Mutagenetix > Incidental Mutation

Incidental Mutation 'R2112:Cog4'

232673

Institutional Source

Beutler Lab

Gene Symbol

Cog4

Ensembl Gene

ENSMUSG00000031753

Gene Name

component of oligomeric golgi complex 4

Synonyms

D8Ertd515e

MMRRC Submission

040116-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.953) question?

Stock #

R2112 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

111573232-111608859 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 111585214 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 292 (Y292C)

Ref Sequence

ENSEMBL: ENSMUSP00000133297 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000034203] [ENSMUST00000165867] [ENSMUST00000172542] [ENSMUST00000172897] [ENSMUST00000174165] [ENSMUST00000174398] [ENSMUST00000174679] [ENSMUST00000174723]

AlphaFold

Q8R1U1

Predicted Effect

possibly damaging
Transcript: ENSMUST00000034203
AA Change: Y293C

PolyPhen 2 Score 0.550 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000034203
Gene: ENSMUSG00000031753
AA Change: Y293C

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: ENSMUST00000165867
AA Change: Y220C

PolyPhen 2 Score 0.117 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000128518
Gene: ENSMUSG00000031753
AA Change: Y220C

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 benign
Transcript: ENSMUST00000172897

SMART Domains

Protein: ENSMUSP00000133583
Gene: ENSMUSG00000031753

Domain	Start	End	E-Value	Type
low complexity region	12	23	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173501

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173794

Predicted Effect

probably benign
Transcript: ENSMUST00000174165

SMART Domains

Protein: ENSMUSP00000134306
Gene: ENSMUSG00000031753

Domain	Start	End	E-Value	Type
low complexity region	12	23	N/A	INTRINSIC
coiled coil region	34	69	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000174398
AA Change: Y292C

PolyPhen 2 Score 0.618 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000133297
Gene: ENSMUSG00000031753
AA Change: Y292C

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: ENSMUST00000174800

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: ENSMUST00000174723

SMART Domains

Protein: ENSMUSP00000133471
Gene: ENSMUSG00000031753

Domain	Start	End	E-Value	Type
low complexity region	12	23	N/A	INTRINSIC
coiled coil region	34	77	N/A	INTRINSIC

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.1%

Validation Efficiency

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: 94 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam1b	A	G	5: 121,638,777 (GRCm39)		probably benign	Het
Adprhl1	A	G	8: 13,298,694 (GRCm39)	Y79H	probably damaging	Het
Ambra1	T	A	2: 91,706,132 (GRCm39)	W746R	probably damaging	Het
Ankhd1	A	T	18: 36,774,679 (GRCm39)	K1420I	probably damaging	Het
Ap1b1	T	C	11: 4,965,613 (GRCm39)	F51L	probably damaging	Het
Arhgap24	A	C	5: 103,040,366 (GRCm39)	R434S	probably damaging	Het
Arhgap29	T	C	3: 121,805,210 (GRCm39)	L525P	probably benign	Het
Arpc1b	T	C	5: 145,060,579 (GRCm39)	Y124H	probably damaging	Het
Arr3	T	A	X: 99,658,247 (GRCm39)	F269L	possibly damaging	Het
Atp11b	G	T	3: 35,891,677 (GRCm39)	V830F	probably damaging	Het
Ccdc71l	T	A	12: 32,429,229 (GRCm39)	F83I	probably damaging	Het
Cdh23	G	T	10: 60,141,362 (GRCm39)	F3127L	probably damaging	Het
Cfap251	G	A	5: 123,392,438 (GRCm39)		probably benign	Het
Cldn15	T	A	5: 136,997,016 (GRCm39)	M19K	possibly damaging	Het
Col12a1	A	G	9: 79,551,181 (GRCm39)	V2145A	possibly damaging	Het
Col5a3	T	C	9: 20,721,073 (GRCm39)	I110V	unknown	Het
Cps1	T	A	1: 67,216,139 (GRCm39)	D821E	probably benign	Het
Crnkl1	A	T	2: 145,772,617 (GRCm39)	Y153*	probably null	Het
Dock10	T	A	1: 80,483,359 (GRCm39)	K2082M	probably damaging	Het
Dock10	T	C	1: 80,483,360 (GRCm39)	K2083E	probably damaging	Het
Dst	T	C	1: 34,208,259 (GRCm39)	S737P	probably damaging	Het
Dthd1	T	C	5: 62,979,251 (GRCm39)	Y304H	probably damaging	Het
Dthd1	T	C	5: 63,000,222 (GRCm39)	S515P	probably damaging	Het
Etf1	A	T	18: 35,042,154 (GRCm39)		probably null	Het
Fmnl2	A	G	2: 52,995,549 (GRCm39)	E424G	probably damaging	Het
Galt	A	G	4: 41,758,245 (GRCm39)	T337A	probably benign	Het
Gbp4	A	G	5: 105,283,042 (GRCm39)	L76P	possibly damaging	Het
Gcfc2	C	A	6: 81,900,759 (GRCm39)	D24E	probably benign	Het
Gigyf2	A	G	1: 87,368,452 (GRCm39)	H1044R	probably damaging	Het
Glg1	T	C	8: 111,919,178 (GRCm39)	D315G	probably damaging	Het
Gm4787	C	T	12: 81,424,607 (GRCm39)	C517Y	probably damaging	Het
Gnl3l	A	G	X: 149,780,290 (GRCm39)	S217P	probably damaging	Het
Gpr37	T	C	6: 25,669,380 (GRCm39)	Y488C	possibly damaging	Het
Hap1	T	C	11: 100,244,825 (GRCm39)	D240G	probably benign	Het
Hhla1	C	G	15: 65,808,232 (GRCm39)	W271S	probably benign	Het
Hmgxb3	T	C	18: 61,288,458 (GRCm39)	R470G	possibly damaging	Het
Inpp5a	A	G	7: 139,154,877 (GRCm39)	D332G	probably damaging	Het
Insr	A	G	8: 3,219,748 (GRCm39)	S925P	probably benign	Het
Isoc2b	T	A	7: 4,852,474 (GRCm39)	D171V	probably damaging	Het
Kif20b	T	C	19: 34,909,132 (GRCm39)	I223T	probably benign	Het
Krt6b	T	C	15: 101,586,999 (GRCm39)	T258A	possibly damaging	Het
Lipo4	G	A	19: 33,488,926 (GRCm39)	P219L	probably benign	Het
Luc7l	T	C	17: 26,474,101 (GRCm39)		probably null	Het
Madd	T	C	2: 91,007,321 (GRCm39)	K264E	possibly damaging	Het
Mcf2l	A	T	8: 13,051,867 (GRCm39)	K433N	probably damaging	Het
Mob3b	A	T	4: 35,083,795 (GRCm39)	N131K	probably damaging	Het
Mtus1	G	T	8: 41,475,608 (GRCm39)	P819T	probably damaging	Het
Myo15a	T	C	11: 60,384,994 (GRCm39)	F1699L	probably damaging	Het
Nav1	C	T	1: 135,376,742 (GRCm39)	R1694Q	probably damaging	Het
Neb	G	C	2: 52,218,776 (GRCm39)	T78S	probably damaging	Het
Nek2	T	C	1: 191,559,320 (GRCm39)	V275A	probably benign	Het
Nfatc1	A	T	18: 80,678,879 (GRCm39)	C836*	probably null	Het
Nos1	T	C	5: 118,074,636 (GRCm39)	V1060A	probably benign	Het
Notch3	T	A	17: 32,363,584 (GRCm39)	I1160F	probably benign	Het
Nox4	T	C	7: 87,021,216 (GRCm39)	L476P	probably damaging	Het
Npc1	A	T	18: 12,346,529 (GRCm39)	N222K	possibly damaging	Het
Nrn1l	C	A	8: 106,621,378 (GRCm39)	H109Q	possibly damaging	Het
Or4c11	T	C	2: 88,695,545 (GRCm39)	S199P	possibly damaging	Het
Or4k15	G	T	14: 50,364,080 (GRCm39)	L15F	probably damaging	Het
Or6d13	T	C	6: 116,517,611 (GRCm39)	Y66H	possibly damaging	Het
Or7a41	T	C	10: 78,871,248 (GRCm39)	L206P	probably damaging	Het
Or8g27	T	C	9: 39,129,075 (GRCm39)	Y141H	probably benign	Het
Or8g33	C	A	9: 39,337,966 (GRCm39)	V134L	probably benign	Het
Pcnt	T	C	10: 76,256,360 (GRCm39)	K627E	probably damaging	Het
Plch1	T	A	3: 63,630,227 (GRCm39)	T514S	probably damaging	Het
Ppargc1b	G	A	18: 61,444,321 (GRCm39)	P297S	probably benign	Het
Ppig	A	G	2: 69,580,451 (GRCm39)	T662A	unknown	Het
Prdm2	A	C	4: 142,858,506 (GRCm39)	S1595A	probably benign	Het
Ptpn5	T	A	7: 46,732,890 (GRCm39)	T318S	probably benign	Het
Ralgps2	A	G	1: 156,660,278 (GRCm39)	Y265H	probably damaging	Het
Seh1l	T	C	18: 67,920,249 (GRCm39)	I182T	probably damaging	Het
Slc12a6	T	C	2: 112,186,830 (GRCm39)	I943T	probably damaging	Het
Slc5a5	A	T	8: 71,342,395 (GRCm39)		probably null	Het
Sparcl1	T	A	5: 104,236,289 (GRCm39)	Q488L	probably damaging	Het
Sphkap	T	G	1: 83,253,602 (GRCm39)	K1382N	probably benign	Het
Sybu	T	C	15: 44,536,731 (GRCm39)	S532G	probably benign	Het
Syde2	G	A	3: 145,704,241 (GRCm39)	G131S	possibly damaging	Het
Taok1	C	T	11: 77,462,472 (GRCm39)	V206I	probably benign	Het
Tas1r2	G	T	4: 139,382,666 (GRCm39)	M101I	probably benign	Het
Trpc6	C	T	9: 8,656,613 (GRCm39)	T680I	probably damaging	Het
Trub1	T	C	19: 57,473,646 (GRCm39)		probably null	Het
Tspan1	G	T	4: 116,020,885 (GRCm39)		probably null	Het
Ttc28	G	A	5: 111,424,139 (GRCm39)	E1438K	probably damaging	Het
Ubr3	A	G	2: 69,808,136 (GRCm39)	T1206A	possibly damaging	Het
Ulbp3	C	T	10: 3,076,459 (GRCm39)		noncoding transcript	Het
Usp40	A	G	1: 87,877,936 (GRCm39)	I1117T	probably benign	Het
Usp43	G	T	11: 67,812,536 (GRCm39)	N113K	probably damaging	Het
Vcan	T	A	13: 89,841,422 (GRCm39)	D414V	probably damaging	Het
Vmn1r202	T	A	13: 22,685,904 (GRCm39)	Y171F	possibly damaging	Het
Zfp142	A	G	1: 74,612,795 (GRCm39)	S451P	probably damaging	Het
Zfp516	A	G	18: 82,975,536 (GRCm39)	D578G	probably damaging	Het
Zfp90	G	A	8: 107,152,120 (GRCm39)	C611Y	probably damaging	Het
Zfp954	A	G	7: 7,118,609 (GRCm39)	C312R	probably damaging	Het
Zmym3	A	T	X: 100,450,993 (GRCm39)	V1208D	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
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
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'- TAGAACTCTGTTTCAGATCGTGAAC -3'
(R):5'- AAGGCCACTCTACCTTCAGC -3'

Sequencing Primer
(F):5'- CGTGAACTAAATCCTTTGCAGGG -3'
(R):5'- TCTAGGCAGTGGGTCCATC -3'

Posted On

2014-09-18