Incidental Mutation 'R0350:Cog4'
| ID |
29657 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Cog4
|
| Ensembl Gene |
ENSMUSG00000031753 |
| Gene Name |
component of oligomeric golgi complex 4 |
| Synonyms |
D8Ertd515e |
| MMRRC Submission |
038557-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.955)
|
| Stock # |
R0350 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
8 |
| Chromosomal Location |
111573232-111608859 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 111580328 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Isoleucine
at position 133
(L133I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000133458
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000034203]
[ENSMUST00000165867]
[ENSMUST00000172668]
[ENSMUST00000172897]
[ENSMUST00000174165]
[ENSMUST00000174398]
[ENSMUST00000174679]
[ENSMUST00000174723]
|
| AlphaFold |
Q8R1U1 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000034203
AA Change: L187I
PolyPhen 2
Score 0.381 (Sensitivity: 0.90; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000034203
Gene: ENSMUSG00000031753
AA Change: L187I
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
12 |
23 |
N/A |
INTRINSIC |
|
coiled coil region
|
34 |
77 |
N/A |
INTRINSIC |
|
Blast:Cog4
|
81 |
178 |
1e-53 |
BLAST |
|
Cog4
|
188 |
498 |
1.81e-140 |
SMART |
|
Pfam:RINT1_TIP1
|
536 |
773 |
3.1e-11 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000165867
AA Change: L114I
PolyPhen 2
Score 0.161 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000128518
Gene: ENSMUSG00000031753
AA Change: L114I
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:Cog4
|
8 |
105 |
6e-54 |
BLAST |
|
Cog4
|
115 |
425 |
1.81e-140 |
SMART |
|
PDB:3HR0|B
|
452 |
712 |
1e-174 |
PDB |
|
Blast:DIL
|
621 |
702 |
6e-38 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000172668
|
| SMART Domains |
Protein: ENSMUSP00000134252
Gene: ENSMUSG00000031753
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
12 |
23 |
N/A |
INTRINSIC |
|
coiled coil region
|
34 |
77 |
N/A |
INTRINSIC |
|
Blast:Cog4
|
81 |
117 |
1e-15 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000172897
|
| SMART Domains |
Protein: ENSMUSP00000133583
Gene: ENSMUSG00000031753
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
12 |
23 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000174165
|
| SMART Domains |
Protein: ENSMUSP00000134306
Gene: ENSMUSG00000031753
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
12 |
23 |
N/A |
INTRINSIC |
|
coiled coil region
|
34 |
69 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000174398
AA Change: L186I
PolyPhen 2
Score 0.263 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000133297
Gene: ENSMUSG00000031753
AA Change: L186I
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
11 |
22 |
N/A |
INTRINSIC |
|
coiled coil region
|
33 |
76 |
N/A |
INTRINSIC |
|
Blast:Cog4
|
80 |
177 |
9e-54 |
BLAST |
|
Cog4
|
187 |
497 |
1.81e-140 |
SMART |
|
PDB:3HR0|B
|
524 |
763 |
1e-153 |
PDB |
|
Blast:DIL
|
672 |
753 |
7e-38 |
BLAST |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000174679
AA Change: L133I
PolyPhen 2
Score 0.731 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000133458
Gene: ENSMUSG00000031753
AA Change: L133I
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:Cog4
|
27 |
174 |
5e-60 |
BLAST |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174702
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174800
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000174723
|
| SMART Domains |
Protein: ENSMUSP00000133471
Gene: ENSMUSG00000031753
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
12 |
23 |
N/A |
INTRINSIC |
|
coiled coil region
|
34 |
77 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 97.9%
- 10x: 95.2%
- 20x: 89.2%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a component of an oligomeric protein complex involved in the structure and function of the Golgi apparatus. Defects in this gene may be a cause of congenital disorder of glycosylation type IIj. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Aug 2010]
|
| Allele List at MGI |
All alleles(13) : Gene trapped(13) |
| Other mutations in this stock |
Total: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abhd13 |
T |
A |
8: 10,037,600 (GRCm39) |
Y66N |
probably damaging |
Het |
| Apol6 |
C |
T |
15: 76,935,147 (GRCm39) |
Q139* |
probably null |
Het |
| Armh1 |
C |
A |
4: 117,072,753 (GRCm39) |
E244* |
probably null |
Het |
| Cd1d1 |
A |
T |
3: 86,904,880 (GRCm39) |
H219Q |
probably benign |
Het |
| Cdca2 |
A |
G |
14: 67,950,568 (GRCm39) |
L121P |
probably benign |
Het |
| Cdin1 |
T |
C |
2: 115,607,411 (GRCm39) |
Y255H |
possibly damaging |
Het |
| Csf1 |
T |
C |
3: 107,655,922 (GRCm39) |
M370V |
probably benign |
Het |
| Ddi2 |
G |
A |
4: 141,412,834 (GRCm39) |
T26M |
probably benign |
Het |
| Dhcr7 |
A |
G |
7: 143,391,507 (GRCm39) |
D32G |
probably damaging |
Het |
| Efcab3 |
T |
C |
11: 104,581,706 (GRCm39) |
V16A |
probably benign |
Het |
| Exd1 |
T |
C |
2: 119,354,047 (GRCm39) |
N337S |
possibly damaging |
Het |
| Flii |
T |
C |
11: 60,612,683 (GRCm39) |
D227G |
probably damaging |
Het |
| Hsf1 |
A |
G |
15: 76,384,679 (GRCm39) |
T485A |
probably benign |
Het |
| Igfn1 |
G |
A |
1: 135,884,505 (GRCm39) |
R2614* |
probably null |
Het |
| Iqch |
T |
C |
9: 63,408,158 (GRCm39) |
T630A |
probably benign |
Het |
| Itgal |
T |
A |
7: 126,921,253 (GRCm39) |
D770E |
probably damaging |
Het |
| Mroh1 |
T |
A |
15: 76,316,449 (GRCm39) |
V759E |
probably damaging |
Het |
| Mrps17 |
A |
G |
5: 129,795,209 (GRCm39) |
|
probably benign |
Het |
| Mtpap |
A |
G |
18: 4,396,195 (GRCm39) |
S496G |
possibly damaging |
Het |
| Nkd1 |
T |
A |
8: 89,311,844 (GRCm39) |
Y39* |
probably null |
Het |
| Nmd3 |
A |
G |
3: 69,650,907 (GRCm39) |
Y359C |
probably damaging |
Het |
| Nr1h3 |
G |
A |
2: 91,022,170 (GRCm39) |
L153F |
possibly damaging |
Het |
| Nuf2 |
T |
A |
1: 169,341,112 (GRCm39) |
|
probably null |
Het |
| Or4b1b |
T |
C |
2: 90,112,926 (GRCm39) |
|
probably null |
Het |
| Or4c113 |
T |
A |
2: 88,885,700 (GRCm39) |
K23N |
probably benign |
Het |
| Or8b12i |
A |
T |
9: 20,082,032 (GRCm39) |
Y278* |
probably null |
Het |
| Pnn |
T |
C |
12: 59,113,903 (GRCm39) |
|
probably null |
Het |
| Ppm1j |
A |
G |
3: 104,690,687 (GRCm39) |
D230G |
probably benign |
Het |
| Ppp1r15a |
A |
T |
7: 45,172,442 (GRCm39) |
L650Q |
probably damaging |
Het |
| Prss37 |
T |
C |
6: 40,491,893 (GRCm39) |
E229G |
probably damaging |
Het |
| Rbm19 |
T |
C |
5: 120,266,372 (GRCm39) |
V465A |
possibly damaging |
Het |
| Rubcnl |
G |
T |
14: 75,278,331 (GRCm39) |
V372F |
probably damaging |
Het |
| Sema6a |
G |
T |
18: 47,403,785 (GRCm39) |
D595E |
probably benign |
Het |
| Slc35c1 |
A |
G |
2: 92,289,377 (GRCm39) |
F43S |
probably damaging |
Het |
| Slc39a5 |
C |
T |
10: 128,232,619 (GRCm39) |
|
probably null |
Het |
| Slco4c1 |
A |
G |
1: 96,756,574 (GRCm39) |
F583L |
probably benign |
Het |
| Sox9 |
A |
G |
11: 112,675,702 (GRCm39) |
Y297C |
probably damaging |
Het |
| Taf1b |
A |
G |
12: 24,564,884 (GRCm39) |
D167G |
possibly damaging |
Het |
| Trpm6 |
T |
C |
19: 18,861,321 (GRCm39) |
|
probably null |
Het |
| Uba6 |
A |
C |
5: 86,292,237 (GRCm39) |
V402G |
possibly damaging |
Het |
| Usp43 |
T |
C |
11: 67,767,324 (GRCm39) |
Y682C |
probably damaging |
Het |
| Vmn1r195 |
A |
G |
13: 22,463,403 (GRCm39) |
D291G |
probably damaging |
Het |
| Xpr1 |
A |
T |
1: 155,206,214 (GRCm39) |
F156Y |
probably damaging |
Het |
| Yju2b |
C |
T |
8: 84,987,277 (GRCm39) |
E99K |
probably damaging |
Het |
| Zfp318 |
T |
A |
17: 46,724,124 (GRCm39) |
H2042Q |
probably benign |
Het |
| Zfp937 |
T |
A |
2: 150,081,222 (GRCm39) |
D417E |
possibly damaging |
Het |
|
| Other mutations in Cog4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01462:Cog4
|
APN |
8 |
111,592,717 (GRCm39) |
missense |
probably benign |
0.44 |
|
IGL01631:Cog4
|
APN |
8 |
111,608,472 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01756:Cog4
|
APN |
8 |
111,580,391 (GRCm39) |
nonsense |
probably null |
|
|
IGL02850:Cog4
|
APN |
8 |
111,593,221 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
IGL02932:Cog4
|
APN |
8 |
111,579,065 (GRCm39) |
missense |
probably benign |
0.16 |
|
IGL03232:Cog4
|
APN |
8 |
111,607,314 (GRCm39) |
splice site |
probably null |
|
|
Deminimis
|
UTSW |
8 |
111,608,112 (GRCm39) |
missense |
probably damaging |
0.98 |
|
PIT4362001:Cog4
|
UTSW |
8 |
111,593,304 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1368:Cog4
|
UTSW |
8 |
111,585,157 (GRCm39) |
unclassified |
probably benign |
|
|
R1531:Cog4
|
UTSW |
8 |
111,606,353 (GRCm39) |
missense |
probably benign |
0.30 |
|
R2110:Cog4
|
UTSW |
8 |
111,585,214 (GRCm39) |
missense |
possibly damaging |
0.62 |
|
R2112:Cog4
|
UTSW |
8 |
111,585,214 (GRCm39) |
missense |
possibly damaging |
0.62 |
|
R2867:Cog4
|
UTSW |
8 |
111,593,291 (GRCm39) |
intron |
probably benign |
|
|
R4239:Cog4
|
UTSW |
8 |
111,585,244 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4867:Cog4
|
UTSW |
8 |
111,593,242 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4967:Cog4
|
UTSW |
8 |
111,578,915 (GRCm39) |
splice site |
probably null |
|
|
R5124:Cog4
|
UTSW |
8 |
111,573,825 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5655:Cog4
|
UTSW |
8 |
111,589,939 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6024:Cog4
|
UTSW |
8 |
111,608,112 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6347:Cog4
|
UTSW |
8 |
111,607,275 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6475:Cog4
|
UTSW |
8 |
111,607,526 (GRCm39) |
missense |
possibly damaging |
0.74 |
|
R6526:Cog4
|
UTSW |
8 |
111,608,418 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6542:Cog4
|
UTSW |
8 |
111,577,994 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6545:Cog4
|
UTSW |
8 |
111,607,577 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7248:Cog4
|
UTSW |
8 |
111,608,834 (GRCm39) |
missense |
unknown |
|
|
R7292:Cog4
|
UTSW |
8 |
111,608,460 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7356:Cog4
|
UTSW |
8 |
111,576,498 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R7440:Cog4
|
UTSW |
8 |
111,606,338 (GRCm39) |
missense |
probably benign |
0.06 |
|
R7751:Cog4
|
UTSW |
8 |
111,607,600 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8170:Cog4
|
UTSW |
8 |
111,592,663 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8181:Cog4
|
UTSW |
8 |
111,578,717 (GRCm39) |
splice site |
probably null |
|
|
R8834:Cog4
|
UTSW |
8 |
111,608,049 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8837:Cog4
|
UTSW |
8 |
111,579,004 (GRCm39) |
missense |
probably benign |
0.45 |
|
R9155:Cog4
|
UTSW |
8 |
111,608,384 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9469:Cog4
|
UTSW |
8 |
111,608,804 (GRCm39) |
missense |
unknown |
|
|
Z1177:Cog4
|
UTSW |
8 |
111,605,647 (GRCm39) |
missense |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TCACACAGAGATTTGACTTTTAGGCACC -3'
(R):5'- CCGAGAACTTGCTCAGGCCATC -3'
Sequencing Primer
(F):5'- GAACACAGGCACAGTTCTTCTTAC -3'
(R):5'- TCCTCATGTAAACCCAGCAGTG -3'
|
| Posted On |
2013-04-24 |
Incidental Mutation