Incidental Mutation 'R4446:Sema6d'
| ID |
329881 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sema6d
|
| Ensembl Gene |
ENSMUSG00000027200 |
| Gene Name |
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D |
| Synonyms |
Sema6D-6, 1110067B02Rik, Sema6D-1, Sema6D-4, Sema6D-5, Sema6D-2 |
| MMRRC Submission |
041707-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4446 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
123931889-124509690 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 124505979 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Valine
at position 596
(M596V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000061123
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000051419]
[ENSMUST00000076335]
[ENSMUST00000077847]
[ENSMUST00000078621]
[ENSMUST00000103238]
[ENSMUST00000103239]
[ENSMUST00000103240]
[ENSMUST00000103241]
|
| AlphaFold |
Q76KF0 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000051419
AA Change: M596V
PolyPhen 2
Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000061123
Gene: ENSMUSG00000027200
AA Change: M596V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Sema
|
57 |
487 |
7.29e-184 |
SMART |
|
PSI
|
514 |
582 |
4.57e-1 |
SMART |
|
transmembrane domain
|
602 |
624 |
N/A |
INTRINSIC |
|
low complexity region
|
743 |
764 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
797 |
898 |
7.43e-5 |
PROSPERO |
|
internal_repeat_1
|
892 |
1004 |
7.43e-5 |
PROSPERO |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000076335
AA Change: M583V
PolyPhen 2
Score 0.649 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000075674
Gene: ENSMUSG00000027200
AA Change: M583V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Sema
|
57 |
487 |
7.29e-184 |
SMART |
|
PSI
|
514 |
569 |
1.12e-1 |
SMART |
|
transmembrane domain
|
589 |
611 |
N/A |
INTRINSIC |
|
low complexity region
|
730 |
751 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
784 |
885 |
7.28e-5 |
PROSPERO |
|
internal_repeat_1
|
879 |
991 |
7.28e-5 |
PROSPERO |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000077847
AA Change: M639V
PolyPhen 2
Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000077014
Gene: ENSMUSG00000027200
AA Change: M639V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Sema
|
57 |
487 |
7.29e-184 |
SMART |
|
PSI
|
514 |
569 |
1.12e-1 |
SMART |
|
low complexity region
|
573 |
584 |
N/A |
INTRINSIC |
|
transmembrane domain
|
645 |
667 |
N/A |
INTRINSIC |
|
low complexity region
|
786 |
807 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
840 |
941 |
5.95e-5 |
PROSPERO |
|
internal_repeat_1
|
935 |
1047 |
5.95e-5 |
PROSPERO |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000078621
AA Change: M615V
PolyPhen 2
Score 0.645 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000077691
Gene: ENSMUSG00000027200
AA Change: M615V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Sema
|
57 |
487 |
7.29e-184 |
SMART |
|
PSI
|
514 |
582 |
4.57e-1 |
SMART |
|
transmembrane domain
|
621 |
643 |
N/A |
INTRINSIC |
|
low complexity region
|
762 |
783 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
816 |
917 |
8.83e-5 |
PROSPERO |
|
internal_repeat_1
|
911 |
1023 |
8.83e-5 |
PROSPERO |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000103238
AA Change: M639V
PolyPhen 2
Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000099528
Gene: ENSMUSG00000027200
AA Change: M639V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Sema
|
57 |
487 |
7.29e-184 |
SMART |
|
PSI
|
514 |
569 |
1.12e-1 |
SMART |
|
low complexity region
|
573 |
584 |
N/A |
INTRINSIC |
|
transmembrane domain
|
645 |
667 |
N/A |
INTRINSIC |
|
low complexity region
|
786 |
807 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
840 |
941 |
5.95e-5 |
PROSPERO |
|
internal_repeat_1
|
935 |
1047 |
5.95e-5 |
PROSPERO |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000103239
AA Change: M658V
PolyPhen 2
Score 0.879 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000099529
Gene: ENSMUSG00000027200
AA Change: M658V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Sema
|
57 |
487 |
7.29e-184 |
SMART |
|
PSI
|
514 |
569 |
1.12e-1 |
SMART |
|
low complexity region
|
587 |
603 |
N/A |
INTRINSIC |
|
transmembrane domain
|
664 |
686 |
N/A |
INTRINSIC |
|
low complexity region
|
805 |
826 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
859 |
960 |
5.78e-5 |
PROSPERO |
|
internal_repeat_1
|
954 |
1066 |
5.78e-5 |
PROSPERO |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000103240
AA Change: M654V
PolyPhen 2
Score 0.518 (Sensitivity: 0.88; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000099530
Gene: ENSMUSG00000027200
AA Change: M654V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Sema
|
57 |
487 |
7.29e-184 |
SMART |
|
PSI
|
514 |
569 |
1.12e-1 |
SMART |
|
low complexity region
|
587 |
603 |
N/A |
INTRINSIC |
|
transmembrane domain
|
660 |
682 |
N/A |
INTRINSIC |
|
low complexity region
|
801 |
822 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
855 |
956 |
5.63e-5 |
PROSPERO |
|
internal_repeat_1
|
950 |
1062 |
5.63e-5 |
PROSPERO |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000103241
AA Change: M583V
PolyPhen 2
Score 0.649 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000099531
Gene: ENSMUSG00000027200
AA Change: M583V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Sema
|
57 |
487 |
7.29e-184 |
SMART |
|
PSI
|
514 |
569 |
1.12e-1 |
SMART |
|
transmembrane domain
|
589 |
611 |
N/A |
INTRINSIC |
|
low complexity region
|
730 |
751 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
784 |
885 |
7.28e-5 |
PROSPERO |
|
internal_repeat_1
|
879 |
991 |
7.28e-5 |
PROSPERO |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000132088
|
| Meta Mutation Damage Score |
0.1109 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.7%
|
| Validation Efficiency |
91% (43/47) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Semaphorins are a large family, including both secreted and membrane associated proteins, many of which have been implicated as inhibitors or chemorepellents in axon pathfinding, fasciculation and branching, and target selection. All semaphorins possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Additional sequence motifs C-terminal to the semaphorin domain allow classification into distinct subfamilies. Results demonstrate that transmembrane semaphorins, like the secreted ones, can act as repulsive axon guidance cues. This gene encodes a class 6 vertebrate transmembrane semaphorin that demonstrates alternative splicing. Several transcript variants have been identified and expression of the distinct encoded isoforms is thought to be regulated in a tissue- and development-dependent manner. [provided by RefSeq, Nov 2010]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit normal dendritic cell trafficking and antigen-specific T cell priming. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A730013G03Rik |
T |
A |
1: 192,515,731 (GRCm39) |
|
noncoding transcript |
Het |
| Adgrg6 |
A |
G |
10: 14,285,507 (GRCm39) |
S1160P |
probably damaging |
Het |
| Akt1 |
C |
T |
12: 112,625,567 (GRCm39) |
R144H |
probably benign |
Het |
| Arrdc3 |
T |
C |
13: 81,037,182 (GRCm39) |
|
probably benign |
Het |
| Asxl2 |
T |
A |
12: 3,551,774 (GRCm39) |
V1172E |
possibly damaging |
Het |
| Atp9a |
C |
T |
2: 168,523,917 (GRCm39) |
A242T |
possibly damaging |
Het |
| C2cd3 |
C |
T |
7: 100,023,684 (GRCm39) |
T90I |
probably damaging |
Het |
| C4bp |
A |
G |
1: 130,570,692 (GRCm39) |
S295P |
probably benign |
Het |
| Cdkl2 |
G |
A |
5: 92,168,168 (GRCm39) |
T342I |
probably benign |
Het |
| Cep131 |
T |
C |
11: 119,955,645 (GRCm39) |
E1025G |
probably damaging |
Het |
| Crot |
T |
C |
5: 9,023,643 (GRCm39) |
H415R |
probably damaging |
Het |
| Cyp17a1 |
A |
G |
19: 46,656,462 (GRCm39) |
F411L |
probably damaging |
Het |
| Dgkb |
G |
T |
12: 38,234,952 (GRCm39) |
G439V |
probably damaging |
Het |
| Dgkh |
A |
G |
14: 78,865,523 (GRCm39) |
V20A |
probably damaging |
Het |
| Dipk1a |
T |
C |
5: 108,072,500 (GRCm39) |
Y52C |
probably damaging |
Het |
| Dysf |
A |
G |
6: 84,182,854 (GRCm39) |
N2035S |
probably damaging |
Het |
| Fzd1 |
A |
G |
5: 4,805,777 (GRCm39) |
Y602H |
probably damaging |
Het |
| Gm38706 |
C |
A |
6: 130,460,273 (GRCm39) |
|
noncoding transcript |
Het |
| Hmmr |
T |
C |
11: 40,606,148 (GRCm39) |
Q274R |
probably damaging |
Het |
| Homer3 |
G |
A |
8: 70,742,793 (GRCm39) |
|
probably null |
Het |
| Igsf9b |
A |
G |
9: 27,245,548 (GRCm39) |
T1172A |
probably benign |
Het |
| Klf5 |
C |
T |
14: 99,539,666 (GRCm39) |
R360C |
probably damaging |
Het |
| Lrat |
A |
G |
3: 82,804,293 (GRCm39) |
M228T |
probably damaging |
Het |
| Mms19 |
A |
T |
19: 41,952,372 (GRCm39) |
M119K |
possibly damaging |
Het |
| Myo3a |
A |
T |
2: 22,490,149 (GRCm39) |
K565N |
probably damaging |
Het |
| Or10n1 |
A |
T |
9: 39,525,294 (GRCm39) |
I144L |
probably benign |
Het |
| Or1ad6 |
C |
T |
11: 50,860,690 (GRCm39) |
P282S |
probably damaging |
Het |
| Or3a1d |
T |
C |
11: 74,237,588 (GRCm39) |
D274G |
probably benign |
Het |
| Pcdha6 |
A |
G |
18: 37,100,813 (GRCm39) |
D2G |
probably benign |
Het |
| Pcdhga3 |
A |
G |
18: 37,808,938 (GRCm39) |
R464G |
probably damaging |
Het |
| Plxna2 |
C |
T |
1: 194,431,625 (GRCm39) |
S538F |
probably damaging |
Het |
| Pramel42 |
T |
A |
5: 94,685,702 (GRCm39) |
I454K |
probably damaging |
Het |
| Rnf13 |
A |
C |
3: 57,728,010 (GRCm39) |
K230T |
probably damaging |
Het |
| Slc25a25 |
T |
C |
2: 32,320,621 (GRCm39) |
K47E |
probably benign |
Het |
| Sptbn1 |
C |
T |
11: 30,089,114 (GRCm39) |
R716H |
possibly damaging |
Het |
| Ssx2ip |
G |
A |
3: 146,132,186 (GRCm39) |
V216I |
probably benign |
Het |
| Tatdn2 |
T |
G |
6: 113,679,501 (GRCm39) |
|
probably null |
Het |
| Tmprss6 |
A |
G |
15: 78,337,039 (GRCm39) |
Y356H |
probably damaging |
Het |
| Ttn |
A |
G |
2: 76,687,210 (GRCm39) |
|
probably benign |
Het |
| Umod |
A |
G |
7: 119,065,279 (GRCm39) |
|
probably null |
Het |
| Vmn2r93 |
T |
A |
17: 18,524,312 (GRCm39) |
I102K |
possibly damaging |
Het |
| Zdhhc6 |
T |
C |
19: 55,291,169 (GRCm39) |
I349V |
probably benign |
Het |
|
| Other mutations in Sema6d |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00155:Sema6d
|
APN |
2 |
124,501,785 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
IGL00508:Sema6d
|
APN |
2 |
124,498,844 (GRCm39) |
splice site |
probably benign |
|
|
IGL00710:Sema6d
|
APN |
2 |
124,504,208 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL00811:Sema6d
|
APN |
2 |
124,500,389 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01457:Sema6d
|
APN |
2 |
124,495,562 (GRCm39) |
missense |
unknown |
|
|
IGL01524:Sema6d
|
APN |
2 |
124,505,995 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
IGL01598:Sema6d
|
APN |
2 |
124,507,018 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01915:Sema6d
|
APN |
2 |
124,500,491 (GRCm39) |
splice site |
probably benign |
|
|
IGL02365:Sema6d
|
APN |
2 |
124,498,788 (GRCm39) |
missense |
probably benign |
0.14 |
|
IGL02698:Sema6d
|
APN |
2 |
124,495,643 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL02865:Sema6d
|
APN |
2 |
124,505,993 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03018:Sema6d
|
APN |
2 |
124,501,520 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL03333:Sema6d
|
APN |
2 |
124,506,290 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R0269:Sema6d
|
UTSW |
2 |
124,502,665 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
R0390:Sema6d
|
UTSW |
2 |
124,500,410 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0541:Sema6d
|
UTSW |
2 |
124,507,197 (GRCm39) |
missense |
probably benign |
0.25 |
|
R0615:Sema6d
|
UTSW |
2 |
124,496,055 (GRCm39) |
splice site |
probably benign |
|
|
R0617:Sema6d
|
UTSW |
2 |
124,502,665 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
R0694:Sema6d
|
UTSW |
2 |
124,505,961 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0854:Sema6d
|
UTSW |
2 |
124,507,222 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R1630:Sema6d
|
UTSW |
2 |
124,506,265 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R1682:Sema6d
|
UTSW |
2 |
124,507,069 (GRCm39) |
missense |
probably benign |
0.21 |
|
R1823:Sema6d
|
UTSW |
2 |
124,501,476 (GRCm39) |
splice site |
probably null |
|
|
R1932:Sema6d
|
UTSW |
2 |
124,501,806 (GRCm39) |
critical splice donor site |
probably null |
|
|
R2249:Sema6d
|
UTSW |
2 |
124,501,508 (GRCm39) |
missense |
possibly damaging |
0.54 |
|
R2256:Sema6d
|
UTSW |
2 |
124,506,070 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2331:Sema6d
|
UTSW |
2 |
124,499,983 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2910:Sema6d
|
UTSW |
2 |
124,506,957 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3683:Sema6d
|
UTSW |
2 |
124,496,146 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R3937:Sema6d
|
UTSW |
2 |
124,498,770 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4135:Sema6d
|
UTSW |
2 |
124,506,040 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R4583:Sema6d
|
UTSW |
2 |
124,506,082 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4599:Sema6d
|
UTSW |
2 |
124,496,151 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4822:Sema6d
|
UTSW |
2 |
124,504,214 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
R4884:Sema6d
|
UTSW |
2 |
124,498,738 (GRCm39) |
splice site |
probably null |
|
|
R5288:Sema6d
|
UTSW |
2 |
124,506,166 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5443:Sema6d
|
UTSW |
2 |
124,498,756 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5504:Sema6d
|
UTSW |
2 |
124,499,941 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5534:Sema6d
|
UTSW |
2 |
124,501,735 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R5615:Sema6d
|
UTSW |
2 |
124,498,821 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5747:Sema6d
|
UTSW |
2 |
124,506,867 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5866:Sema6d
|
UTSW |
2 |
124,506,262 (GRCm39) |
missense |
probably benign |
0.26 |
|
R5980:Sema6d
|
UTSW |
2 |
124,506,628 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6670:Sema6d
|
UTSW |
2 |
124,496,762 (GRCm39) |
small deletion |
probably benign |
|
|
R6803:Sema6d
|
UTSW |
2 |
124,505,970 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R7023:Sema6d
|
UTSW |
2 |
124,506,831 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7068:Sema6d
|
UTSW |
2 |
124,499,741 (GRCm39) |
missense |
probably benign |
|
|
R7426:Sema6d
|
UTSW |
2 |
124,496,078 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7556:Sema6d
|
UTSW |
2 |
124,496,109 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7569:Sema6d
|
UTSW |
2 |
124,499,892 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R8427:Sema6d
|
UTSW |
2 |
124,507,197 (GRCm39) |
missense |
probably benign |
0.25 |
|
R8690:Sema6d
|
UTSW |
2 |
124,506,937 (GRCm39) |
missense |
probably benign |
0.07 |
|
R8711:Sema6d
|
UTSW |
2 |
124,502,232 (GRCm39) |
missense |
possibly damaging |
0.54 |
|
R8757:Sema6d
|
UTSW |
2 |
124,497,134 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8759:Sema6d
|
UTSW |
2 |
124,497,134 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8868:Sema6d
|
UTSW |
2 |
124,496,114 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9511:Sema6d
|
UTSW |
2 |
124,499,943 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9586:Sema6d
|
UTSW |
2 |
124,496,096 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9731:Sema6d
|
UTSW |
2 |
124,506,117 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- CAGCAAGCATACGTGTTTCTG -3'
(R):5'- TCAAAGAGGCCGTTCAGCTTG -3'
Sequencing Primer
(F):5'- AAATTTAATTGTGACTTCAGGGGGC -3'
(R):5'- CCGTTCAGCTTGGCGAAG -3'
|
| Posted On |
2015-07-21 |
Incidental Mutation