
probably null |
Het |
Cacng5 |
C |
G |
11: 107,768,215 (GRCm39) |
C264S |
possibly damaging |
Het |
Calr4 |
T |
A |
4: 109,101,859 (GRCm39) |
|
probably benign |
Het |
Cdhr1 |
T |
A |
14: 36,811,422 (GRCm39) |
T230S |
probably benign |
Het |
Cdk16 |
T |
C |
X: 20,562,566 (GRCm39) |
|
probably benign |
Het |
Cenpj |
T |
C |
14: 56,791,148 (GRCm39) |
E337G |
probably damaging |
Het |
Chd9 |
A |
G |
8: 91,704,147 (GRCm39) |
I694V |
possibly damaging |
Het |
Chsy3 |
T |
A |
18: 59,312,607 (GRCm39) |
V360D |
probably damaging |
Het |
Col16a1 |
C |
T |
4: 129,972,988 (GRCm39) |
T643M |
probably benign |
Het |
Col5a1 |
G |
A |
2: 27,908,614 (GRCm39) |
W67* |
probably null |
Het |
Cyp20a1 |
A |
T |
1: 60,402,509 (GRCm39) |
H198L |
probably damaging |
Het |
Dnai1 |
T |
A |
4: 41,597,630 (GRCm39) |
S38T |
probably benign |
Het |
Dnai1 |
T |
G |
4: 41,632,251 (GRCm39) |
S562A |
probably benign |
Het |
Dpy19l4 |
G |
T |
4: 11,303,357 (GRCm39) |
T188K |
probably damaging |
Het |
Ergic2 |
A |
G |
6: 148,084,621 (GRCm39) |
V304A |
probably damaging |
Het |
Fam83a |
A |
G |
15: 57,873,196 (GRCm39) |
T342A |
probably benign |
Het |
Fbxo7 |
A |
G |
10: 85,857,784 (GRCm39) |
|
probably benign |
Het |
Gins4 |
T |
C |
8: 23,727,084 (GRCm39) |
E3G |
possibly damaging |
Het |
Glis3 |
G |
A |
19: 28,508,979 (GRCm39) |
P335L |
probably benign |
Het |
Golph3l |
A |
T |
3: 95,524,501 (GRCm39) |
T251S |
possibly damaging |
Het |
Hnf4g |
C |
T |
3: 3,722,181 (GRCm39) |
A445V |
probably benign |
Het |
Hykk |
A |
G |
9: 54,853,763 (GRCm39) |
I362V |
probably benign |
Het |
Il6st |
G |
A |
13: 112,627,089 (GRCm39) |
V294M |
probably damaging |
Het |
Itpr1 |
A |
G |
6: 108,366,348 (GRCm39) |
I92V |
probably damaging |
Het |
Kdm4c |
T |
C |
4: 74,252,936 (GRCm39) |
L501P |
probably benign |
Het |
Mpi |
G |
A |
9: 57,457,887 (GRCm39) |
T105M |
probably damaging |
Het |
Mrpl37 |
A |
T |
4: 106,921,919 (GRCm39) |
L132H |
probably damaging |
Het |
Muc5ac |
A |
T |
7: 141,350,056 (GRCm39) |
T600S |
possibly damaging |
Het |
Npl |
A |
T |
1: 153,384,890 (GRCm39) |
I249N |
possibly damaging |
Het |
Or10j27 |
C |
T |
1: 172,958,606 (GRCm39) |
M59I |
probably damaging |
Het |
Or7g30 |
A |
G |
9: 19,353,067 (GRCm39) |
N286S |
probably damaging |
Het |
Pkd1 |
A |
G |
17: 24,809,812 (GRCm39) |
K3497E |
possibly damaging |
Het |
Ptprt |
T |
C |
2: 162,080,095 (GRCm39) |
N235D |
probably benign |
Het |
Rangap1 |
A |
C |
15: 81,594,664 (GRCm39) |
D388E |
probably benign |
Het |
Rcvrn |
A |
T |
11: 67,586,340 (GRCm39) |
Q33L |
probably benign |
Het |
Rif1 |
A |
T |
2: 51,982,307 (GRCm39) |
K524I |
possibly damaging |
Het |
Rnf139 |
A |
T |
15: 58,771,790 (GRCm39) |
N605I |
possibly damaging |
Het |
Ryr2 |
C |
A |
13: 11,727,129 (GRCm39) |
G2411* |
probably null |
Het |
Scn3a |
A |
T |
2: 65,302,643 (GRCm39) |
S1268T |
probably damaging |
Het |
Sgms2 |
C |
T |
3: 131,124,005 (GRCm39) |
V232M |
probably benign |
Het |
Skint7 |
T |
C |
4: 111,837,627 (GRCm39) |
I135T |
possibly damaging |
Het |
Smchd1 |
A |
T |
17: 71,738,343 (GRCm39) |
N507K |
possibly damaging |
Het |
Spata31d1a |
A |
C |
13: 59,848,966 (GRCm39) |
|
probably null |
Het |
Spata7 |
A |
T |
12: 98,635,761 (GRCm39) |
D527V |
probably benign |
Het |
Srcap |
A |
G |
7: 127,140,833 (GRCm39) |
T1477A |
probably benign |
Het |
Srl |
C |
A |
16: 4,300,633 (GRCm39) |
D375Y |
probably damaging |
Het |
Stk4 |
A |
T |
2: 163,925,608 (GRCm39) |
K58* |
probably null |
Het |
Svep1 |
T |
G |
4: 58,120,648 (GRCm39) |
H795P |
possibly damaging |
Het |
Trak2 |
T |
A |
1: 58,974,967 (GRCm39) |
Q75L |
probably benign |
Het |
Ubxn2a |
T |
A |
12: 4,933,904 (GRCm39) |
N169I |
probably damaging |
Het |
Vmn1r216 |
T |
A |
13: 23,283,473 (GRCm39) |
L52* |
probably null |
Het |
Vmn2r108 |
A |
T |
17: 20,690,454 (GRCm39) |
N459K |
possibly damaging |
Het |
Vstm5 |
A |
G |
9: 15,168,601 (GRCm39) |
D55G |
possibly damaging |
Het |
Wdr24 |
T |
A |
17: 26,047,181 (GRCm39) |
|
probably null |
Het |
Zfp13 |
C |
A |
17: 23,796,035 (GRCm39) |
E179* |
probably null |
Het |
Zfp839 |
T |
C |
12: 110,834,610 (GRCm39) |
S546P |
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 |
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 |
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'- ACCACCTCGCTCATTTTGGG -3'
(R):5'- AGTGTCACCAAGCTCAGTG -3'
Sequencing Primer
(F):5'- CATTTTGGGCTGATCTACGTAC -3'
(R):5'- CAAGCTCAGTGGCCTCTTTGG -3'
|
Posted On |
2016-06-06 |