Mutagenetix > Incidental Mutation

Incidental Mutation 'R7292:Cog4'

566494

Institutional Source

Beutler Lab

Gene Symbol

Cog4

Ensembl Gene

ENSMUSG00000031753

Gene Name

component of oligomeric golgi complex 4

Synonyms

D8Ertd515e

MMRRC Submission

045397-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.955) question?

Stock #

R7292 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

111573232-111608859 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 111608460 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 774 (D774G)

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: D774G

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

SMART Domains

Protein: ENSMUSP00000034203
Gene: ENSMUSG00000031753
AA Change: D774G

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: D701G

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

SMART Domains

Protein: ENSMUSP00000128518
Gene: ENSMUSG00000031753
AA Change: D701G

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: D752G

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

SMART Domains

Protein: ENSMUSP00000133297
Gene: ENSMUSG00000031753
AA Change: D752G

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

Meta Mutation Damage Score

0.4937

Coding Region Coverage

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

Validation Efficiency

100% (66/66)

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700010I14Rik	T	A	17: 9,215,861 (GRCm39)	C322*	probably null	Het
4930553M12Rik	G	A	4: 88,786,568 (GRCm39)	R17C	unknown	Het
Abcc8	G	A	7: 45,784,950 (GRCm39)	T726I	probably benign	Het
Adamts18	T	C	8: 114,436,277 (GRCm39)	T981A	probably benign	Het
Adgrb3	A	G	1: 25,570,957 (GRCm39)	C507R	probably damaging	Het
Bloc1s6	T	A	2: 122,584,615 (GRCm39)	D63E	probably damaging	Het
Cdc25b	C	T	2: 131,033,093 (GRCm39)	R135W	probably damaging	Het
Cdca2	G	T	14: 67,915,326 (GRCm39)	Y644*	probably null	Het
Ceacam10	G	T	7: 24,477,775 (GRCm39)	G97C	probably damaging	Het
Cenpf	G	A	1: 189,382,891 (GRCm39)	L2668F	probably damaging	Het
Col11a2	G	A	17: 34,270,482 (GRCm39)	G511E	unknown	Het
Col19a1	T	A	1: 24,569,089 (GRCm39)	I220F	unknown	Het
Cubn	G	T	2: 13,429,550 (GRCm39)	T1317K	probably damaging	Het
Dnaaf5	T	C	5: 139,136,072 (GRCm39)	L24P	unknown	Het
Eif4a3l2	G	A	6: 116,528,438 (GRCm39)	R105Q	probably damaging	Het
Fan1	T	A	7: 64,022,234 (GRCm39)	N340Y	probably damaging	Het
Foxn4	C	A	5: 114,396,716 (GRCm39)	E256*	probably null	Het
Gm5930	A	G	14: 44,574,014 (GRCm39)	S108P	probably damaging	Het
Gnl3	A	G	14: 30,735,189 (GRCm39)	S468P	probably benign	Het
Gzmb	A	T	14: 56,499,576 (GRCm39)	S11T	probably benign	Het
Hmcn1	T	C	1: 150,608,880 (GRCm39)		probably null	Het
Ifi206	A	G	1: 173,301,428 (GRCm39)	L750P	unknown	Het
Ifi213	T	A	1: 173,422,691 (GRCm39)	E58V	probably damaging	Het
Igkv4-78	A	T	6: 69,036,752 (GRCm39)	Y94N	probably damaging	Het
Igsf9	G	T	1: 172,319,324 (GRCm39)		probably null	Het
Itpr2	G	T	6: 146,060,447 (GRCm39)	L2490M	possibly damaging	Het
Kdm2b	A	G	5: 123,018,854 (GRCm39)	F862S	probably damaging	Het
Kif19b	A	G	5: 140,457,425 (GRCm39)	D398G	probably benign	Het
Meis1	A	G	11: 18,961,351 (GRCm39)	I174T	probably damaging	Het
Micu3	A	G	8: 40,835,166 (GRCm39)	Q507R	probably benign	Het
Mpp4	C	T	1: 59,182,969 (GRCm39)	E313K	possibly damaging	Het
Nfatc4	G	A	14: 56,062,512 (GRCm39)	E7K	probably damaging	Het
Or7g16	A	T	9: 18,727,486 (GRCm39)	Y35N	probably damaging	Het
Or9s18	T	A	13: 65,300,656 (GRCm39)	V206D	possibly damaging	Het
Osbpl5	G	A	7: 143,255,015 (GRCm39)	P470S	probably damaging	Het
Pak6	A	G	2: 118,524,072 (GRCm39)	D409G	possibly damaging	Het
Pierce1	TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC	TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC	2: 28,356,122 (GRCm39)		probably benign	Het
Pkhd1l1	T	A	15: 44,361,986 (GRCm39)	M553K	probably benign	Het
Ppp2r3d	T	C	9: 101,089,871 (GRCm39)	N151D	probably damaging	Het
Prdm12	T	C	2: 31,533,862 (GRCm39)	W160R	probably damaging	Het
Prdm2	G	A	4: 142,859,471 (GRCm39)	T1273M	possibly damaging	Het
Prl2a1	A	G	13: 27,991,353 (GRCm39)		probably null	Het
Prob1	G	A	18: 35,787,603 (GRCm39)	P217L	possibly damaging	Het
Ramp1	A	C	1: 91,124,499 (GRCm39)	H20P	probably benign	Het
Rbm47	T	A	5: 66,184,093 (GRCm39)	E170V	possibly damaging	Het
Relch	G	T	1: 105,649,141 (GRCm39)		probably null	Het
Rpn1	C	T	6: 88,067,066 (GRCm39)	P142L	probably damaging	Het
Rsu1	C	T	2: 13,174,827 (GRCm39)	R238H	probably damaging	Het
Sh3rf3	C	T	10: 58,907,795 (GRCm39)	P441L	probably damaging	Het
Slc1a6	A	G	10: 78,650,438 (GRCm39)	S559G	possibly damaging	Het
Slc35f5	C	A	1: 125,500,222 (GRCm39)	S245R	probably damaging	Het
Spcs3	T	C	8: 54,979,554 (GRCm39)	N76D	probably benign	Het
Spmip5	A	T	19: 58,777,539 (GRCm39)	Y90*	probably null	Het
Svep1	T	C	4: 58,111,395 (GRCm39)	T1075A	possibly damaging	Het
Sympk	A	T	7: 18,769,955 (GRCm39)	I211F	probably benign	Het
Tk1	C	T	11: 117,716,603 (GRCm39)	M1I	probably null	Het
Tln2	A	G	9: 67,253,743 (GRCm39)	V776A	probably benign	Het
Tmem94	G	T	11: 115,677,082 (GRCm39)	R118L	possibly damaging	Het
Tnk2	T	C	16: 32,499,618 (GRCm39)	V977A	probably benign	Het
Toporsl	A	T	4: 52,611,630 (GRCm39)	S508C	probably benign	Het
Trank1	A	C	9: 111,206,938 (GRCm39)	R1690S	probably benign	Het
Trio	T	A	15: 27,828,437 (GRCm39)	Q1409L	possibly damaging	Het
Vit	T	C	17: 78,912,927 (GRCm39)	F287L	probably benign	Het
Vmn2r109	G	C	17: 20,761,700 (GRCm39)	D552E	probably benign	Het
Zw10	T	C	9: 48,972,491 (GRCm39)	V186A	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
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
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'- TCTCAGTAAAGCCCAGGAGC -3'
(R):5'- GGAAAAGCTCTCCCTTTTAGCC -3'

Sequencing Primer
(F):5'- AGGAGCTTCCCTCAGAATGGAC -3'
(R):5'- AACTGCTCCTGGGAAGAACTTTG -3'

Posted On

2019-06-26