Incidental Mutation 'R6024:Cog4'
| ID |
479090 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Cog4
|
| Ensembl Gene |
ENSMUSG00000031753 |
| Gene Name |
component of oligomeric golgi complex 4 |
| Synonyms |
D8Ertd515e |
| MMRRC Submission |
044196-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.955)
|
| Stock # |
R6024 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
111573232-111608859 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 111608112 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Isoleucine
at position 735
(T735I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000034203
(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: T735I
PolyPhen 2
Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000034203
Gene: ENSMUSG00000031753
AA Change: T735I
| 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: T662I
PolyPhen 2
Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000128518
Gene: ENSMUSG00000031753
AA Change: T662I
| 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 |
possibly damaging
Transcript: ENSMUST00000174398
AA Change: T713I
PolyPhen 2
Score 0.910 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000133297
Gene: ENSMUSG00000031753
AA Change: T713I
| 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 |
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
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000180679
|
| Meta Mutation Damage Score |
0.2706 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.7%
- 20x: 93.0%
|
| Validation Efficiency |
100% (56/56) |
| 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: 55 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgrv1 |
A |
G |
13: 81,624,624 (GRCm39) |
F3782L |
probably benign |
Het |
| Akr1d1 |
T |
C |
6: 37,535,417 (GRCm39) |
I267T |
probably benign |
Het |
| Aoc1l1 |
A |
T |
6: 48,953,030 (GRCm39) |
K318N |
possibly damaging |
Het |
| Arhgef5 |
T |
C |
6: 43,252,068 (GRCm39) |
S940P |
probably benign |
Het |
| Art2b |
A |
G |
7: 101,229,587 (GRCm39) |
I104T |
probably benign |
Het |
| Avpr1a |
A |
G |
10: 122,285,053 (GRCm39) |
Y115C |
probably damaging |
Het |
| Cdc42bpg |
T |
A |
19: 6,367,526 (GRCm39) |
L995Q |
probably damaging |
Het |
| Cenatac |
T |
C |
9: 44,329,249 (GRCm39) |
T13A |
possibly damaging |
Het |
| Clip1 |
T |
C |
5: 123,753,152 (GRCm39) |
K210E |
possibly damaging |
Het |
| Creb3l4 |
G |
A |
3: 90,146,006 (GRCm39) |
S206L |
probably damaging |
Het |
| Csf3r |
C |
A |
4: 125,931,310 (GRCm39) |
|
probably null |
Het |
| Dnah11 |
G |
T |
12: 117,994,007 (GRCm39) |
S2346R |
probably benign |
Het |
| Dnai2 |
A |
T |
11: 114,643,734 (GRCm39) |
I467F |
possibly damaging |
Het |
| Dpy19l4 |
A |
T |
4: 11,276,876 (GRCm39) |
M523K |
probably damaging |
Het |
| Ebf3 |
T |
C |
7: 136,802,264 (GRCm39) |
D407G |
probably damaging |
Het |
| Fbn2 |
A |
G |
18: 58,209,908 (GRCm39) |
I991T |
probably benign |
Het |
| Gcc1 |
T |
C |
6: 28,419,299 (GRCm39) |
T345A |
probably benign |
Het |
| Gm1527 |
C |
T |
3: 28,974,752 (GRCm39) |
H522Y |
probably benign |
Het |
| Gm4846 |
T |
A |
1: 166,317,696 (GRCm39) |
Y240F |
probably benign |
Het |
| Hmgcl |
T |
C |
4: 135,682,926 (GRCm39) |
V126A |
probably benign |
Het |
| Ifit1bl2 |
G |
T |
19: 34,597,438 (GRCm39) |
S59R |
probably benign |
Het |
| Itga6 |
A |
G |
2: 71,617,577 (GRCm39) |
N32S |
probably benign |
Het |
| Lcor |
C |
A |
19: 41,572,396 (GRCm39) |
P384T |
possibly damaging |
Het |
| Macc1 |
T |
C |
12: 119,414,160 (GRCm39) |
S779P |
probably benign |
Het |
| Mctp1 |
G |
T |
13: 76,533,280 (GRCm39) |
L209F |
probably damaging |
Het |
| Mink1 |
A |
G |
11: 70,489,915 (GRCm39) |
N97S |
possibly damaging |
Het |
| Mst1r |
T |
A |
9: 107,785,350 (GRCm39) |
V336E |
probably benign |
Het |
| Muc16 |
A |
T |
9: 18,557,967 (GRCm39) |
S2775R |
unknown |
Het |
| Muc6 |
T |
A |
7: 141,227,841 (GRCm39) |
T1316S |
possibly damaging |
Het |
| Myh11 |
T |
A |
16: 14,095,567 (GRCm39) |
N65I |
probably damaging |
Het |
| Myo9a |
A |
G |
9: 59,762,671 (GRCm39) |
N801D |
possibly damaging |
Het |
| Nkain2 |
A |
T |
10: 31,827,281 (GRCm39) |
M103K |
probably damaging |
Het |
| Nkx2-2 |
T |
A |
2: 147,025,961 (GRCm39) |
Y259F |
probably benign |
Het |
| Nrxn1 |
T |
C |
17: 90,897,526 (GRCm39) |
M877V |
possibly damaging |
Het |
| Nxf1 |
C |
T |
19: 8,745,108 (GRCm39) |
L453F |
probably damaging |
Het |
| Pcnt |
T |
C |
10: 76,255,871 (GRCm39) |
S790G |
possibly damaging |
Het |
| Phf3 |
T |
C |
1: 30,902,307 (GRCm39) |
D2G |
probably damaging |
Het |
| Phrf1 |
T |
C |
7: 140,838,898 (GRCm39) |
|
probably benign |
Het |
| Ptpn3 |
C |
A |
4: 57,248,653 (GRCm39) |
|
probably null |
Het |
| Pygl |
T |
C |
12: 70,243,841 (GRCm39) |
T625A |
probably benign |
Het |
| R3hdm2 |
T |
A |
10: 127,295,349 (GRCm39) |
F239I |
probably damaging |
Het |
| Sesn1 |
A |
T |
10: 41,772,196 (GRCm39) |
I242F |
probably damaging |
Het |
| Shank2 |
C |
T |
7: 143,733,768 (GRCm39) |
T105I |
probably benign |
Het |
| Skint3 |
T |
C |
4: 112,147,543 (GRCm39) |
F350S |
possibly damaging |
Het |
| Slco5a1 |
T |
C |
1: 13,014,294 (GRCm39) |
Y320C |
probably damaging |
Het |
| Syt11 |
A |
G |
3: 88,669,416 (GRCm39) |
S159P |
probably benign |
Het |
| Tanc2 |
G |
A |
11: 105,758,543 (GRCm39) |
R768Q |
probably damaging |
Het |
| Tanc2 |
T |
C |
11: 105,814,498 (GRCm39) |
S1981P |
probably damaging |
Het |
| Tmem200c |
A |
C |
17: 69,148,722 (GRCm39) |
D435A |
possibly damaging |
Het |
| Trappc8 |
A |
G |
18: 20,966,066 (GRCm39) |
V1125A |
probably damaging |
Het |
| Ttn |
A |
G |
2: 76,644,487 (GRCm39) |
V4762A |
possibly damaging |
Het |
| Unc5d |
A |
G |
8: 29,365,539 (GRCm39) |
S149P |
possibly damaging |
Het |
| Usf3 |
A |
T |
16: 44,040,203 (GRCm39) |
N1561I |
probably damaging |
Het |
| Wdr4 |
A |
T |
17: 31,720,272 (GRCm39) |
|
probably benign |
Het |
| Wdr49 |
T |
G |
3: 75,209,133 (GRCm39) |
E612D |
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 |
|
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'- AATCTAGACCCTGCTCTGGC -3'
(R):5'- GCTTTACTGAGACAAGGCAGAG -3'
Sequencing Primer
(F):5'- TCAGACTCAGACCATCGGGATTG -3'
(R):5'- CTTTACTGAGACAAGGCAGAGACATG -3'
|
| Posted On |
2017-06-26 |
Incidental Mutation