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) question?
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
Blast:Cog4 27 174 5e-60 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000212971
Meta Mutation Damage Score 0.3317 question?
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
GeneRefVarChr/LocMutationPredicted EffectZygosity
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
AlleleSourceChrCoordTypePredicted EffectPPH 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