Mutagenetix > Incidental Mutation

Incidental Mutation 'R7751:Cog4'

597238

Institutional Source

Beutler Lab

Gene Symbol

Cog4

Ensembl Gene

ENSMUSG00000031753

Gene Name

component of oligomeric golgi complex 4

Synonyms

D8Ertd515e

MMRRC Submission

045807-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.955) question?

Stock #

R7751 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

111573232-111608859 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 111607600 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 696 (F696L)

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: F696L

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000034203
Gene: ENSMUSG00000031753
AA Change: F696L

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: F623L

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000128518
Gene: ENSMUSG00000031753
AA Change: F623L

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

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: F674L

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000133297
Gene: ENSMUSG00000031753
AA Change: F674L

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

98% (82/84)

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: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca15	A	T	7: 119,965,044 (GRCm39)	I769F	possibly damaging	Het
Ackr1	A	C	1: 173,159,779 (GRCm39)	W247G	probably damaging	Het
Adgrl4	G	A	3: 151,197,946 (GRCm39)	G69S	probably damaging	Het
Agrn	C	T	4: 156,260,886 (GRCm39)	S710N	probably damaging	Het
Aox3	A	G	1: 58,218,494 (GRCm39)	M1103V	probably benign	Het
Asb18	G	A	1: 89,896,206 (GRCm39)	A278V	probably benign	Het
B3gat2	A	G	1: 23,801,945 (GRCm39)	E77G	probably benign	Het
Camta1	T	C	4: 151,232,863 (GRCm39)		probably null	Het
Cbll1	A	T	12: 31,537,579 (GRCm39)	I392N	probably damaging	Het
Ccdc113	A	G	8: 96,264,829 (GRCm39)	D113G	possibly damaging	Het
Cd79a	T	C	7: 24,599,092 (GRCm39)	F148L	probably benign	Het
Chad	T	A	11: 94,455,999 (GRCm39)	C26S	probably damaging	Het
Csf2rb	T	G	15: 78,225,839 (GRCm39)	S303R	probably damaging	Het
Cstpp1	A	T	2: 91,214,118 (GRCm39)	L79H	probably damaging	Het
Cubn	C	T	2: 13,365,176 (GRCm39)	G1621R	probably damaging	Het
Dennd4c	T	A	4: 86,747,179 (GRCm39)	N1454K	probably benign	Het
Dennd5b	T	C	6: 148,918,604 (GRCm39)	I853V	probably benign	Het
Dnaaf11	T	C	15: 66,321,412 (GRCm39)	E243G	probably benign	Het
Dop1a	A	T	9: 86,389,783 (GRCm39)	D561V	probably benign	Het
Dpysl4	A	G	7: 138,669,456 (GRCm39)	I45V	probably benign	Het
Ect2l	A	C	10: 18,045,153 (GRCm39)	S301A	possibly damaging	Het
Elf2	A	G	3: 51,165,035 (GRCm39)	V323A	probably damaging	Het
Epcam	C	T	17: 87,947,904 (GRCm39)	R125*	probably null	Het
Ephb4	T	C	5: 137,363,937 (GRCm39)	V612A	probably damaging	Het
Erich3	C	T	3: 154,469,426 (GRCm39)	R1293C	unknown	Het
F830045P16Rik	C	A	2: 129,302,367 (GRCm39)	L408F	probably damaging	Het
Gask1a	G	A	9: 121,793,887 (GRCm39)	V14I	probably benign	Het
Gm13102	T	C	4: 143,835,787 (GRCm39)	I485T	probably benign	Het
Gm16494	A	T	17: 47,327,800 (GRCm39)	L28*	probably null	Het
Grin2c	A	G	11: 115,144,696 (GRCm39)	V610A	probably damaging	Het
Hacd2	T	A	16: 34,922,434 (GRCm39)	Y208N	probably damaging	Het
Hlf	A	T	11: 90,278,821 (GRCm39)	F81Y	probably damaging	Het
Igfbp7	G	A	5: 77,499,134 (GRCm39)	A257V	probably damaging	Het
Il12a	A	T	3: 68,605,235 (GRCm39)	N167I	probably damaging	Het
Il1r2	G	A	1: 40,162,371 (GRCm39)	C338Y	probably damaging	Het
Irf2bpl	G	T	12: 86,930,489 (GRCm39)	H61Q	probably damaging	Het
Kansl1	A	G	11: 104,314,890 (GRCm39)	F383L	probably benign	Het
Kcnh8	A	G	17: 53,268,871 (GRCm39)	T863A	probably damaging	Het
Klhl36	C	A	8: 120,596,397 (GRCm39)	Q33K	probably benign	Het
Lrig2	A	T	3: 104,401,985 (GRCm39)	Y113*	probably null	Het
Lrrc36	T	A	8: 106,178,667 (GRCm39)	S287R	possibly damaging	Het
Mr1	A	T	1: 155,005,054 (GRCm39)	Y329N	probably damaging	Het
Muc5ac	G	C	7: 141,363,040 (GRCm39)	G2117A	unknown	Het
Nectin4	G	A	1: 171,211,326 (GRCm39)		probably null	Het
Nsrp1	A	G	11: 76,940,097 (GRCm39)		probably null	Het
Or1e21	A	T	11: 73,344,372 (GRCm39)	I222N	possibly damaging	Het
Or9g3	A	G	2: 85,583,836 (GRCm39)	T44A	probably benign	Het
Pcdh8	A	T	14: 80,008,143 (GRCm39)	I140N	probably damaging	Het
Pdzd8	A	G	19: 59,333,208 (GRCm39)	V271A	probably damaging	Het
Pex3	T	A	10: 13,403,550 (GRCm39)	I324L	possibly damaging	Het
Pira12	T	A	7: 3,898,603 (GRCm39)	I282F	probably damaging	Het
Pitpnm1	T	A	19: 4,153,470 (GRCm39)	F209I	probably benign	Het
Pkd1l3	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	8: 110,350,827 (GRCm39)		probably benign	Het
Pkhd1	T	A	1: 20,271,149 (GRCm39)	T3135S	probably damaging	Het
Pramel32	T	C	4: 88,547,356 (GRCm39)	D192G	probably benign	Het
Prdm16	T	C	4: 154,412,756 (GRCm39)	N1082S	probably damaging	Het
Psmd12	A	T	11: 107,370,439 (GRCm39)	I13F	possibly damaging	Het
Ptgs2	A	T	1: 149,980,258 (GRCm39)	I399F	probably benign	Het
Rasa3	A	T	8: 13,618,708 (GRCm39)	S830T	probably benign	Het
Rasgef1c	A	T	11: 49,861,120 (GRCm39)	R362W	probably damaging	Het
Resf1	A	G	6: 149,226,936 (GRCm39)		probably benign	Het
Rictor	C	T	15: 6,801,635 (GRCm39)	S441L	probably benign	Het
Rnf217	C	A	10: 31,393,415 (GRCm39)	G389W	probably damaging	Het
Sec16b	A	T	1: 157,385,630 (GRCm39)	D675V	probably damaging	Het
Serpinb12	A	G	1: 106,877,401 (GRCm39)	Y137C	probably damaging	Het
Slc2a5	T	A	4: 150,227,591 (GRCm39)	I470N	probably damaging	Het
Slc5a1	T	C	5: 33,290,761 (GRCm39)	I115T	possibly damaging	Het
Slco1a4	A	T	6: 141,780,413 (GRCm39)	S126T	possibly damaging	Het
St6galnac2	T	C	11: 116,568,410 (GRCm39)	D351G	probably damaging	Het
Stat4	G	A	1: 52,121,711 (GRCm39)	V357M	possibly damaging	Het
Taf4	G	A	2: 179,573,822 (GRCm39)	T682M	probably damaging	Het
Tdrd9	T	A	12: 111,958,982 (GRCm39)	C139S	probably benign	Het
Tmed9	G	A	13: 55,741,054 (GRCm39)	R23Q	not run	Het
Tmem150a	A	C	6: 72,336,028 (GRCm39)	H205P	probably damaging	Het
Tns2	C	A	15: 102,018,163 (GRCm39)	L350I	probably benign	Het
Tpr	A	G	1: 150,295,646 (GRCm39)	T964A	probably benign	Het
Traf3ip1	G	T	1: 91,422,479 (GRCm39)		probably benign	Het
Trem2	G	T	17: 48,653,567 (GRCm39)		probably benign	Het
Ttc14	G	A	3: 33,863,590 (GRCm39)	G666D	unknown	Het
Ulk1	T	C	5: 110,957,078 (GRCm39)	D40G	probably damaging	Het
Vmn1r30	A	G	6: 58,412,397 (GRCm39)	V145A	probably benign	Het
Vmn1r79	C	T	7: 11,910,762 (GRCm39)	Q215*	probably null	Het
Wnk2	G	A	13: 49,231,493 (GRCm39)	T16I	unknown	Het
Yme1l1	T	C	2: 23,077,856 (GRCm39)		probably null	Het
Zbtb16	T	A	9: 48,654,769 (GRCm39)	H454L	probably damaging	Het
Zkscan5	A	C	5: 145,157,676 (GRCm39)	H726P	probably damaging	Het
Zrsr2-ps1	A	G	11: 22,923,595 (GRCm39)	Q123R	possibly 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
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
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'- GTCTCACTGGAAGACTGTCAG -3'
(R):5'- TGAAGCAGAATTCAGTGGCC -3'

Sequencing Primer
(F):5'- CACTGGAAGACTGTCAGTATTAAAG -3'
(R):5'- AGCTACAGGTTGTCCACATG -3'

Posted On

2019-11-26