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) question?
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

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 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

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 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

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
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
GeneRefVarChr/LocMutationPredicted EffectZygosity
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
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
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