Incidental Mutation 'R6545:Cog4'
ID |
521111 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Cog4
|
Ensembl Gene |
ENSMUSG00000031753 |
Gene Name |
component of oligomeric golgi complex 4 |
Synonyms |
D8Ertd515e |
MMRRC Submission |
044671-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.955)
|
Stock # |
R6545 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
8 |
Chromosomal Location |
111573232-111608859 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 111607577 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Glutamic Acid to Glycine
at position 666
(E666G)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000133297
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000034203]
[ENSMUST00000041382]
[ENSMUST00000165867]
[ENSMUST00000172542]
[ENSMUST00000174398]
[ENSMUST00000174679]
[ENSMUST00000212971]
|
AlphaFold |
Q8R1U1 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000034203
AA Change: E688G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000034203 Gene: ENSMUSG00000031753 AA Change: E688G
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: ENSMUST00000041382
|
SMART Domains |
Protein: ENSMUSP00000039271 Gene: ENSMUSG00000033703
Domain | Start | End | E-Value | Type |
low complexity region
|
22 |
37 |
N/A |
INTRINSIC |
Pfam:Fucokinase
|
94 |
496 |
1.7e-101 |
PFAM |
low complexity region
|
807 |
821 |
N/A |
INTRINSIC |
Pfam:GHMP_kinases_N
|
827 |
894 |
3.6e-9 |
PFAM |
Pfam:GHMP_kinases_C
|
970 |
1052 |
1e-8 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000165867
AA Change: E615G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000128518 Gene: ENSMUSG00000031753 AA Change: E615G
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 |
noncoding transcript
Transcript: ENSMUST00000172497
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000172542
|
SMART Domains |
Protein: ENSMUSP00000133283 Gene: ENSMUSG00000031753
Domain | Start | End | E-Value | Type |
Pfam:COG4
|
1 |
156 |
6.3e-43 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000174398
AA Change: E666G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000133297 Gene: ENSMUSG00000031753 AA Change: E666G
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 |
noncoding transcript
Transcript: ENSMUST00000180679
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000174679
|
SMART Domains |
Protein: ENSMUSP00000133458 Gene: ENSMUSG00000031753
Domain | Start | End | E-Value | Type |
Blast:Cog4
|
27 |
174 |
5e-60 |
BLAST |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000212971
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.3%
- 20x: 97.6%
|
Validation Efficiency |
95% (42/44) |
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 |
Ago1 |
C |
T |
4: 126,348,145 (GRCm39) |
A58T |
possibly damaging |
Het |
Ago4 |
T |
A |
4: 126,405,811 (GRCm39) |
Q366L |
probably benign |
Het |
Card10 |
C |
A |
15: 78,661,010 (GRCm39) |
G950V |
probably damaging |
Het |
Ceacam1 |
A |
T |
7: 25,173,279 (GRCm39) |
V303D |
probably damaging |
Het |
Cfap54 |
C |
T |
10: 92,672,319 (GRCm39) |
R2917H |
probably benign |
Het |
Cit |
A |
G |
5: 115,984,493 (GRCm39) |
S22G |
probably null |
Het |
Crocc2 |
A |
G |
1: 93,140,659 (GRCm39) |
D1103G |
probably benign |
Het |
Cttnbp2 |
A |
T |
6: 18,405,278 (GRCm39) |
|
probably null |
Het |
Dctn3 |
T |
C |
4: 41,723,084 (GRCm39) |
E16G |
probably damaging |
Het |
Dnah6 |
A |
G |
6: 73,021,715 (GRCm39) |
S3536P |
probably damaging |
Het |
Eef2 |
T |
A |
10: 81,016,948 (GRCm39) |
I675N |
probably damaging |
Het |
Gga3 |
A |
G |
11: 115,477,995 (GRCm39) |
F531S |
possibly damaging |
Het |
Gm19410 |
A |
G |
8: 36,257,652 (GRCm39) |
R697G |
possibly damaging |
Het |
Gm3173 |
T |
A |
14: 15,728,395 (GRCm39) |
M18K |
possibly damaging |
Het |
Gm5800 |
A |
T |
14: 51,949,419 (GRCm39) |
S175R |
possibly damaging |
Het |
Gria2 |
T |
C |
3: 80,648,451 (GRCm39) |
K95R |
probably damaging |
Het |
Gstm6 |
A |
G |
3: 107,849,681 (GRCm39) |
I76T |
probably damaging |
Het |
Harbi1 |
T |
G |
2: 91,542,640 (GRCm39) |
Y34D |
probably damaging |
Het |
Hectd2 |
C |
A |
19: 36,564,778 (GRCm39) |
Q20K |
probably benign |
Het |
Inpp5f |
C |
A |
7: 128,296,280 (GRCm39) |
A250D |
possibly damaging |
Het |
Irf9 |
T |
C |
14: 55,842,684 (GRCm39) |
F59L |
probably damaging |
Het |
Itgam |
T |
A |
7: 127,707,044 (GRCm39) |
M625K |
probably damaging |
Het |
Kcnh5 |
C |
T |
12: 75,054,432 (GRCm39) |
R504Q |
probably damaging |
Het |
Lama2 |
T |
C |
10: 27,052,793 (GRCm39) |
T1389A |
probably benign |
Het |
Lin54 |
T |
A |
5: 100,632,996 (GRCm39) |
|
probably null |
Het |
Mettl23 |
A |
G |
11: 116,740,042 (GRCm39) |
D171G |
possibly damaging |
Het |
Mgll |
A |
G |
6: 88,802,685 (GRCm39) |
N296S |
probably benign |
Het |
Mpv17 |
T |
A |
5: 31,302,041 (GRCm39) |
|
probably benign |
Het |
Myof |
A |
T |
19: 37,930,745 (GRCm39) |
M1001K |
possibly damaging |
Het |
Myom1 |
A |
T |
17: 71,389,300 (GRCm39) |
Q850L |
probably benign |
Het |
Or10ab5 |
A |
T |
7: 108,245,662 (GRCm39) |
N40K |
probably damaging |
Het |
Pias2 |
A |
G |
18: 77,217,781 (GRCm39) |
I328V |
possibly damaging |
Het |
Polh |
G |
A |
17: 46,493,685 (GRCm39) |
P311S |
possibly damaging |
Het |
Prss34 |
A |
T |
17: 25,517,809 (GRCm39) |
R61S |
probably benign |
Het |
Rassf2 |
A |
T |
2: 131,840,237 (GRCm39) |
M280K |
probably damaging |
Het |
Rpsa |
A |
G |
9: 119,959,323 (GRCm39) |
H47R |
probably benign |
Het |
Rtp3 |
A |
G |
9: 110,815,894 (GRCm39) |
V219A |
possibly damaging |
Het |
Smarcc2 |
T |
C |
10: 128,319,997 (GRCm39) |
I790T |
probably benign |
Het |
Stag3 |
A |
G |
5: 138,296,614 (GRCm39) |
T491A |
possibly damaging |
Het |
Svil |
C |
T |
18: 5,108,621 (GRCm39) |
H2007Y |
probably benign |
Het |
Togaram1 |
T |
G |
12: 65,024,981 (GRCm39) |
C750G |
possibly damaging |
Het |
Vmn2r13 |
A |
T |
5: 109,304,806 (GRCm39) |
|
probably null |
Het |
Vmn2r4 |
A |
T |
3: 64,313,777 (GRCm39) |
D401E |
possibly damaging |
Het |
Wdr97 |
C |
T |
15: 76,247,578 (GRCm39) |
R1585C |
probably damaging |
Het |
Wsb1 |
A |
T |
11: 79,141,881 (GRCm39) |
D45E |
probably damaging |
Het |
Zfp808 |
T |
A |
13: 62,319,709 (GRCm39) |
Y313N |
probably benign |
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 |
R0350:Cog4
|
UTSW |
8 |
111,580,328 (GRCm39) |
missense |
possibly damaging |
0.73 |
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 |
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'- GGCACTGCCTCTTCATGTAAC -3'
(R):5'- AAGCAGAATTCAGTGGCCC -3'
Sequencing Primer
(F):5'- ACTGTCTCACTGGAAGACTGTCAG -3'
(R):5'- AGCTACAGGTTGTCCACATG -3'
|
Posted On |
2018-06-06 |