Incidental Mutation 'R5263:Sema6c'
| ID |
401544 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sema6c
|
| Ensembl Gene |
ENSMUSG00000038777 |
| Gene Name |
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C |
| Synonyms |
Sema Y, Semay |
| MMRRC Submission |
042831-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.303)
|
| Stock # |
R5263 (G1)
|
| Quality Score |
115 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
95067768-95081335 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 95080463 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Proline
at position 887
(L887P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000144039
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000090821]
[ENSMUST00000090823]
[ENSMUST00000107217]
[ENSMUST00000131620]
[ENSMUST00000168321]
[ENSMUST00000202315]
[ENSMUST00000204709]
[ENSMUST00000142449]
|
| AlphaFold |
Q9WTM3 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000090821
AA Change: L887P
PolyPhen 2
Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000088331
Gene: ENSMUSG00000038777
AA Change: L887P
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
25 |
N/A |
INTRINSIC |
|
Sema
|
62 |
488 |
2.55e-165 |
SMART |
|
transmembrane domain
|
604 |
626 |
N/A |
INTRINSIC |
|
low complexity region
|
627 |
638 |
N/A |
INTRINSIC |
|
low complexity region
|
646 |
658 |
N/A |
INTRINSIC |
|
low complexity region
|
660 |
669 |
N/A |
INTRINSIC |
|
low complexity region
|
693 |
709 |
N/A |
INTRINSIC |
|
low complexity region
|
744 |
761 |
N/A |
INTRINSIC |
|
low complexity region
|
907 |
924 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000090823
AA Change: L919P
PolyPhen 2
Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000088333
Gene: ENSMUSG00000038777
AA Change: L919P
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
25 |
N/A |
INTRINSIC |
|
Sema
|
62 |
488 |
2.55e-165 |
SMART |
|
low complexity region
|
591 |
603 |
N/A |
INTRINSIC |
|
transmembrane domain
|
636 |
658 |
N/A |
INTRINSIC |
|
low complexity region
|
659 |
670 |
N/A |
INTRINSIC |
|
low complexity region
|
678 |
690 |
N/A |
INTRINSIC |
|
low complexity region
|
692 |
701 |
N/A |
INTRINSIC |
|
low complexity region
|
725 |
741 |
N/A |
INTRINSIC |
|
low complexity region
|
776 |
793 |
N/A |
INTRINSIC |
|
low complexity region
|
939 |
956 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000107217
AA Change: L879P
PolyPhen 2
Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000102835
Gene: ENSMUSG00000038777
AA Change: L879P
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
25 |
N/A |
INTRINSIC |
|
Sema
|
62 |
448 |
1.23e-126 |
SMART |
|
low complexity region
|
551 |
563 |
N/A |
INTRINSIC |
|
transmembrane domain
|
596 |
618 |
N/A |
INTRINSIC |
|
low complexity region
|
619 |
630 |
N/A |
INTRINSIC |
|
low complexity region
|
638 |
650 |
N/A |
INTRINSIC |
|
low complexity region
|
652 |
661 |
N/A |
INTRINSIC |
|
low complexity region
|
685 |
701 |
N/A |
INTRINSIC |
|
low complexity region
|
736 |
753 |
N/A |
INTRINSIC |
|
low complexity region
|
899 |
916 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000126597
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130662
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000131620
|
| SMART Domains |
Protein: ENSMUSP00000138154
Gene: ENSMUSG00000038777
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
25 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000134125
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000168321
AA Change: L919P
PolyPhen 2
Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000129081
Gene: ENSMUSG00000038777
AA Change: L919P
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
25 |
N/A |
INTRINSIC |
|
Sema
|
62 |
488 |
2.55e-165 |
SMART |
|
transmembrane domain
|
604 |
626 |
N/A |
INTRINSIC |
|
low complexity region
|
627 |
638 |
N/A |
INTRINSIC |
|
low complexity region
|
646 |
658 |
N/A |
INTRINSIC |
|
low complexity region
|
660 |
669 |
N/A |
INTRINSIC |
|
low complexity region
|
693 |
709 |
N/A |
INTRINSIC |
|
low complexity region
|
744 |
761 |
N/A |
INTRINSIC |
|
low complexity region
|
907 |
924 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000202315
AA Change: L887P
PolyPhen 2
Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000144039
Gene: ENSMUSG00000038777
AA Change: L887P
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
25 |
N/A |
INTRINSIC |
|
Sema
|
62 |
488 |
2.55e-165 |
SMART |
|
transmembrane domain
|
604 |
626 |
N/A |
INTRINSIC |
|
low complexity region
|
627 |
638 |
N/A |
INTRINSIC |
|
low complexity region
|
646 |
658 |
N/A |
INTRINSIC |
|
low complexity region
|
660 |
669 |
N/A |
INTRINSIC |
|
low complexity region
|
693 |
709 |
N/A |
INTRINSIC |
|
low complexity region
|
744 |
761 |
N/A |
INTRINSIC |
|
low complexity region
|
907 |
924 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000204709
|
| SMART Domains |
Protein: ENSMUSP00000144702
Gene: ENSMUSG00000038777
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
10 |
20 |
N/A |
INTRINSIC |
|
PDB:3OKY|B
|
25 |
117 |
8e-8 |
PDB |
|
Blast:Sema
|
62 |
119 |
9e-34 |
BLAST |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141607
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000142449
|
| SMART Domains |
Protein: ENSMUSP00000123457
Gene: ENSMUSG00000038777
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
25 |
N/A |
INTRINSIC |
|
Sema
|
62 |
488 |
2.55e-165 |
SMART |
|
low complexity region
|
591 |
603 |
N/A |
INTRINSIC |
|
transmembrane domain
|
636 |
658 |
N/A |
INTRINSIC |
|
low complexity region
|
659 |
670 |
N/A |
INTRINSIC |
|
low complexity region
|
678 |
690 |
N/A |
INTRINSIC |
|
low complexity region
|
692 |
701 |
N/A |
INTRINSIC |
|
low complexity region
|
725 |
741 |
N/A |
INTRINSIC |
|
low complexity region
|
776 |
793 |
N/A |
INTRINSIC |
|
low complexity region
|
939 |
956 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.9%
- 20x: 94.4%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the semaphorin family. Semaphorins represent important molecular signals controlling multiple aspects of the cellular response that follows CNS injury, and thus may play an important role in neural regeneration. [provided by RefSeq, May 2010]
PHENOTYPE: Mice homozygous for a targeted mutation display a decrease in pain threshold. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 35 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adh4 |
G |
T |
3: 138,133,816 (GRCm39) |
V309L |
probably benign |
Het |
| Agmo |
T |
C |
12: 37,407,680 (GRCm39) |
V188A |
probably benign |
Het |
| Aqr |
A |
G |
2: 113,947,059 (GRCm39) |
M1041T |
probably damaging |
Het |
| Arhgef4 |
T |
A |
1: 34,764,078 (GRCm39) |
S1111R |
possibly damaging |
Het |
| Ascc3 |
A |
C |
10: 50,592,757 (GRCm39) |
E1144D |
probably benign |
Het |
| Cct3 |
T |
C |
3: 88,228,672 (GRCm39) |
|
probably null |
Het |
| Cd209f |
T |
C |
8: 4,154,506 (GRCm39) |
T114A |
probably benign |
Het |
| Cgnl1 |
G |
A |
9: 71,539,936 (GRCm39) |
Q1103* |
probably null |
Het |
| Cop1 |
G |
A |
1: 159,152,507 (GRCm39) |
D586N |
probably damaging |
Het |
| Dcaf5 |
A |
G |
12: 80,395,120 (GRCm39) |
S350P |
probably damaging |
Het |
| Dhx29 |
T |
C |
13: 113,084,755 (GRCm39) |
C658R |
probably damaging |
Het |
| Dync1i1 |
G |
A |
6: 5,969,446 (GRCm39) |
V424I |
possibly damaging |
Het |
| Gfap |
C |
T |
11: 102,787,756 (GRCm39) |
R63Q |
probably damaging |
Het |
| Gm10563 |
CTTT |
CTTTATTT |
4: 155,698,940 (GRCm39) |
|
probably null |
Het |
| Gprc6a |
C |
A |
10: 51,502,900 (GRCm39) |
G321V |
probably damaging |
Het |
| Itgb4 |
C |
T |
11: 115,874,983 (GRCm39) |
R447W |
probably benign |
Het |
| Izumo1r |
A |
G |
9: 14,812,976 (GRCm39) |
C99R |
probably damaging |
Het |
| Lrp1b |
T |
C |
2: 41,850,691 (GRCm39) |
D102G |
probably damaging |
Het |
| Mettl4 |
G |
A |
17: 95,047,937 (GRCm39) |
Q235* |
probably null |
Het |
| Mmrn2 |
A |
G |
14: 34,121,541 (GRCm39) |
T804A |
probably benign |
Het |
| Mrgprb5 |
A |
G |
7: 47,817,937 (GRCm39) |
V266A |
probably damaging |
Het |
| Ntng1 |
T |
C |
3: 109,842,188 (GRCm39) |
D195G |
probably damaging |
Het |
| Pld4 |
T |
C |
12: 112,731,465 (GRCm39) |
L206P |
probably damaging |
Het |
| Polr3a |
T |
C |
14: 24,505,009 (GRCm39) |
I1084V |
possibly damaging |
Het |
| Prkd1 |
A |
G |
12: 50,435,089 (GRCm39) |
L546P |
probably damaging |
Het |
| Rhob |
A |
T |
12: 8,549,232 (GRCm39) |
M134K |
probably benign |
Het |
| Ryr3 |
A |
G |
2: 112,548,347 (GRCm39) |
S3087P |
possibly damaging |
Het |
| Sltm |
T |
C |
9: 70,492,081 (GRCm39) |
S648P |
unknown |
Het |
| Sucnr1 |
A |
G |
3: 59,994,190 (GRCm39) |
I239M |
possibly damaging |
Het |
| Tgtp2 |
T |
A |
11: 48,950,090 (GRCm39) |
M161L |
probably damaging |
Het |
| Trpm7 |
A |
G |
2: 126,663,137 (GRCm39) |
V1037A |
probably benign |
Het |
| Vmn2r13 |
A |
T |
5: 109,321,841 (GRCm39) |
H285Q |
probably benign |
Het |
| Zfp971 |
T |
A |
2: 177,675,555 (GRCm39) |
C385S |
probably damaging |
Het |
| Zfpm2 |
T |
A |
15: 40,962,791 (GRCm39) |
V283E |
probably benign |
Het |
| Zranb1 |
CTGATGATGATG |
CTGATGATGATGATG |
7: 132,584,556 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Sema6c |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01547:Sema6c
|
APN |
3 |
95,079,709 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01631:Sema6c
|
APN |
3 |
95,077,714 (GRCm39) |
missense |
probably benign |
0.10 |
|
IGL01799:Sema6c
|
APN |
3 |
95,078,142 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02237:Sema6c
|
APN |
3 |
95,077,430 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02852:Sema6c
|
APN |
3 |
95,077,295 (GRCm39) |
splice site |
probably benign |
|
|
IGL02874:Sema6c
|
APN |
3 |
95,077,688 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03003:Sema6c
|
APN |
3 |
95,076,925 (GRCm39) |
missense |
probably damaging |
1.00 |
|
BB005:Sema6c
|
UTSW |
3 |
95,079,620 (GRCm39) |
missense |
probably damaging |
1.00 |
|
BB015:Sema6c
|
UTSW |
3 |
95,079,620 (GRCm39) |
missense |
probably damaging |
1.00 |
|
PIT4418001:Sema6c
|
UTSW |
3 |
95,077,401 (GRCm39) |
missense |
possibly damaging |
0.57 |
|
R0558:Sema6c
|
UTSW |
3 |
95,076,002 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0582:Sema6c
|
UTSW |
3 |
95,076,508 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0590:Sema6c
|
UTSW |
3 |
95,079,934 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0685:Sema6c
|
UTSW |
3 |
95,080,021 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R1056:Sema6c
|
UTSW |
3 |
95,078,527 (GRCm39) |
missense |
probably benign |
0.15 |
|
R1721:Sema6c
|
UTSW |
3 |
95,078,099 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1867:Sema6c
|
UTSW |
3 |
95,078,099 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1868:Sema6c
|
UTSW |
3 |
95,078,124 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2016:Sema6c
|
UTSW |
3 |
95,078,545 (GRCm39) |
missense |
probably benign |
0.00 |
|
R2343:Sema6c
|
UTSW |
3 |
95,074,394 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2898:Sema6c
|
UTSW |
3 |
95,080,129 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4095:Sema6c
|
UTSW |
3 |
95,080,505 (GRCm39) |
missense |
probably benign |
0.03 |
|
R4999:Sema6c
|
UTSW |
3 |
95,075,674 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6914:Sema6c
|
UTSW |
3 |
95,080,519 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6942:Sema6c
|
UTSW |
3 |
95,080,519 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7104:Sema6c
|
UTSW |
3 |
95,076,156 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R7524:Sema6c
|
UTSW |
3 |
95,074,371 (GRCm39) |
missense |
probably benign |
0.20 |
|
R7724:Sema6c
|
UTSW |
3 |
95,080,510 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7928:Sema6c
|
UTSW |
3 |
95,079,620 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8045:Sema6c
|
UTSW |
3 |
95,080,535 (GRCm39) |
missense |
probably benign |
0.27 |
|
R8243:Sema6c
|
UTSW |
3 |
95,079,916 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8790:Sema6c
|
UTSW |
3 |
95,075,341 (GRCm39) |
missense |
probably benign |
0.34 |
|
R9607:Sema6c
|
UTSW |
3 |
95,076,545 (GRCm39) |
missense |
probably benign |
0.03 |
|
R9653:Sema6c
|
UTSW |
3 |
95,080,525 (GRCm39) |
missense |
probably benign |
0.40 |
|
Z1177:Sema6c
|
UTSW |
3 |
95,075,639 (GRCm39) |
missense |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TAGAGGTGACCACGCTGGAG -3'
(R):5'- GAGTTCCTCGCCAAAGGAC -3'
Sequencing Primer
(F):5'- AACTGCTGCGCTACCTG -3'
(R):5'- CGGGAGAGTCTCGGAGTC -3'
|
| Posted On |
2016-07-06 |
Incidental Mutation