Mutagenetix > Incidental Mutation

Incidental Mutation 'R6526:Cog4'

521876

Institutional Source

Beutler Lab

Gene Symbol

Cog4

Ensembl Gene

ENSMUSG00000031753

Gene Name

component of oligomeric golgi complex 4

Synonyms

D8Ertd515e

MMRRC Submission

044652-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.955) question?

Stock #

R6526 (G1)

Quality Score

195.009

Status

Validated

Chromosome

Chromosomal Location

111573232-111608859 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 111608418 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 738 (L738P)

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: L760P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000034203
Gene: ENSMUSG00000031753
AA Change: L760P

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: L687P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000128518
Gene: ENSMUSG00000031753
AA Change: L687P

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

probably damaging
Transcript: ENSMUST00000174398
AA Change: L738P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000133297
Gene: ENSMUSG00000031753
AA Change: L738P

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

0.5664

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.4%
20x: 91.5%

Validation Efficiency

100% (72/72)

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aamp	A	G	1: 74,323,331 (GRCm39)		probably null	Het
Abcc3	C	T	11: 94,250,198 (GRCm39)	G975D	probably benign	Het
Abhd13	G	A	8: 10,037,777 (GRCm39)	G125S	probably damaging	Het
Ache	T	A	5: 137,288,906 (GRCm39)	L204Q	probably damaging	Het
Acnat2	A	G	4: 49,383,497 (GRCm39)	S19P	probably benign	Het
Adprh	A	G	16: 38,267,638 (GRCm39)	Y216H	probably benign	Het
Anapc1	T	A	2: 128,514,055 (GRCm39)	K429*	probably null	Het
Anxa13	T	C	15: 58,208,353 (GRCm39)		noncoding transcript	Het
Aprt	A	C	8: 123,303,555 (GRCm39)	L6W	probably damaging	Het
Arhgef15	T	C	11: 68,840,820 (GRCm39)	T569A	probably damaging	Het
Atp11a	T	C	8: 12,914,999 (GRCm39)	L1139P	probably benign	Het
Atp2b4	A	G	1: 133,639,467 (GRCm39)	S1136P	probably damaging	Het
B9d1	T	A	11: 61,399,923 (GRCm39)	Y90*	probably null	Het
Btla	G	A	16: 45,059,457 (GRCm39)	A54T	probably damaging	Het
Cd63	T	C	10: 128,747,358 (GRCm39)	V35A	probably benign	Het
Chek2	T	C	5: 110,996,556 (GRCm39)	F173L	probably damaging	Het
Cntnap3	T	A	13: 64,929,702 (GRCm39)	N499I	possibly damaging	Het
Cops6	T	C	5: 138,162,162 (GRCm39)		probably null	Het
Cpeb1	T	A	7: 81,011,417 (GRCm39)	I175F	probably benign	Het
Cyp3a16	C	T	5: 145,392,705 (GRCm39)	D174N	probably benign	Het
Dnah6	T	G	6: 73,051,687 (GRCm39)	I2984L	probably benign	Het
Dock10	A	T	1: 80,564,068 (GRCm39)	I540N	probably damaging	Het
Elf5	A	G	2: 103,269,578 (GRCm39)	Y53C	probably damaging	Het
Elmod2	T	C	8: 84,046,086 (GRCm39)	T164A	probably damaging	Het
Elp1	T	C	4: 56,798,812 (GRCm39)		probably null	Het
Epn3	A	G	11: 94,385,758 (GRCm39)		probably null	Het
Fam151a	A	T	4: 106,591,201 (GRCm39)	I15F	possibly damaging	Het
Gm11115	T	A	5: 88,301,909 (GRCm39)		probably null	Het
Golga3	T	A	5: 110,352,761 (GRCm39)	I884N	probably damaging	Het
Gria2	A	T	3: 80,599,776 (GRCm39)	F703I	probably damaging	Het
Gtf2h3	C	T	5: 124,722,360 (GRCm39)	T121I	probably benign	Het
Gtpbp2	A	T	17: 46,475,037 (GRCm39)		probably null	Het
Herc2	T	C	7: 55,807,078 (GRCm39)	S2419P	probably damaging	Het
Inpp5d	T	C	1: 87,603,972 (GRCm39)		probably benign	Het
Kdm2b	C	A	5: 123,099,532 (GRCm39)	V136F	probably damaging	Het
Klra2	T	A	6: 131,198,839 (GRCm39)	D234V	probably benign	Het
Lct	A	T	1: 128,228,215 (GRCm39)	S1093T	probably benign	Het
Marchf9	A	G	10: 126,892,558 (GRCm39)	L310P	probably benign	Het
Morc1	G	T	16: 48,407,487 (GRCm39)	E668*	probably null	Het
Nbas	A	T	12: 13,455,426 (GRCm39)	L1213F	probably damaging	Het
Neto1	A	G	18: 86,516,873 (GRCm39)	T397A	possibly damaging	Het
Oit3	A	G	10: 59,265,462 (GRCm39)	C268R	probably damaging	Het
Or5p55	A	G	7: 107,566,669 (GRCm39)	T22A	probably benign	Het
Pcx	T	C	19: 4,654,523 (GRCm39)	F312L	probably benign	Het
Pitx2	T	C	3: 129,008,432 (GRCm39)		probably null	Het
Pkhd1l1	G	A	15: 44,361,485 (GRCm39)		probably null	Het
Polr1a	C	A	6: 71,906,427 (GRCm39)	D414E	possibly damaging	Het
Pramel27	A	G	4: 143,579,384 (GRCm39)	D323G	probably damaging	Het
Prkch	T	C	12: 73,749,549 (GRCm39)	Y381H	probably damaging	Het
Ptger3	T	A	3: 157,273,139 (GRCm39)	V162E	probably damaging	Het
Ptgr2	T	G	12: 84,360,726 (GRCm39)	M332R	probably damaging	Het
Ptprq	G	T	10: 107,378,514 (GRCm39)	S2009*	probably null	Het
Pwwp3a	A	G	10: 80,068,113 (GRCm39)	T86A	probably benign	Het
Rangrf	C	T	11: 68,864,514 (GRCm39)	G11R	probably damaging	Het
Rbl2	A	T	8: 91,823,467 (GRCm39)	Q465L	probably benign	Het
Rhbdd1	A	T	1: 82,318,380 (GRCm39)	M88L	probably benign	Het
Setd2	G	A	9: 110,361,785 (GRCm39)	M13I	probably benign	Het
Sirpb1a	T	C	3: 15,444,080 (GRCm39)	Y384C	probably damaging	Het
Slc13a1	C	T	6: 24,097,611 (GRCm39)	G439S	probably damaging	Het
Slc41a1	T	A	1: 131,768,887 (GRCm39)	I239N	probably damaging	Het
Slit2	T	A	5: 48,461,509 (GRCm39)	C1502S	probably damaging	Het
Slit3	G	A	11: 35,552,119 (GRCm39)	E888K	probably benign	Het
Srrm3	G	T	5: 135,864,088 (GRCm39)	R62L	probably damaging	Het
Synm	A	G	7: 67,385,331 (GRCm39)	V777A	possibly damaging	Het
Trmt13	T	A	3: 116,385,864 (GRCm39)	N31I	probably damaging	Het
Trpm8	G	A	1: 88,289,720 (GRCm39)	E893K	probably damaging	Het
Uqcc1	A	G	2: 155,693,343 (GRCm39)	F197S	probably damaging	Het
Vmn1r67	T	A	7: 10,181,598 (GRCm39)	N287K	probably benign	Het
Vmn2r44	A	T	7: 8,381,098 (GRCm39)	M265K	probably benign	Het
Wwc1	C	T	11: 35,744,264 (GRCm39)	E853K	probably benign	Het
Xdh	C	A	17: 74,207,546 (GRCm39)	C937F	probably damaging	Het
Zfp846	T	A	9: 20,505,167 (GRCm39)	N342K	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
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
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'- GCACAGTTCTACAAGGCACC -3'
(R):5'- TTCCTGGTTTCCATGCAGTG -3'

Sequencing Primer
(F):5'- AGGCACCCCCTTCCTATATG -3'
(R):5'- TAGCCTGGACCTTTGGCTGAC -3'

Posted On

2018-06-06