Incidental Mutation 'R6475:Cog4'
ID |
517384 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Cog4
|
Ensembl Gene |
ENSMUSG00000031753 |
Gene Name |
component of oligomeric golgi complex 4 |
Synonyms |
D8Ertd515e |
MMRRC Submission |
044608-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.955)
|
Stock # |
R6475 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
8 |
Chromosomal Location |
111573232-111608859 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 111607526 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Isoleucine to Asparagine
at position 671
(I671N)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000034203
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000034203]
[ENSMUST00000041382]
[ENSMUST00000165867]
[ENSMUST00000172542]
[ENSMUST00000174398]
[ENSMUST00000174679]
[ENSMUST00000212971]
|
AlphaFold |
Q8R1U1 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000034203
AA Change: I671N
PolyPhen 2
Score 0.738 (Sensitivity: 0.85; Specificity: 0.92)
|
SMART Domains |
Protein: ENSMUSP00000034203 Gene: ENSMUSG00000031753 AA Change: I671N
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 benign
Transcript: ENSMUST00000165867
AA Change: I598N
PolyPhen 2
Score 0.062 (Sensitivity: 0.94; Specificity: 0.84)
|
SMART Domains |
Protein: ENSMUSP00000128518 Gene: ENSMUSG00000031753 AA Change: I598N
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 benign
Transcript: ENSMUST00000174398
AA Change: I649N
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
SMART Domains |
Protein: ENSMUSP00000133297 Gene: ENSMUSG00000031753 AA Change: I649N
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
|
Meta Mutation Damage Score |
0.3317 |
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.5%
- 20x: 92.0%
|
Validation Efficiency |
96% (54/56) |
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: 58 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Asb5 |
T |
A |
8: 55,003,610 (GRCm39) |
V44E |
probably damaging |
Het |
Bmpr2 |
T |
A |
1: 59,907,503 (GRCm39) |
D865E |
probably damaging |
Het |
Ccr4 |
A |
G |
9: 114,322,047 (GRCm39) |
V6A |
probably benign |
Het |
Cd209a |
A |
T |
8: 3,797,031 (GRCm39) |
D102E |
probably damaging |
Het |
Cdh18 |
A |
G |
15: 23,227,022 (GRCm39) |
D161G |
possibly damaging |
Het |
Col14a1 |
T |
G |
15: 55,309,218 (GRCm39) |
|
probably benign |
Het |
Cpne6 |
A |
G |
14: 55,751,110 (GRCm39) |
D173G |
probably damaging |
Het |
Daglb |
G |
T |
5: 143,467,406 (GRCm39) |
V275L |
probably benign |
Het |
Defb43 |
G |
T |
14: 63,249,321 (GRCm39) |
|
probably null |
Het |
Dhx30 |
A |
G |
9: 109,914,120 (GRCm39) |
V1022A |
possibly damaging |
Het |
Egfem1 |
A |
T |
3: 29,711,312 (GRCm39) |
K297M |
probably damaging |
Het |
Egfr |
A |
G |
11: 16,841,259 (GRCm39) |
I717V |
probably benign |
Het |
Eif2ak1 |
T |
G |
5: 143,803,765 (GRCm39) |
|
probably null |
Het |
Epb42 |
T |
C |
2: 120,857,614 (GRCm39) |
Y307C |
possibly damaging |
Het |
Erlec1 |
G |
A |
11: 30,898,442 (GRCm39) |
Q10* |
probably null |
Het |
Fam185a |
A |
G |
5: 21,630,281 (GRCm39) |
D39G |
probably benign |
Het |
Fbxl4 |
T |
A |
4: 22,433,661 (GRCm39) |
D599E |
probably damaging |
Het |
Fgfr2 |
T |
A |
7: 129,802,850 (GRCm39) |
T268S |
probably benign |
Het |
Gabra1 |
A |
T |
11: 42,053,382 (GRCm39) |
M84K |
probably benign |
Het |
Gba1 |
A |
G |
3: 89,113,235 (GRCm39) |
D222G |
probably benign |
Het |
Gm3409 |
T |
A |
5: 146,474,596 (GRCm39) |
H37Q |
possibly damaging |
Het |
Gm4559 |
A |
G |
7: 141,827,887 (GRCm39) |
C72R |
unknown |
Het |
Grik4 |
T |
C |
9: 42,540,304 (GRCm39) |
N292S |
probably benign |
Het |
Haao |
A |
G |
17: 84,139,113 (GRCm39) |
S274P |
possibly damaging |
Het |
Hsd17b4 |
T |
A |
18: 50,305,329 (GRCm39) |
|
probably null |
Het |
Igdcc4 |
A |
T |
9: 65,027,603 (GRCm39) |
S222C |
probably damaging |
Het |
Iqub |
T |
A |
6: 24,449,744 (GRCm39) |
N707I |
probably damaging |
Het |
Itgb7 |
T |
A |
15: 102,124,701 (GRCm39) |
D772V |
probably benign |
Het |
Kif14 |
T |
C |
1: 136,455,149 (GRCm39) |
L1607P |
probably damaging |
Het |
Klf5 |
A |
G |
14: 99,538,817 (GRCm39) |
T77A |
probably benign |
Het |
Klhl29 |
C |
T |
12: 5,141,030 (GRCm39) |
V605I |
probably damaging |
Het |
Map4k1 |
T |
C |
7: 28,686,447 (GRCm39) |
V105A |
probably damaging |
Het |
Mctp2 |
A |
T |
7: 71,850,092 (GRCm39) |
|
probably null |
Het |
Med12l |
A |
G |
3: 59,164,500 (GRCm39) |
E1364G |
probably damaging |
Het |
Mup9 |
A |
T |
4: 60,375,805 (GRCm39) |
D30E |
possibly damaging |
Het |
Naip1 |
T |
C |
13: 100,545,596 (GRCm39) |
R1311G |
probably damaging |
Het |
Or2ag2 |
A |
G |
7: 106,485,604 (GRCm39) |
V140A |
probably benign |
Het |
Or2v1 |
C |
T |
11: 49,025,760 (GRCm39) |
T247I |
probably benign |
Het |
Or4f14 |
G |
A |
2: 111,743,204 (GRCm39) |
Q24* |
probably null |
Het |
Or8g28 |
T |
A |
9: 39,169,378 (GRCm39) |
M197L |
probably benign |
Het |
Pkd1l3 |
A |
C |
8: 110,349,844 (GRCm39) |
T230P |
unknown |
Het |
Pthlh |
G |
T |
6: 147,158,688 (GRCm39) |
H91N |
probably damaging |
Het |
Rapgef5 |
T |
A |
12: 117,681,942 (GRCm39) |
V239D |
probably damaging |
Het |
Rita1 |
G |
A |
5: 120,749,635 (GRCm39) |
T26I |
probably damaging |
Het |
Robo3 |
T |
C |
9: 37,334,586 (GRCm39) |
T615A |
probably damaging |
Het |
Rpp38 |
T |
C |
2: 3,330,644 (GRCm39) |
D86G |
probably benign |
Het |
Sec31a |
T |
C |
5: 100,533,129 (GRCm39) |
T539A |
probably damaging |
Het |
Senp2 |
G |
T |
16: 21,842,550 (GRCm39) |
V205L |
probably damaging |
Het |
Septin10 |
T |
C |
10: 59,028,133 (GRCm39) |
N63D |
possibly damaging |
Het |
Sez6 |
A |
G |
11: 77,864,670 (GRCm39) |
|
|
Het |
Spesp1 |
C |
T |
9: 62,179,715 (GRCm39) |
V398I |
probably benign |
Het |
Tmbim7 |
G |
A |
5: 3,714,319 (GRCm39) |
G19S |
probably benign |
Het |
Tnni3k |
A |
T |
3: 154,646,695 (GRCm39) |
L431* |
probably null |
Het |
Trdn |
T |
A |
10: 33,340,551 (GRCm39) |
|
probably null |
Het |
Tubb2a |
A |
G |
13: 34,259,442 (GRCm39) |
V116A |
possibly damaging |
Het |
Ush1c |
T |
C |
7: 45,878,643 (GRCm39) |
D124G |
probably damaging |
Het |
Zfp768 |
A |
T |
7: 126,943,827 (GRCm39) |
F103L |
probably damaging |
Het |
Zfp799 |
A |
G |
17: 33,039,820 (GRCm39) |
S149P |
probably 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 |
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 |
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'- CAGAGTTCAAGGTGAGGGTC -3'
(R):5'- CAGGGTCTAGATTAGCAGGGTG -3'
Sequencing Primer
(F):5'- GGAGTTCCCATAATGCCCTCAC -3'
(R):5'- CAGGGTGTGCTGGTGGC -3'
|
Posted On |
2018-05-21 |