Incidental Mutation 'R6734:Sema6a'
| ID |
528366 |
| 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 |
044852-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R6734 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
47378321-47504267 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 47412236 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Isoleucine
at position 526
(T526I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000111109
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000019791]
[ENSMUST00000076043]
[ENSMUST00000115449]
[ENSMUST00000135790]
[ENSMUST00000156422]
|
| AlphaFold |
O35464 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000019791
AA Change: T552I
PolyPhen 2
Score 0.058 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647
AA Change: T552I
| 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
AA Change: T552I
PolyPhen 2
Score 0.075 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647
AA Change: T552I
| 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
AA Change: T526I
PolyPhen 2
Score 0.306 (Sensitivity: 0.90; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
AA Change: T526I
| 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 |
unknown
Transcript: ENSMUST00000123228
AA Change: T27I
|
| SMART Domains |
Protein: ENSMUSP00000120249
Gene: ENSMUSG00000019647
AA Change: T27I
| 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
AA Change: T552I
PolyPhen 2
Score 0.018 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
AA Change: T552I
| 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
AA Change: T552I
PolyPhen 2
Score 0.058 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647
AA Change: T552I
| 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 |
0.0730 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 98.4%
- 20x: 95.6%
|
| Validation Efficiency |
100% (52/52) |
| 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: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acot11 |
C |
T |
4: 106,617,327 (GRCm39) |
G240R |
probably damaging |
Het |
| Ano6 |
A |
G |
15: 95,847,417 (GRCm39) |
K554R |
probably damaging |
Het |
| Arhgef10 |
A |
T |
8: 15,025,053 (GRCm39) |
I703F |
probably damaging |
Het |
| Bbs1 |
T |
C |
19: 4,953,924 (GRCm39) |
S80G |
probably benign |
Het |
| Bhlhe40 |
TG |
TGG |
6: 108,641,818 (GRCm39) |
254 |
probably null |
Het |
| Camk1 |
C |
A |
6: 113,311,345 (GRCm39) |
R352L |
probably benign |
Het |
| Cand1 |
G |
A |
10: 119,047,897 (GRCm39) |
P531L |
possibly damaging |
Het |
| Cnot2 |
G |
A |
10: 116,334,058 (GRCm39) |
P371S |
possibly damaging |
Het |
| Col24a1 |
C |
A |
3: 145,214,429 (GRCm39) |
P1384Q |
probably benign |
Het |
| Csmd2 |
C |
A |
4: 128,357,606 (GRCm39) |
T1689K |
probably benign |
Het |
| Cyp26a1 |
T |
A |
19: 37,689,660 (GRCm39) |
L452H |
probably damaging |
Het |
| Dcpp2 |
T |
C |
17: 24,119,545 (GRCm39) |
Y120H |
probably damaging |
Het |
| Dennd6a |
G |
T |
14: 26,329,774 (GRCm39) |
R115L |
possibly damaging |
Het |
| Eml2 |
T |
A |
7: 18,934,432 (GRCm39) |
V377E |
probably benign |
Het |
| Fam135b |
T |
C |
15: 71,334,629 (GRCm39) |
E855G |
probably benign |
Het |
| Fam149a |
A |
T |
8: 45,834,478 (GRCm39) |
I107K |
probably benign |
Het |
| Fam227b |
A |
T |
2: 125,968,896 (GRCm39) |
Y59* |
probably null |
Het |
| Fbn2 |
T |
C |
18: 58,169,032 (GRCm39) |
E2249G |
probably damaging |
Het |
| Flrt1 |
T |
C |
19: 7,073,524 (GRCm39) |
D341G |
possibly damaging |
Het |
| Galnt9 |
G |
A |
5: 110,768,465 (GRCm39) |
R587H |
probably damaging |
Het |
| Gsdma2 |
A |
G |
11: 98,540,416 (GRCm39) |
T112A |
possibly damaging |
Het |
| Klhl24 |
T |
C |
16: 19,926,279 (GRCm39) |
V269A |
probably damaging |
Het |
| Lcorl |
A |
G |
5: 45,890,839 (GRCm39) |
S505P |
probably damaging |
Het |
| Liph |
A |
G |
16: 21,802,707 (GRCm39) |
S121P |
probably damaging |
Het |
| Lrp4 |
G |
A |
2: 91,316,242 (GRCm39) |
V787M |
possibly damaging |
Het |
| Lrrd1 |
A |
C |
5: 3,900,226 (GRCm39) |
D177A |
possibly damaging |
Het |
| Mbd1 |
G |
A |
18: 74,409,114 (GRCm39) |
R399H |
probably damaging |
Het |
| Naa25 |
C |
T |
5: 121,576,888 (GRCm39) |
T879M |
possibly damaging |
Het |
| Naa35 |
T |
G |
13: 59,756,005 (GRCm39) |
L147R |
possibly damaging |
Het |
| Ninl |
C |
A |
2: 150,787,003 (GRCm39) |
|
probably null |
Het |
| Nrap |
T |
C |
19: 56,333,941 (GRCm39) |
D972G |
probably damaging |
Het |
| Or9k7 |
A |
G |
10: 130,046,126 (GRCm39) |
F291S |
probably benign |
Het |
| Pdzd2 |
T |
C |
15: 12,592,551 (GRCm39) |
E31G |
probably damaging |
Het |
| Plec |
C |
T |
15: 76,078,603 (GRCm39) |
E41K |
probably damaging |
Het |
| Plxnb1 |
A |
T |
9: 108,937,988 (GRCm39) |
K1245* |
probably null |
Het |
| Ppfia1 |
T |
C |
7: 144,032,790 (GRCm39) |
T1263A |
probably damaging |
Het |
| Prex2 |
G |
A |
1: 11,150,283 (GRCm39) |
V152I |
probably damaging |
Het |
| Prpf40b |
C |
T |
15: 99,212,784 (GRCm39) |
R627W |
probably damaging |
Het |
| Prss3l |
T |
C |
6: 41,422,321 (GRCm39) |
Y28C |
probably damaging |
Het |
| Prune2 |
T |
G |
19: 16,981,097 (GRCm39) |
F85V |
probably damaging |
Het |
| Rrp1b |
T |
G |
17: 32,274,278 (GRCm39) |
|
probably benign |
Het |
| Sec62 |
A |
G |
3: 30,864,609 (GRCm39) |
T158A |
probably benign |
Het |
| Shank1 |
G |
T |
7: 44,003,110 (GRCm39) |
A1610S |
probably benign |
Het |
| Slc24a4 |
T |
C |
12: 102,185,259 (GRCm39) |
V123A |
probably damaging |
Het |
| Stk11ip |
T |
C |
1: 75,509,013 (GRCm39) |
V714A |
probably benign |
Het |
| Tas1r3 |
T |
C |
4: 155,945,257 (GRCm39) |
T655A |
probably damaging |
Het |
| Tns2 |
G |
T |
15: 102,011,551 (GRCm39) |
L10F |
probably damaging |
Het |
| Trmt10c |
A |
G |
16: 55,854,489 (GRCm39) |
V382A |
probably benign |
Het |
| Unc45a |
G |
C |
7: 79,986,746 (GRCm39) |
T149R |
probably damaging |
Het |
| Zhx3 |
T |
G |
2: 160,623,640 (GRCm39) |
I176L |
probably damaging |
Het |
| Zscan12 |
T |
A |
13: 21,552,966 (GRCm39) |
C263* |
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 |
|
|
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 |
|
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 |
|
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'- ATCCAGACTCAGATGCGTTG -3'
(R):5'- ATTCTGCTCTGAGCTCACTG -3'
Sequencing Primer
(F):5'- CAGACTCAGATGCGTTGTTTTACAC -3'
(R):5'- CATAGCTAGCTTCTCCTCAGAG -3'
|
| Posted On |
2018-07-24 |
Incidental Mutation