Incidental Mutation 'R4845:Sema3f'
| ID |
372115 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sema3f
|
| Ensembl Gene |
ENSMUSG00000034684 |
| Gene Name |
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F |
| Synonyms |
Sema IV, Semak |
| MMRRC Submission |
042458-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4845 (G1)
|
| Quality Score |
207 |
|
Status
|
Not validated
|
| Chromosome |
9 |
| Chromosomal Location |
107558699-107587674 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 107562700 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Cysteine
at position 427
(Y427C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141865
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000080560]
[ENSMUST00000192727]
[ENSMUST00000192783]
[ENSMUST00000193108]
[ENSMUST00000194039]
|
| AlphaFold |
O88632 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000080560
AA Change: Y396C
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000079400
Gene: ENSMUSG00000034684
AA Change: Y396C
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
18 |
N/A |
INTRINSIC |
|
Sema
|
57 |
498 |
5.46e-206 |
SMART |
|
PSI
|
516 |
568 |
1.87e-12 |
SMART |
|
IGc2
|
586 |
654 |
3.79e-4 |
SMART |
|
low complexity region
|
673 |
695 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000192157
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000192712
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000192727
AA Change: Y427C
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000141865
Gene: ENSMUSG00000034684
AA Change: Y427C
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
18 |
N/A |
INTRINSIC |
|
Sema
|
57 |
529 |
3.31e-205 |
SMART |
|
PSI
|
547 |
599 |
1.87e-12 |
SMART |
|
IGc2
|
617 |
685 |
3.79e-4 |
SMART |
|
low complexity region
|
704 |
726 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000192783
|
| SMART Domains |
Protein: ENSMUSP00000141668
Gene: ENSMUSG00000034684
| Domain | Start | End | E-Value | Type |
|---|
|
Sema
|
1 |
276 |
3.6e-7 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000193108
|
| SMART Domains |
Protein: ENSMUSP00000141878
Gene: ENSMUSG00000034684
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
18 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
57 |
191 |
9.9e-46 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000193665
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000194424
AA Change: Y58C
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000194146
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000194846
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000195267
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000195023
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194039
|
| SMART Domains |
Protein: ENSMUSP00000142221
Gene: ENSMUSG00000034684
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
18 |
N/A |
INTRINSIC |
|
Pfam:Sema
|
57 |
185 |
2e-42 |
PFAM |
|
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.7%
- 20x: 93.6%
|
| 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 III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin loop and a C-terminal basic domain. This gene is expressed by the endothelial cells where it was found to act in an autocrine fashion to induce apoptosis, inhibit cell proliferation and survival, and function as an anti-tumorigenic agent. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
PHENOTYPE: Inactivation of this locus results in neuronal defects including impaired CNS axon pathfinding, and PNS and limbic system circuitry. Mice homozygous for a knock-out allele exhibit increased lymphatic branching complexity and LEC numbers. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcg1 |
C |
T |
17: 31,333,057 (GRCm39) |
S600F |
possibly damaging |
Het |
| Arhgap21 |
T |
A |
2: 20,885,998 (GRCm39) |
N393I |
probably damaging |
Het |
| Atp5pf |
T |
A |
16: 84,628,365 (GRCm39) |
I6F |
possibly damaging |
Het |
| B4galt6 |
A |
G |
18: 20,821,517 (GRCm39) |
L337S |
probably benign |
Het |
| C8b |
G |
T |
4: 104,649,009 (GRCm39) |
V308F |
possibly damaging |
Het |
| Cables1 |
A |
G |
18: 12,077,545 (GRCm39) |
R558G |
probably damaging |
Het |
| Chmp2b |
T |
A |
16: 65,347,862 (GRCm39) |
Q38L |
probably damaging |
Het |
| Clca3b |
A |
T |
3: 144,531,031 (GRCm39) |
I773K |
probably benign |
Het |
| Cnmd |
T |
C |
14: 79,899,448 (GRCm39) |
T2A |
probably benign |
Het |
| Crb1 |
C |
T |
1: 139,170,772 (GRCm39) |
D812N |
probably benign |
Het |
| Dnah7c |
T |
A |
1: 46,832,692 (GRCm39) |
D3901E |
probably damaging |
Het |
| Dst |
T |
C |
1: 34,232,208 (GRCm39) |
V3445A |
probably benign |
Het |
| Epn1 |
T |
A |
7: 5,096,908 (GRCm39) |
I230N |
possibly damaging |
Het |
| Exoc6b |
G |
T |
6: 84,812,119 (GRCm39) |
D627E |
probably benign |
Het |
| Exosc1 |
T |
C |
19: 41,919,797 (GRCm39) |
K74E |
possibly damaging |
Het |
| Extl3 |
T |
C |
14: 65,315,024 (GRCm39) |
T53A |
probably benign |
Het |
| Fam227a |
C |
T |
15: 79,533,912 (GRCm39) |
R17H |
probably damaging |
Het |
| Faxc |
G |
T |
4: 21,993,358 (GRCm39) |
W334L |
probably damaging |
Het |
| Gabrr3 |
T |
C |
16: 59,246,833 (GRCm39) |
I94T |
probably damaging |
Het |
| Ifi203 |
A |
T |
1: 173,754,595 (GRCm39) |
M298K |
probably benign |
Het |
| Igkv4-78 |
A |
T |
6: 69,037,207 (GRCm39) |
M1K |
probably null |
Het |
| Iqcm |
G |
T |
8: 76,472,980 (GRCm39) |
R273I |
probably damaging |
Het |
| Itga1 |
G |
T |
13: 115,110,708 (GRCm39) |
S961* |
probably null |
Het |
| Jmy |
T |
A |
13: 93,576,246 (GRCm39) |
M886L |
possibly damaging |
Het |
| Lrp2 |
T |
C |
2: 69,339,585 (GRCm39) |
T1109A |
possibly damaging |
Het |
| Mastl |
A |
G |
2: 23,030,010 (GRCm39) |
S239P |
probably benign |
Het |
| Mettl14 |
T |
A |
3: 123,165,004 (GRCm39) |
E112V |
probably damaging |
Het |
| Mfng |
C |
T |
15: 78,648,588 (GRCm39) |
R163H |
probably benign |
Het |
| Musk |
A |
G |
4: 58,296,679 (GRCm39) |
D93G |
probably damaging |
Het |
| Myoc |
C |
T |
1: 162,475,034 (GRCm39) |
T195M |
possibly damaging |
Het |
| Ncapg2 |
A |
G |
12: 116,404,208 (GRCm39) |
D893G |
probably damaging |
Het |
| Nrap |
C |
T |
19: 56,339,902 (GRCm39) |
V908M |
probably benign |
Het |
| Or4a79 |
T |
C |
2: 89,552,120 (GRCm39) |
I112V |
probably benign |
Het |
| Or52n5 |
T |
C |
7: 104,588,570 (GRCm39) |
V279A |
possibly damaging |
Het |
| Or5g9 |
T |
A |
2: 85,551,836 (GRCm39) |
L29* |
probably null |
Het |
| Orc4 |
T |
C |
2: 48,799,478 (GRCm39) |
N333S |
probably benign |
Het |
| Otx1 |
C |
A |
11: 21,947,037 (GRCm39) |
A91S |
probably damaging |
Het |
| Pcdhb8 |
G |
A |
18: 37,489,771 (GRCm39) |
G483D |
probably benign |
Het |
| Pclo |
A |
T |
5: 14,729,132 (GRCm39) |
|
probably benign |
Het |
| Ppm1k |
A |
T |
6: 57,499,753 (GRCm39) |
Y174* |
probably null |
Het |
| Ptprq |
A |
T |
10: 107,489,393 (GRCm39) |
S911T |
probably benign |
Het |
| Rp1 |
C |
A |
1: 4,419,451 (GRCm39) |
A554S |
probably benign |
Het |
| Slc12a1 |
A |
T |
2: 125,030,146 (GRCm39) |
I573F |
probably damaging |
Het |
| Slc17a1 |
A |
T |
13: 24,060,601 (GRCm39) |
Y201F |
probably damaging |
Het |
| Slc4a7 |
A |
T |
14: 14,733,803 (GRCm38) |
H71L |
probably damaging |
Het |
| Spata6l |
G |
T |
19: 28,905,148 (GRCm39) |
D305E |
probably benign |
Het |
| St13 |
G |
C |
15: 81,283,786 (GRCm39) |
R4G |
probably benign |
Het |
| Tab1 |
C |
T |
15: 80,036,964 (GRCm39) |
R217W |
probably damaging |
Het |
| Taf6 |
T |
A |
5: 138,180,909 (GRCm39) |
Y224F |
possibly damaging |
Het |
| Tmc5 |
C |
G |
7: 118,241,604 (GRCm39) |
F432L |
probably damaging |
Het |
| Trbc1 |
A |
T |
6: 41,516,169 (GRCm39) |
|
probably benign |
Het |
| Trbv21 |
A |
G |
6: 41,179,879 (GRCm39) |
N65S |
probably benign |
Het |
| Trim15 |
G |
A |
17: 37,177,875 (GRCm39) |
P40L |
probably benign |
Het |
| Txnip |
T |
C |
3: 96,466,916 (GRCm39) |
S197P |
probably benign |
Het |
| Vmn1r167 |
T |
A |
7: 23,204,158 (GRCm39) |
Q286L |
probably benign |
Het |
| Wnt9a |
A |
G |
11: 59,222,067 (GRCm39) |
I322V |
probably benign |
Het |
| Zfp879 |
T |
C |
11: 50,724,672 (GRCm39) |
E128G |
probably damaging |
Het |
|
| Other mutations in Sema3f |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00945:Sema3f
|
APN |
9 |
107,562,721 (GRCm39) |
missense |
probably benign |
0.44 |
|
IGL01940:Sema3f
|
APN |
9 |
107,560,896 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02070:Sema3f
|
APN |
9 |
107,569,440 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02381:Sema3f
|
APN |
9 |
107,569,594 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02472:Sema3f
|
APN |
9 |
107,564,935 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02557:Sema3f
|
APN |
9 |
107,564,411 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02614:Sema3f
|
APN |
9 |
107,559,710 (GRCm39) |
missense |
probably benign |
0.28 |
|
IGL02660:Sema3f
|
APN |
9 |
107,561,183 (GRCm39) |
missense |
probably benign |
0.05 |
|
R1468:Sema3f
|
UTSW |
9 |
107,564,771 (GRCm39) |
unclassified |
probably benign |
|
|
R1905:Sema3f
|
UTSW |
9 |
107,561,575 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4728:Sema3f
|
UTSW |
9 |
107,582,639 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4772:Sema3f
|
UTSW |
9 |
107,566,919 (GRCm39) |
nonsense |
probably null |
|
|
R4786:Sema3f
|
UTSW |
9 |
107,559,881 (GRCm39) |
missense |
probably benign |
0.45 |
|
R5418:Sema3f
|
UTSW |
9 |
107,569,820 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5780:Sema3f
|
UTSW |
9 |
107,559,788 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5849:Sema3f
|
UTSW |
9 |
107,559,815 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5929:Sema3f
|
UTSW |
9 |
107,569,392 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6968:Sema3f
|
UTSW |
9 |
107,568,648 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R7043:Sema3f
|
UTSW |
9 |
107,568,599 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R7449:Sema3f
|
UTSW |
9 |
107,561,235 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7526:Sema3f
|
UTSW |
9 |
107,566,927 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R7559:Sema3f
|
UTSW |
9 |
107,561,777 (GRCm39) |
missense |
possibly damaging |
0.52 |
|
R7640:Sema3f
|
UTSW |
9 |
107,560,774 (GRCm39) |
missense |
probably benign |
0.20 |
|
R7771:Sema3f
|
UTSW |
9 |
107,569,625 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R7789:Sema3f
|
UTSW |
9 |
107,582,631 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8058:Sema3f
|
UTSW |
9 |
107,559,800 (GRCm39) |
missense |
probably benign |
0.42 |
|
R8113:Sema3f
|
UTSW |
9 |
107,565,275 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R9574:Sema3f
|
UTSW |
9 |
107,566,972 (GRCm39) |
missense |
possibly damaging |
0.50 |
|
R9641:Sema3f
|
UTSW |
9 |
107,565,454 (GRCm39) |
missense |
unknown |
|
|
R9674:Sema3f
|
UTSW |
9 |
107,566,947 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R9799:Sema3f
|
UTSW |
9 |
107,562,562 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGTGTCTGAGAGCAGCAGTG -3'
(R):5'- CGTGTGACAGCATAGATCTGTG -3'
Sequencing Primer
(F):5'- TCTGAGAGCAGCAGTGGGTAC -3'
(R):5'- CAGCATAGATCTGTGGGGAG -3'
|
| Posted On |
2016-03-01 |
Incidental Mutation