Mutagenetix > Incidental Mutation

Incidental Mutation 'R9155:Cog4'

695309

Institutional Source

Beutler Lab

Gene Symbol

Cog4

Ensembl Gene

ENSMUSG00000031753

Gene Name

component of oligomeric golgi complex 4

Synonyms

D8Ertd515e

MMRRC Submission

068941-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.953) question?

Stock #

R9155 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

111573232-111608859 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 111608384 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tryptophan to Arginine at position 749 (W749R)

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: W749R

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

SMART Domains

Protein: ENSMUSP00000034203
Gene: ENSMUSG00000031753
AA Change: W749R

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: W676R

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

SMART Domains

Protein: ENSMUSP00000128518
Gene: ENSMUSG00000031753
AA Change: W676R

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: W727R

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

SMART Domains

Protein: ENSMUSP00000133297
Gene: ENSMUSG00000031753
AA Change: W727R

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

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700028K03Rik	A	G	5: 107,691,811 (GRCm39)	E34G	probably damaging	Het
Aldh1a3	A	T	7: 66,058,867 (GRCm39)	L157*	probably null	Het
Asic2	T	A	11: 80,784,872 (GRCm39)	T356S	probably benign	Het
Ate1	T	C	7: 129,996,463 (GRCm39)	D459G	probably damaging	Het
Cacna1g	T	A	11: 94,350,423 (GRCm39)	Q474L		Het
Calhm6	T	C	10: 34,002,363 (GRCm39)	E240G	probably damaging	Het
Carf	C	A	1: 60,189,842 (GRCm39)	T689K	possibly damaging	Het
Carmil2	A	G	8: 106,412,922 (GRCm39)	D6G	probably benign	Het
Ccnd2	A	C	6: 127,127,663 (GRCm39)	V25G	probably damaging	Het
Ccnk	T	A	12: 108,159,978 (GRCm39)	F153L	probably damaging	Het
Cdh23	C	T	10: 60,249,485 (GRCm39)	G808E	probably damaging	Het
Clec11a	C	T	7: 43,954,317 (GRCm39)	R212Q	probably damaging	Het
Col6a3	T	A	1: 90,738,301 (GRCm39)	T1073S	probably benign	Het
Col6a4	T	A	9: 105,952,209 (GRCm39)	D563V	probably benign	Het
Coq5	A	G	5: 115,433,839 (GRCm39)		probably null	Het
Crebbp	A	C	16: 3,914,346 (GRCm39)	H1292Q	probably damaging	Het
Csmd3	C	A	15: 47,449,051 (GRCm39)	G2737W		Het
Ddrgk1	T	C	2: 130,500,227 (GRCm39)	Y223C	probably damaging	Het
Dennd1c	T	C	17: 57,373,796 (GRCm39)	Q589R	probably benign	Het
Dnah10	A	G	5: 124,907,475 (GRCm39)	D4336G	probably damaging	Het
Dnah11	C	T	12: 117,991,251 (GRCm39)	E2372K	probably damaging	Het
E330034G19Rik	A	T	14: 24,346,938 (GRCm39)	Q140L	possibly damaging	Het
Ergic3	A	G	2: 155,850,780 (GRCm39)	Y83C	probably damaging	Het
Fam171a2	A	T	11: 102,329,497 (GRCm39)	S421T	probably benign	Het
Fndc3a	T	A	14: 72,921,162 (GRCm39)	H4L	possibly damaging	Het
Gid8	T	A	2: 180,359,756 (GRCm39)	Y213*	probably null	Het
Hephl1	G	T	9: 15,000,375 (GRCm39)	H292Q	probably damaging	Het
Hexb	T	C	13: 97,314,414 (GRCm39)	Y443C	probably damaging	Het
Htr1f	C	T	16: 64,746,788 (GRCm39)	R168H	probably benign	Het
Hus1	A	G	11: 8,956,056 (GRCm39)	I159T	probably damaging	Het
Inha	A	G	1: 75,486,133 (GRCm39)	T143A	probably benign	Het
Itga8	A	G	2: 12,194,330 (GRCm39)	I690T	probably benign	Het
Itgae	G	T	11: 73,016,089 (GRCm39)	C766F	possibly damaging	Het
Kank4	T	C	4: 98,666,563 (GRCm39)	E628G	probably benign	Het
Kctd19	T	C	8: 106,120,571 (GRCm39)	H221R	probably benign	Het
Llgl1	A	G	11: 60,597,934 (GRCm39)	E351G	probably benign	Het
Lrba	A	G	3: 86,202,508 (GRCm39)	Y253C	probably damaging	Het
Lrp2	T	A	2: 69,291,713 (GRCm39)	R3489*	probably null	Het
Lrriq1	T	C	10: 103,050,640 (GRCm39)	N704S	probably benign	Het
Mbtps1	T	C	8: 120,235,693 (GRCm39)	N995S	probably benign	Het
Mga	T	C	2: 119,757,013 (GRCm39)	C1077R	probably damaging	Het
Muc21	G	A	17: 35,932,131 (GRCm39)	P685L	unknown	Het
Ndufv1	A	T	19: 4,059,912 (GRCm39)	C142S	probably damaging	Het
Nkx3-1	T	C	14: 69,429,660 (GRCm39)	L226P	probably damaging	Het
Nsd1	C	T	13: 55,361,253 (GRCm39)	R74W	probably damaging	Het
Or12k8	A	C	2: 36,975,016 (GRCm39)	M248R	probably benign	Het
Or1d2	A	G	11: 74,255,791 (GRCm39)	T99A	probably benign	Het
Or2n1d	A	T	17: 38,646,224 (GRCm39)	M59L	probably damaging	Het
Or5b99	G	A	19: 12,976,428 (GRCm39)	C26Y	probably benign	Het
Or7g35	A	T	9: 19,496,379 (GRCm39)	D182V	probably benign	Het
Phc3	A	G	3: 30,968,691 (GRCm39)	V812A	probably benign	Het
Pigt	CCAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGATCTGTAACCACAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGATCTGTAACCACAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGAT	CCAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGATCTGTAACCACAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGAT	2: 164,341,589 (GRCm39)		probably null	Het
Ppp4c	A	T	7: 126,386,419 (GRCm39)	C193S	possibly damaging	Het
Rbbp5	C	A	1: 132,422,023 (GRCm39)	P308T	probably damaging	Het
Rhot1	A	G	11: 80,148,380 (GRCm39)	T607A	probably null	Het
Secisbp2l	G	A	2: 125,617,623 (GRCm39)	P18L	probably damaging	Het
Slc27a4	G	A	2: 29,701,294 (GRCm39)	G362S	probably damaging	Het
Slc4a8	T	C	15: 100,672,571 (GRCm39)	Y36H	probably damaging	Het
Sox17	T	C	1: 4,562,447 (GRCm39)	Y251C	probably damaging	Het
Spata31h1	A	T	10: 82,120,203 (GRCm39)	I4269N	probably damaging	Het
Taf4b	T	C	18: 14,946,296 (GRCm39)	V373A	probably benign	Het
Tecpr2	T	A	12: 110,881,184 (GRCm39)	V107E	probably damaging	Het
Them7	A	G	2: 105,209,124 (GRCm39)	Y148C	probably damaging	Het
Tktl2	T	A	8: 66,965,858 (GRCm39)	M472K	possibly damaging	Het
Ttn	C	T	2: 76,625,937 (GRCm39)	V15041I	probably damaging	Het
Ubr1	A	G	2: 120,754,615 (GRCm39)	V751A	possibly damaging	Het
Vmn1r213	A	T	13: 23,196,343 (GRCm39)	R309*	probably null	Het
Vmn2r10	A	T	5: 109,144,212 (GRCm39)	D579E	probably benign	Het
Vmn2r118	T	C	17: 55,917,207 (GRCm39)	Q435R	probably null	Het
Vmn2r50	A	T	7: 9,781,571 (GRCm39)	H391Q	probably damaging	Het
Zbtb44	A	T	9: 30,965,309 (GRCm39)	I240F	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
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
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'- GTCCATCACCAAGTTTCGAGC -3'
(R):5'- AGCCAGACAGTTTTGCATAGC -3'

Sequencing Primer
(F):5'- GCGCCCTTACTTGCTAGCAG -3'
(R):5'- GCATAGCTCTTTGGCTGTAAC -3'

Posted On

2022-01-20