Mutagenetix > Incidental Mutation

Incidental Mutation 'R4254:Copa'

321726

Institutional Source

Beutler Lab

Gene Symbol

Copa

Ensembl Gene

ENSMUSG00000026553

Gene Name

coatomer protein complex subunit alpha

Synonyms

xenin

MMRRC Submission

041067-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.970) question?

Stock #

R4254 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

171910096-171949897 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 171929811 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 293 (R293C)

Ref Sequence

ENSEMBL: ENSMUSP00000118179 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000027833] [ENSMUST00000124289] [ENSMUST00000135192]

AlphaFold

Q8CIE6

Predicted Effect

probably damaging
Transcript: ENSMUST00000027833
AA Change: R293C

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

SMART Domains

Protein: ENSMUSP00000027833
Gene: ENSMUSG00000026553
AA Change: R293C

Domain	Start	End	E-Value	Type
WD40	2	37	2.86e0	SMART
WD40	40	79	1.11e-6	SMART
WD40	82	121	4.76e-6	SMART
WD40	124	163	2.24e-11	SMART
WD40	194	233	2.98e-7	SMART
WD40	238	277	8.42e-7	SMART
WD40	280	318	1.38e1	SMART
Pfam:Coatomer_WDAD	338	776	5.4e-144	PFAM
Pfam:COPI_C	824	1233	1.4e-190	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000124289

SMART Domains

Protein: ENSMUSP00000118899
Gene: ENSMUSG00000026553

Domain	Start	End	E-Value	Type
Blast:WD40	1	37	2e-19	BLAST
PDB:4J8G\|B	1	52	2e-23	PDB
SCOP:d1erja_	1	52	1e-6	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126634

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134468
AA Change: R654C

Predicted Effect

probably damaging
Transcript: ENSMUST00000135192
AA Change: R293C

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

SMART Domains

Protein: ENSMUSP00000118179
Gene: ENSMUSG00000026553
AA Change: R293C

Domain	Start	End	E-Value	Type
WD40	2	37	2.86e0	SMART
WD40	40	79	1.11e-6	SMART
WD40	82	121	4.76e-6	SMART
WD40	124	163	2.24e-11	SMART
WD40	194	233	2.98e-7	SMART
WD40	238	277	8.42e-7	SMART
WD40	280	318	1.38e1	SMART
Pfam:Coatomer_WDAD	338	767	1.1e-148	PFAM
Pfam:COPI_C	815	1224	3.6e-216	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150298

Predicted Effect

unknown
Transcript: ENSMUST00000152403
AA Change: R68C

SMART Domains

Protein: ENSMUSP00000123214
Gene: ENSMUSG00000026553
AA Change: R68C

Domain	Start	End	E-Value	Type
WD40	14	53	8.42e-7	SMART
WD40	56	94	1.38e1	SMART

Meta Mutation Damage Score

0.9279

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.4%

Validation Efficiency

98% (40/41)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] In eukaryotic cells, protein transport between the endoplasmic reticulum and Golgi compartments is mediated in part by non-clathrin-coated vesicular coat proteins (COPs). Seven coat proteins have been identified, and they represent subunits of a complex known as coatomer. The subunits are designated alpha-COP, beta-COP, beta-prime-COP, gamma-COP, delta-COP, epsilon-COP, and zeta-COP. The alpha-COP, encoded by COPA, shares high sequence similarity with RET1P, the alpha subunit of the coatomer complex in yeast. Also, the N-terminal 25 amino acids of alpha-COP encode the bioactive peptide, xenin, which stimulates exocrine pancreatic secretion and may act as a gastrointestinal hormone. Alternative splicing results in multiple splice forms encoding distinct isoforms. [provided by RefSeq, Jul 2008]

Allele List at MGI

All alleles(6) : Gene trapped(6)

Other mutations in this stock

Total: 34 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrg1	T	G	8: 95,732,530 (GRCm39)		probably null	Het
Adgrg2	T	G	X: 159,265,404 (GRCm39)	S551R	possibly damaging	Het
Anapc2	T	C	2: 25,163,357 (GRCm39)	V198A	probably benign	Het
Asxl3	T	C	18: 22,657,423 (GRCm39)	I1811T	possibly damaging	Het
Atp5mc3	A	C	2: 73,740,319 (GRCm39)		probably benign	Het
Ccdc27	A	C	4: 154,123,976 (GRCm39)	S186A	unknown	Het
Ccdc28a	A	G	10: 18,100,683 (GRCm39)	L48P	probably damaging	Het
Cdh19	C	T	1: 110,852,760 (GRCm39)	A392T	probably damaging	Het
Cfap65	T	C	1: 74,942,517 (GRCm39)	D1679G	probably benign	Het
Depdc1a	A	G	3: 159,204,124 (GRCm39)	R58G	probably damaging	Het
Dnah5	T	A	15: 28,438,248 (GRCm39)	S3960T	probably benign	Het
Dsg4	A	T	18: 20,604,595 (GRCm39)	T1021S	probably benign	Het
Hrh1	T	A	6: 114,456,962 (GRCm39)	M81K	probably damaging	Het
Ipo11	G	A	13: 107,029,017 (GRCm39)	T312I	probably benign	Het
Itgb2l	T	C	16: 96,231,777 (GRCm39)	N330D	probably benign	Het
Itsn1	G	A	16: 91,615,440 (GRCm39)		probably benign	Het
Kcnb1	A	G	2: 166,947,651 (GRCm39)	I399T	probably damaging	Het
Muc13	G	A	16: 33,636,221 (GRCm39)	M568I	probably benign	Het
Nlrp1a	A	C	11: 71,013,854 (GRCm39)	Y465*	probably null	Het
Nwd2	G	A	5: 63,963,889 (GRCm39)	V1158I	possibly damaging	Het
Or2h1b	A	G	17: 37,462,530 (GRCm39)	I111T	possibly damaging	Het
Or5d14	C	T	2: 87,880,123 (GRCm39)	V282I	possibly damaging	Het
Or8b101	T	A	9: 38,020,546 (GRCm39)	L183H	probably damaging	Het
Ptprr	T	A	10: 115,998,348 (GRCm39)		probably null	Het
Rasd2	G	A	8: 75,948,538 (GRCm39)	E155K	probably damaging	Het
Rufy4	T	C	1: 74,186,822 (GRCm39)	C537R	probably damaging	Het
Serinc3	T	A	2: 163,478,888 (GRCm39)	M80L	probably benign	Het
Sf1	T	C	19: 6,421,677 (GRCm39)	V140A	probably damaging	Het
Slc15a2	A	T	16: 36,574,852 (GRCm39)	V519E	probably benign	Het
Slc16a10	A	G	10: 39,952,997 (GRCm39)	Y166H	probably damaging	Het
Slc38a1	T	C	15: 96,483,431 (GRCm39)	D299G	probably benign	Het
Smim29	A	T	17: 27,784,696 (GRCm39)		probably null	Het
Tmbim1	C	A	1: 74,333,090 (GRCm39)	V92F	probably damaging	Het
Vsig4	C	A	X: 95,334,107 (GRCm39)	R134L	probably benign	Het

Other mutations in Copa

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00848:Copa	APN	1	171,938,255 (GRCm39)	missense	possibly damaging	0.87
IGL01360:Copa	APN	1	171,915,155 (GRCm39)	splice site	probably null
IGL01434:Copa	APN	1	171,947,128 (GRCm39)	missense	probably benign	0.00
IGL01744:Copa	APN	1	171,940,756 (GRCm39)	missense	probably benign	0.01
IGL01837:Copa	APN	1	171,946,419 (GRCm39)	missense	probably benign	0.01
IGL01988:Copa	APN	1	171,945,831 (GRCm39)	missense	probably benign	0.09
IGL02059:Copa	APN	1	171,927,320 (GRCm39)	missense	probably damaging	0.96
IGL02123:Copa	APN	1	171,939,695 (GRCm39)	missense	probably damaging	1.00
IGL02731:Copa	APN	1	171,929,785 (GRCm39)	missense	possibly damaging	0.77
IGL03114:Copa	APN	1	171,946,835 (GRCm39)	nonsense	probably null
P0027:Copa	UTSW	1	171,939,515 (GRCm39)	missense	possibly damaging	0.87
PIT4434001:Copa	UTSW	1	171,933,742 (GRCm39)	missense	probably benign	0.00
R0233:Copa	UTSW	1	171,915,234 (GRCm39)	critical splice donor site	probably null
R0465:Copa	UTSW	1	171,945,872 (GRCm39)	missense	probably damaging	1.00
R0547:Copa	UTSW	1	171,949,254 (GRCm39)	splice site	probably benign
R0568:Copa	UTSW	1	171,939,704 (GRCm39)	missense	possibly damaging	0.91
R0628:Copa	UTSW	1	171,918,592 (GRCm39)	splice site	probably benign
R1328:Copa	UTSW	1	171,949,258 (GRCm39)	splice site	probably benign
R1494:Copa	UTSW	1	171,931,694 (GRCm39)	missense	probably benign	0.27
R1728:Copa	UTSW	1	171,939,554 (GRCm39)	missense	probably benign
R1758:Copa	UTSW	1	171,931,711 (GRCm39)	missense	probably damaging	1.00
R1784:Copa	UTSW	1	171,939,554 (GRCm39)	missense	probably benign
R1942:Copa	UTSW	1	171,939,455 (GRCm39)	missense	probably damaging	1.00
R2054:Copa	UTSW	1	171,946,524 (GRCm39)	nonsense	probably null
R2299:Copa	UTSW	1	171,949,292 (GRCm39)	missense	probably benign	0.10
R2518:Copa	UTSW	1	171,947,468 (GRCm39)	missense	probably benign
R2680:Copa	UTSW	1	171,948,971 (GRCm39)	nonsense	probably null
R3080:Copa	UTSW	1	171,940,716 (GRCm39)	missense	probably damaging	1.00
R3160:Copa	UTSW	1	171,918,800 (GRCm39)	missense	probably damaging	1.00
R3161:Copa	UTSW	1	171,918,800 (GRCm39)	missense	probably damaging	1.00
R3162:Copa	UTSW	1	171,918,800 (GRCm39)	missense	probably damaging	1.00
R3162:Copa	UTSW	1	171,918,800 (GRCm39)	missense	probably damaging	1.00
R3973:Copa	UTSW	1	171,948,812 (GRCm39)	missense	probably benign	0.00
R3975:Copa	UTSW	1	171,948,812 (GRCm39)	missense	probably benign	0.00
R4031:Copa	UTSW	1	171,935,942 (GRCm39)	missense	probably damaging	1.00
R4155:Copa	UTSW	1	171,928,992 (GRCm39)	missense	probably damaging	1.00
R4227:Copa	UTSW	1	171,945,682 (GRCm39)	intron	probably benign
R4244:Copa	UTSW	1	171,938,285 (GRCm39)	missense	probably benign	0.00
R4291:Copa	UTSW	1	171,919,964 (GRCm39)	intron	probably benign
R4323:Copa	UTSW	1	171,946,831 (GRCm39)	missense	probably damaging	1.00
R4402:Copa	UTSW	1	171,929,791 (GRCm39)	missense	probably damaging	1.00
R4711:Copa	UTSW	1	171,947,555 (GRCm39)	missense	probably damaging	1.00
R4721:Copa	UTSW	1	171,931,841 (GRCm39)	splice site	probably benign
R4773:Copa	UTSW	1	171,932,787 (GRCm39)	missense	probably damaging	1.00
R4794:Copa	UTSW	1	171,946,888 (GRCm39)	missense	probably damaging	1.00
R4887:Copa	UTSW	1	171,919,843 (GRCm39)	missense	probably benign	0.39
R4953:Copa	UTSW	1	171,910,453 (GRCm39)	unclassified	probably benign
R5139:Copa	UTSW	1	171,948,896 (GRCm39)	missense	probably damaging	0.99
R5152:Copa	UTSW	1	171,945,628 (GRCm39)	missense	probably benign	0.34
R5297:Copa	UTSW	1	171,940,675 (GRCm39)	missense	probably damaging	1.00
R5586:Copa	UTSW	1	171,932,789 (GRCm39)	missense	probably damaging	1.00
R5698:Copa	UTSW	1	171,946,511 (GRCm39)	nonsense	probably null
R6283:Copa	UTSW	1	171,946,415 (GRCm39)	missense	possibly damaging	0.79
R6921:Copa	UTSW	1	171,939,491 (GRCm39)	missense	possibly damaging	0.63
R6934:Copa	UTSW	1	171,938,253 (GRCm39)	missense	possibly damaging	0.64
R7009:Copa	UTSW	1	171,918,567 (GRCm39)	missense	probably damaging	0.96
R7194:Copa	UTSW	1	171,947,511 (GRCm39)	missense	probably damaging	0.99
R7348:Copa	UTSW	1	171,929,790 (GRCm39)	missense	possibly damaging	0.96
R7710:Copa	UTSW	1	171,937,411 (GRCm39)	missense	possibly damaging	0.50
R7745:Copa	UTSW	1	171,939,509 (GRCm39)	missense	probably damaging	1.00
R7893:Copa	UTSW	1	171,947,132 (GRCm39)	nonsense	probably null
R8168:Copa	UTSW	1	171,927,239 (GRCm39)	missense	probably damaging	1.00
R8273:Copa	UTSW	1	171,946,546 (GRCm39)	critical splice donor site	probably null
R8704:Copa	UTSW	1	171,931,693 (GRCm39)	missense	probably benign	0.01
R8754:Copa	UTSW	1	171,935,926 (GRCm39)	missense	probably damaging	1.00
R8757:Copa	UTSW	1	171,947,081 (GRCm39)	missense	probably benign	0.04
R8759:Copa	UTSW	1	171,947,081 (GRCm39)	missense	probably benign	0.04
R8885:Copa	UTSW	1	171,925,312 (GRCm39)	missense	probably damaging	1.00
R8891:Copa	UTSW	1	171,946,818 (GRCm39)	missense	probably damaging	1.00
R8927:Copa	UTSW	1	171,931,737 (GRCm39)	missense	probably null	0.03
R8928:Copa	UTSW	1	171,931,737 (GRCm39)	missense	probably null	0.03
R8956:Copa	UTSW	1	171,937,480 (GRCm39)	missense	possibly damaging	0.65
R9063:Copa	UTSW	1	171,944,529 (GRCm39)	missense	probably benign	0.00
R9295:Copa	UTSW	1	171,939,823 (GRCm39)	missense	probably damaging	0.99
R9364:Copa	UTSW	1	171,944,831 (GRCm39)	missense	probably benign	0.00
R9437:Copa	UTSW	1	171,931,712 (GRCm39)	missense	possibly damaging	0.93
R9673:Copa	UTSW	1	171,945,648 (GRCm39)	missense	probably benign	0.11
T0722:Copa	UTSW	1	171,939,515 (GRCm39)	missense	possibly damaging	0.87
Z1177:Copa	UTSW	1	171,933,690 (GRCm39)	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- TAGTGTGAAGCCTTCCCTCC -3'
(R):5'- GGTGGCTCTGAAAACTCTGC -3'

Sequencing Primer
(F):5'- GGTCCTGATCCTTAGCTGAGTGC -3'
(R):5'- GTGGCTCTGAAAACTCTGCTTCTC -3'

Posted On

2015-06-20