Incidental Mutation 'R0497:Sema4c'
| ID |
40510 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sema4c
|
| Ensembl Gene |
ENSMUSG00000026121 |
| Gene Name |
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C |
| Synonyms |
M-Sema F, Semacl1, Semaf, Semai, Semacl1 |
| MMRRC Submission |
038693-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R0497 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
36587720-36597430 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 36588689 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glutamic Acid
at position 812
(D812E)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141527
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001172]
[ENSMUST00000114991]
[ENSMUST00000191642]
[ENSMUST00000191677]
[ENSMUST00000193382]
[ENSMUST00000195620]
[ENSMUST00000207843]
[ENSMUST00000194894]
|
| AlphaFold |
Q64151 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000001172
|
| SMART Domains |
Protein: ENSMUSP00000001172
Gene: ENSMUSG00000079610
| Domain | Start | End | E-Value | Type |
|---|
|
ANK
|
30 |
59 |
8.77e2 |
SMART |
|
ANK
|
63 |
92 |
1.08e-5 |
SMART |
|
ANK
|
96 |
127 |
1.27e-2 |
SMART |
|
ANK
|
129 |
158 |
5.62e-4 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000114990
AA Change: D812E
PolyPhen 2
Score 0.036 (Sensitivity: 0.94; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000110641
Gene: ENSMUSG00000026121
AA Change: D812E
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Sema
|
53 |
481 |
2.54e-183 |
SMART |
|
PSI
|
499 |
552 |
4.52e-11 |
SMART |
|
IG
|
563 |
647 |
1.77e-4 |
SMART |
|
transmembrane domain
|
665 |
687 |
N/A |
INTRINSIC |
|
low complexity region
|
754 |
774 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000114991
AA Change: D812E
PolyPhen 2
Score 0.036 (Sensitivity: 0.94; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000110643
Gene: ENSMUSG00000026121
AA Change: D812E
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Sema
|
53 |
481 |
2.54e-183 |
SMART |
|
PSI
|
499 |
552 |
4.52e-11 |
SMART |
|
IG
|
563 |
647 |
1.77e-4 |
SMART |
|
transmembrane domain
|
665 |
687 |
N/A |
INTRINSIC |
|
low complexity region
|
754 |
774 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000191642
AA Change: D812E
PolyPhen 2
Score 0.036 (Sensitivity: 0.94; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000142284
Gene: ENSMUSG00000026121
AA Change: D812E
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Sema
|
53 |
481 |
2.54e-183 |
SMART |
|
PSI
|
499 |
552 |
4.52e-11 |
SMART |
|
IG
|
563 |
647 |
1.77e-4 |
SMART |
|
transmembrane domain
|
665 |
687 |
N/A |
INTRINSIC |
|
low complexity region
|
754 |
774 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000191677
AA Change: D812E
PolyPhen 2
Score 0.036 (Sensitivity: 0.94; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000141263
Gene: ENSMUSG00000026121
AA Change: D812E
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Sema
|
53 |
481 |
2.54e-183 |
SMART |
|
PSI
|
499 |
552 |
4.52e-11 |
SMART |
|
IG
|
563 |
647 |
1.77e-4 |
SMART |
|
transmembrane domain
|
665 |
687 |
N/A |
INTRINSIC |
|
low complexity region
|
754 |
774 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000191785
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000193382
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000195620
AA Change: D812E
PolyPhen 2
Score 0.036 (Sensitivity: 0.94; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000141527
Gene: ENSMUSG00000026121
AA Change: D812E
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Sema
|
53 |
481 |
2.54e-183 |
SMART |
|
PSI
|
499 |
552 |
4.52e-11 |
SMART |
|
IG
|
563 |
647 |
1.77e-4 |
SMART |
|
transmembrane domain
|
665 |
687 |
N/A |
INTRINSIC |
|
low complexity region
|
754 |
774 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000207843
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000208269
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000195160
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000208690
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194894
|
| SMART Domains |
Protein: ENSMUSP00000141712
Gene: ENSMUSG00000079610
| Domain | Start | End | E-Value | Type |
|---|
|
ANK
|
30 |
59 |
5.6e0 |
SMART |
|
ANK
|
63 |
92 |
7.1e-8 |
SMART |
|
ANK
|
96 |
127 |
8.2e-5 |
SMART |
|
| Meta Mutation Damage Score |
0.0983 |
| Coding Region Coverage |
- 1x: 99.6%
- 3x: 98.7%
- 10x: 96.6%
- 20x: 93.1%
|
| Validation Efficiency |
100% (68/68) |
| MGI Phenotype |
FUNCTION: This gene encodes a member of the semaphorin family of proteins that have diverse functions in neuronal development, heart morphogenesis, vascular growth, tumor progression and immune cell regulation. Lack of the encoded protein in some mice causes exencephaly resulting in neonatal lethality. Mice that bypass exencephaly show no obvious behavioral defects but display distinct pigmentation defects. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2015]
PHENOTYPE: Mice homozygous for a targeted mutation exhibit exencephaly, neonatal lethality, and abnormal cerebellum morphology. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 67 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aatk |
A |
C |
11: 119,909,606 (GRCm39) |
V110G |
probably damaging |
Het |
| Adcy6 |
A |
C |
15: 98,495,606 (GRCm39) |
|
probably null |
Het |
| Adm |
A |
G |
7: 110,228,328 (GRCm39) |
T170A |
probably benign |
Het |
| Afap1l2 |
G |
T |
19: 56,918,641 (GRCm39) |
N171K |
probably benign |
Het |
| Aph1b |
G |
T |
9: 66,697,900 (GRCm39) |
S112* |
probably null |
Het |
| Arhgap23 |
A |
G |
11: 97,342,989 (GRCm39) |
S424G |
probably damaging |
Het |
| Asah2 |
T |
A |
19: 32,032,031 (GRCm39) |
N46I |
probably benign |
Het |
| Braf |
G |
A |
6: 39,617,483 (GRCm39) |
|
probably benign |
Het |
| Brd2 |
C |
T |
17: 34,333,334 (GRCm39) |
R47Q |
probably damaging |
Het |
| C2cd5 |
A |
G |
6: 142,957,819 (GRCm39) |
V972A |
probably benign |
Het |
| Car9 |
T |
A |
4: 43,511,881 (GRCm39) |
L300H |
probably damaging |
Het |
| Chmp3 |
T |
C |
6: 71,529,395 (GRCm39) |
S20P |
probably damaging |
Het |
| Chp1 |
A |
G |
2: 119,402,263 (GRCm39) |
N79S |
possibly damaging |
Het |
| Cnot2 |
A |
T |
10: 116,334,260 (GRCm39) |
I335N |
probably damaging |
Het |
| Cntnap4 |
T |
C |
8: 113,296,783 (GRCm39) |
V6A |
probably benign |
Het |
| Ctcf |
T |
A |
8: 106,401,672 (GRCm39) |
|
probably benign |
Het |
| Dennd1b |
A |
G |
1: 138,967,724 (GRCm39) |
|
probably benign |
Het |
| Dnmbp |
A |
G |
19: 43,845,079 (GRCm39) |
|
probably benign |
Het |
| Eef2 |
T |
C |
10: 81,017,420 (GRCm39) |
F782L |
probably benign |
Het |
| Eogt |
T |
A |
6: 97,112,194 (GRCm39) |
Y153F |
probably benign |
Het |
| Fam81a |
G |
T |
9: 70,003,401 (GRCm39) |
Q237K |
possibly damaging |
Het |
| Fat2 |
T |
A |
11: 55,174,228 (GRCm39) |
T2162S |
probably benign |
Het |
| Fcgbpl1 |
T |
A |
7: 27,846,890 (GRCm39) |
C1158S |
probably damaging |
Het |
| Gas6 |
T |
C |
8: 13,520,387 (GRCm39) |
I434V |
possibly damaging |
Het |
| Gm42417 |
A |
T |
1: 36,571,248 (GRCm39) |
L77Q |
probably damaging |
Het |
| Grik3 |
A |
T |
4: 125,517,303 (GRCm39) |
N49Y |
possibly damaging |
Het |
| Gucy2e |
A |
T |
11: 69,114,985 (GRCm39) |
V974E |
probably damaging |
Het |
| Helz2 |
A |
G |
2: 180,871,449 (GRCm39) |
V2721A |
probably damaging |
Het |
| Klhl6 |
GT |
G |
16: 19,775,716 (GRCm39) |
279 |
probably null |
Het |
| Krt73 |
A |
G |
15: 101,710,665 (GRCm39) |
L23P |
probably damaging |
Het |
| L3mbtl3 |
T |
C |
10: 26,158,772 (GRCm39) |
|
probably benign |
Het |
| Lrrc15 |
A |
T |
16: 30,091,710 (GRCm39) |
V543E |
probably damaging |
Het |
| Med13 |
G |
A |
11: 86,167,809 (GRCm39) |
|
probably benign |
Het |
| Med25 |
T |
C |
7: 44,541,524 (GRCm39) |
D60G |
probably damaging |
Het |
| Mgam |
T |
A |
6: 40,641,826 (GRCm39) |
Y560N |
probably damaging |
Het |
| Mlkl |
A |
G |
8: 112,054,505 (GRCm39) |
Y211H |
probably damaging |
Het |
| Msl2 |
A |
G |
9: 100,978,493 (GRCm39) |
N289S |
probably benign |
Het |
| Nwd2 |
G |
T |
5: 63,963,686 (GRCm39) |
W1090L |
probably damaging |
Het |
| Omt2b |
T |
C |
9: 78,235,513 (GRCm39) |
|
probably benign |
Het |
| Or4k37 |
A |
G |
2: 111,159,175 (GRCm39) |
D137G |
probably benign |
Het |
| Pald1 |
A |
G |
10: 61,177,094 (GRCm39) |
L652P |
probably damaging |
Het |
| Pard3b |
T |
A |
1: 62,479,167 (GRCm39) |
|
probably null |
Het |
| Prdm15 |
G |
A |
16: 97,595,534 (GRCm39) |
T1098I |
possibly damaging |
Het |
| Rock2 |
A |
G |
12: 17,004,954 (GRCm39) |
T436A |
probably benign |
Het |
| Sla |
A |
T |
15: 66,664,098 (GRCm39) |
I91K |
probably benign |
Het |
| Slc22a16 |
T |
G |
10: 40,460,963 (GRCm39) |
M255R |
probably damaging |
Het |
| Slc49a4 |
A |
T |
16: 35,555,974 (GRCm39) |
V162D |
probably benign |
Het |
| Smg8 |
C |
T |
11: 86,976,910 (GRCm39) |
D224N |
possibly damaging |
Het |
| Spdef |
A |
T |
17: 27,937,032 (GRCm39) |
D190E |
probably benign |
Het |
| Taok1 |
A |
G |
11: 77,464,630 (GRCm39) |
I152T |
probably damaging |
Het |
| Tmem220 |
A |
G |
11: 66,916,748 (GRCm39) |
D36G |
probably damaging |
Het |
| Tmem235 |
A |
C |
11: 117,755,177 (GRCm39) |
I210L |
probably benign |
Het |
| Tmem266 |
C |
T |
9: 55,288,168 (GRCm39) |
|
probably null |
Het |
| Tmprss12 |
A |
G |
15: 100,178,920 (GRCm39) |
|
probably benign |
Het |
| Trim32 |
G |
A |
4: 65,531,491 (GRCm39) |
R16Q |
probably damaging |
Het |
| Usp38 |
T |
A |
8: 81,711,053 (GRCm39) |
|
probably benign |
Het |
| Usp44 |
C |
T |
10: 93,682,668 (GRCm39) |
P373S |
possibly damaging |
Het |
| Vmn1r209 |
G |
T |
13: 22,990,118 (GRCm39) |
Q191K |
probably damaging |
Het |
| Vmn1r70 |
T |
C |
7: 10,367,953 (GRCm39) |
I147T |
probably benign |
Het |
| Vmn2r107 |
T |
A |
17: 20,595,394 (GRCm39) |
I649N |
probably damaging |
Het |
| Vmn2r12 |
A |
T |
5: 109,239,755 (GRCm39) |
Y269* |
probably null |
Het |
| Zan |
C |
T |
5: 137,410,938 (GRCm39) |
|
probably benign |
Het |
| Zfp616 |
G |
T |
11: 73,974,306 (GRCm39) |
V192L |
probably benign |
Het |
| Zfp644 |
A |
T |
5: 106,786,199 (GRCm39) |
V116D |
probably damaging |
Het |
| Zgrf1 |
T |
C |
3: 127,378,299 (GRCm39) |
|
probably benign |
Het |
| Zhx3 |
A |
T |
2: 160,621,914 (GRCm39) |
L751* |
probably null |
Het |
| Znfx1 |
T |
A |
2: 166,897,331 (GRCm39) |
Q531L |
probably benign |
Het |
|
| Other mutations in Sema4c |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00420:Sema4c
|
APN |
1 |
36,593,001 (GRCm39) |
critical splice donor site |
probably benign |
0.00 |
|
IGL01824:Sema4c
|
APN |
1 |
36,592,110 (GRCm39) |
missense |
possibly damaging |
0.76 |
|
IGL02236:Sema4c
|
APN |
1 |
36,592,166 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02262:Sema4c
|
APN |
1 |
36,589,422 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02282:Sema4c
|
APN |
1 |
36,589,284 (GRCm39) |
splice site |
probably null |
|
|
IGL02476:Sema4c
|
APN |
1 |
36,595,031 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL02900:Sema4c
|
APN |
1 |
36,589,826 (GRCm39) |
nonsense |
probably null |
|
|
swirl
|
UTSW |
1 |
36,589,392 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02837:Sema4c
|
UTSW |
1 |
36,591,965 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0427:Sema4c
|
UTSW |
1 |
36,592,892 (GRCm39) |
nonsense |
probably null |
|
|
R1066:Sema4c
|
UTSW |
1 |
36,589,281 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R1099:Sema4c
|
UTSW |
1 |
36,591,191 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1146:Sema4c
|
UTSW |
1 |
36,589,646 (GRCm39) |
missense |
probably benign |
0.04 |
|
R1146:Sema4c
|
UTSW |
1 |
36,589,646 (GRCm39) |
missense |
probably benign |
0.04 |
|
R1639:Sema4c
|
UTSW |
1 |
36,592,615 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1644:Sema4c
|
UTSW |
1 |
36,589,885 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3176:Sema4c
|
UTSW |
1 |
36,588,960 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
R3177:Sema4c
|
UTSW |
1 |
36,588,960 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
R3276:Sema4c
|
UTSW |
1 |
36,588,960 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
R3277:Sema4c
|
UTSW |
1 |
36,588,960 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
R3551:Sema4c
|
UTSW |
1 |
36,592,804 (GRCm39) |
missense |
probably benign |
0.02 |
|
R4452:Sema4c
|
UTSW |
1 |
36,592,837 (GRCm39) |
missense |
probably benign |
0.31 |
|
R4883:Sema4c
|
UTSW |
1 |
36,591,097 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4895:Sema4c
|
UTSW |
1 |
36,592,651 (GRCm39) |
splice site |
probably null |
|
|
R4913:Sema4c
|
UTSW |
1 |
36,589,266 (GRCm39) |
missense |
probably benign |
0.11 |
|
R4944:Sema4c
|
UTSW |
1 |
36,589,392 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5062:Sema4c
|
UTSW |
1 |
36,592,059 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5077:Sema4c
|
UTSW |
1 |
36,590,812 (GRCm39) |
missense |
probably benign |
0.20 |
|
R5109:Sema4c
|
UTSW |
1 |
36,591,381 (GRCm39) |
frame shift |
probably null |
|
|
R5208:Sema4c
|
UTSW |
1 |
36,589,407 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5551:Sema4c
|
UTSW |
1 |
36,591,398 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5912:Sema4c
|
UTSW |
1 |
36,593,469 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R6578:Sema4c
|
UTSW |
1 |
36,589,834 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7111:Sema4c
|
UTSW |
1 |
36,592,160 (GRCm39) |
missense |
possibly damaging |
0.48 |
|
R7141:Sema4c
|
UTSW |
1 |
36,592,101 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7252:Sema4c
|
UTSW |
1 |
36,589,096 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7495:Sema4c
|
UTSW |
1 |
36,589,774 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7891:Sema4c
|
UTSW |
1 |
36,588,995 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7895:Sema4c
|
UTSW |
1 |
36,592,199 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8264:Sema4c
|
UTSW |
1 |
36,591,966 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8478:Sema4c
|
UTSW |
1 |
36,590,871 (GRCm39) |
missense |
probably benign |
0.04 |
|
R8680:Sema4c
|
UTSW |
1 |
36,589,867 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8733:Sema4c
|
UTSW |
1 |
36,591,954 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9017:Sema4c
|
UTSW |
1 |
36,592,079 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9344:Sema4c
|
UTSW |
1 |
36,592,395 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9488:Sema4c
|
UTSW |
1 |
36,591,067 (GRCm39) |
missense |
probably benign |
|
|
X0019:Sema4c
|
UTSW |
1 |
36,592,077 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0028:Sema4c
|
UTSW |
1 |
36,589,047 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGGTAGCTGGTGCCTGTGCAAAAG -3'
(R):5'- CTGGCCCCGAAACTGATGAGAAAC -3'
Sequencing Primer
(F):5'- CTGGTGCCTGTGCAAAAGTTAAG -3'
(R):5'- TCAAGATTGTGCCTGGTCAC -3'
|
| Posted On |
2013-05-23 |
Incidental Mutation