Mutagenetix > Incidental Mutation

Incidental Mutation 'R3162:Copa'

271661

Institutional Source

Beutler Lab

Gene Symbol

Copa

Ensembl Gene

ENSMUSG00000026553

Gene Name

coatomer protein complex subunit alpha

Synonyms

xenin

MMRRC Submission

040613-MU

Accession Numbers

Genbank: NM_009938; MGI: 1334462

Is this an essential gene?

Probably essential (E-score: 0.971) question?

Stock #

R3162 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

172082529-172122330 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 172091233 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 127 (C127S)

Ref Sequence

ENSEMBL: ENSMUSP00000027833 (fasta)

Gene Model

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

AlphaFold

Q8CIE6

Predicted Effect

probably damaging
Transcript: ENSMUST00000027833
AA Change: C127S

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

SMART Domains

Protein: ENSMUSP00000027833
Gene: ENSMUSG00000026553
AA Change: C127S

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

probably damaging
Transcript: ENSMUST00000135192
AA Change: C127S

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000118179
Gene: ENSMUSG00000026553
AA Change: C127S

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: ENSMUST00000138407

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150298

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000191834

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000192810

Meta Mutation Damage Score

0.1894

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.0%

Validation Efficiency

98% (49/50)

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: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610040J01Rik	T	C	5: 63,896,490		probably benign	Het
1700074P13Rik	A	G	6: 40,926,069	M123T	probably benign	Het
4933412E24Rik	T	A	15: 60,016,285	E102V	probably damaging	Het
Adcy9	A	G	16: 4,311,588	L715P	probably damaging	Het
Adgre4	T	C	17: 55,802,218		probably benign	Het
Amer2	A	G	14: 60,378,551	D65G	probably damaging	Het
Atad2b	C	A	12: 4,939,689	N133K	possibly damaging	Het
AW551984	C	A	9: 39,593,029	R547L	probably damaging	Het
B3galt6	A	G	4: 155,992,007	Y204H	probably benign	Het
Btnl2	T	C	17: 34,358,065	W65R	probably damaging	Het
Camk1g	T	C	1: 193,359,807	T45A	possibly damaging	Het
Caps2	C	A	10: 112,182,486	Y180*	probably null	Het
Ccdc181	T	A	1: 164,280,296	S183T	probably damaging	Het
Cdc14b	A	G	13: 64,246,608		probably benign	Het
Cep350	T	C	1: 155,863,164	H2311R	probably benign	Het
Cfap54	T	A	10: 93,045,278	K349N	probably damaging	Het
Crbn	T	C	6: 106,790,866	Q221R	probably benign	Het
Dapk2	T	G	9: 66,254,611	V267G	probably damaging	Het
Ddb1	T	C	19: 10,625,971	L881P	probably damaging	Het
Decr1	T	A	4: 15,930,972	D120V	probably damaging	Het
Dennd1c	C	T	17: 57,066,562	G637D	possibly damaging	Het
Dhrs3	A	G	4: 144,919,446	D108G	possibly damaging	Het
Disp1	T	C	1: 183,087,242	K1205E	probably benign	Het
Dnajc13	G	T	9: 104,219,898	N510K	possibly damaging	Het
Dusp6	T	C	10: 99,264,082	Y131H	probably damaging	Het
Eif2b2	A	T	12: 85,219,661	M34L	probably benign	Het
Epsti1	A	T	14: 77,974,513		probably benign	Het
Errfi1	G	A	4: 150,867,359	E415K	probably damaging	Het
Ext1	T	C	15: 53,344,604	N254D	possibly damaging	Het
Fam84b	A	T	15: 60,823,447	V150E	probably damaging	Het
Gm7337	A	C	5: 87,851,557		noncoding transcript	Het
Hnrnpu	T	C	1: 178,331,125		probably benign	Het
Hyal3	T	A	9: 107,586,806	C407S	probably damaging	Het
Insr	T	G	8: 3,161,416	N1141T	possibly damaging	Het
Ipo9	T	C	1: 135,409,476	T174A	probably benign	Het
Iqgap1	G	A	7: 80,752,338	A393V	probably benign	Het
Irak2	G	T	6: 113,672,760	A119S	probably benign	Het
Itgb2l	A	G	16: 96,437,389	L70P	probably damaging	Het
Itsn1	C	A	16: 91,853,044	S202*	probably null	Het
Ivd	T	C	2: 118,862,169		probably null	Het
Leprot	C	T	4: 101,657,893	T89I	probably damaging	Het
Mill2	A	C	7: 18,856,174	E127A	probably benign	Het
Msh6	T	C	17: 87,985,481	Y555H	probably damaging	Het
Myo18b	A	C	5: 112,692,728	S2400A	probably damaging	Het
Naa25	A	G	5: 121,435,072		probably null	Het
Nop2	A	G	6: 125,134,592	N96S	probably benign	Het
Nup155	G	T	15: 8,148,383	R1083S	possibly damaging	Het
Nusap1	A	T	2: 119,630,404	Q126L	possibly damaging	Het
Olfr1042	T	C	2: 86,160,095	I92V	probably benign	Het
Olfr1263	T	G	2: 90,015,021	Y30*	probably null	Het
Olfr1351	C	A	10: 79,017,604	T94N	probably benign	Het
Olfr156	T	A	4: 43,820,544	K272N	probably benign	Het
Olfr30	T	C	11: 58,455,227	T241A	probably damaging	Het
Olfr739	T	A	14: 50,425,031	C171S	probably damaging	Het
Olfr986	G	T	9: 40,187,605	Q163H	probably benign	Het
Pde5a	T	A	3: 122,781,628	L356*	probably null	Het
Pdik1l	A	G	4: 134,284,250	L94S	probably damaging	Het
Pkdrej	T	A	15: 85,816,617	D1706V	probably damaging	Het
Pkhd1l1	A	G	15: 44,505,528	I856M	probably damaging	Het
Prkcz	A	T	4: 155,290,524	D114E	probably benign	Het
Psap	T	C	10: 60,277,753	L4P	possibly damaging	Het
Ptprk	T	C	10: 28,592,826	V1402A	probably benign	Het
Rai14	T	C	15: 10,633,164	T47A	possibly damaging	Het
Ralgapa1	A	T	12: 55,709,586	N1075K	probably damaging	Het
Rlf	A	G	4: 121,148,847	S979P	probably damaging	Het
Rps2	G	T	17: 24,720,978	A129S	probably benign	Het
Serinc2	A	G	4: 130,260,735	S175P	probably benign	Het
Skiv2l	C	T	17: 34,847,813	W88*	probably null	Het
Socs5	A	T	17: 87,134,718	Q362L	probably damaging	Het
Srbd1	A	T	17: 86,130,215	D233E	probably benign	Het
Srgap3	A	G	6: 112,729,658	V826A	probably benign	Het
Tacr2	A	G	10: 62,265,245	D378G	probably benign	Het
Taok2	A	G	7: 126,875,175	I294T	possibly damaging	Het
Tert	A	G	13: 73,627,409	E93G	possibly damaging	Het
Tns2	A	G	15: 102,113,336	E1118G	possibly damaging	Het
Topaz1	T	C	9: 122,749,381	I452T	probably benign	Het
Trak1	C	T	9: 121,451,734		probably benign	Het
Ttc22	A	T	4: 106,623,079	I177F	probably damaging	Het
Tuba8	A	G	6: 121,222,738	D127G	possibly damaging	Het
Tulp4	A	G	17: 6,198,708	M1V	probably null	Het
Urb1	A	G	16: 90,797,903	L247P	probably damaging	Het
Usp32	A	G	11: 85,025,536	W861R	probably damaging	Het
Vmn1r48	G	A	6: 90,036,378	T155I	probably benign	Het
Vmn2r117	A	G	17: 23,460,378	L624P	probably damaging	Het
Vmn2r86	T	C	10: 130,455,804	R31G	probably damaging	Het
Vstm5	T	G	9: 15,257,298	S53A	probably benign	Het
Wnt5a	T	C	14: 28,522,488	Y231H	probably benign	Het
Yeats2	T	C	16: 20,193,645	V531A	probably damaging	Het
Zw10	T	C	9: 49,077,560	Y709H	probably damaging	Het

Other mutations in Copa

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00848:Copa	APN	1	172110688	missense	possibly damaging	0.87
IGL01360:Copa	APN	1	172087588	splice site	probably null
IGL01434:Copa	APN	1	172119561	missense	probably benign	0.00
IGL01744:Copa	APN	1	172113189	missense	probably benign	0.01
IGL01837:Copa	APN	1	172118852	missense	probably benign	0.01
IGL01988:Copa	APN	1	172118264	missense	probably benign	0.09
IGL02059:Copa	APN	1	172099753	missense	probably damaging	0.96
IGL02123:Copa	APN	1	172112128	missense	probably damaging	1.00
IGL02731:Copa	APN	1	172102218	missense	possibly damaging	0.77
IGL03114:Copa	APN	1	172119268	nonsense	probably null
P0027:Copa	UTSW	1	172111948	missense	possibly damaging	0.87
PIT4434001:Copa	UTSW	1	172106175	missense	probably benign	0.00
R0233:Copa	UTSW	1	172087667	critical splice donor site	probably null
R0465:Copa	UTSW	1	172118305	missense	probably damaging	1.00
R0547:Copa	UTSW	1	172121687	splice site	probably benign
R0568:Copa	UTSW	1	172112137	missense	possibly damaging	0.91
R0628:Copa	UTSW	1	172091025	splice site	probably benign
R1328:Copa	UTSW	1	172121691	splice site	probably benign
R1494:Copa	UTSW	1	172104127	missense	probably benign	0.27
R1728:Copa	UTSW	1	172111987	missense	probably benign
R1758:Copa	UTSW	1	172104144	missense	probably damaging	1.00
R1784:Copa	UTSW	1	172111987	missense	probably benign
R1942:Copa	UTSW	1	172111888	missense	probably damaging	1.00
R2054:Copa	UTSW	1	172118957	nonsense	probably null
R2299:Copa	UTSW	1	172121725	missense	probably benign	0.10
R2518:Copa	UTSW	1	172119901	missense	probably benign
R2680:Copa	UTSW	1	172121404	nonsense	probably null
R3080:Copa	UTSW	1	172113149	missense	probably damaging	1.00
R3160:Copa	UTSW	1	172091233	missense	probably damaging	1.00
R3161:Copa	UTSW	1	172091233	missense	probably damaging	1.00
R3162:Copa	UTSW	1	172091233	missense	probably damaging	1.00
R3973:Copa	UTSW	1	172121245	missense	probably benign	0.00
R3975:Copa	UTSW	1	172121245	missense	probably benign	0.00
R4031:Copa	UTSW	1	172108375	missense	probably damaging	1.00
R4155:Copa	UTSW	1	172101425	missense	probably damaging	1.00
R4227:Copa	UTSW	1	172118115	intron	probably benign
R4244:Copa	UTSW	1	172110718	missense	probably benign	0.00
R4254:Copa	UTSW	1	172102244	missense	probably damaging	1.00
R4291:Copa	UTSW	1	172092397	intron	probably benign
R4323:Copa	UTSW	1	172119264	missense	probably damaging	1.00
R4402:Copa	UTSW	1	172102224	missense	probably damaging	1.00
R4711:Copa	UTSW	1	172119988	missense	probably damaging	1.00
R4721:Copa	UTSW	1	172104274	splice site	probably benign
R4773:Copa	UTSW	1	172105220	missense	probably damaging	1.00
R4794:Copa	UTSW	1	172119321	missense	probably damaging	1.00
R4887:Copa	UTSW	1	172092276	missense	probably benign	0.39
R4953:Copa	UTSW	1	172082886	unclassified	probably benign
R5139:Copa	UTSW	1	172121329	missense	probably damaging	0.99
R5152:Copa	UTSW	1	172118061	missense	probably benign	0.34
R5297:Copa	UTSW	1	172113108	missense	probably damaging	1.00
R5586:Copa	UTSW	1	172105222	missense	probably damaging	1.00
R5698:Copa	UTSW	1	172118944	nonsense	probably null
R6283:Copa	UTSW	1	172118848	missense	possibly damaging	0.79
R6921:Copa	UTSW	1	172111924	missense	possibly damaging	0.63
R6934:Copa	UTSW	1	172110686	missense	possibly damaging	0.64
R7009:Copa	UTSW	1	172091000	missense	probably damaging	0.96
R7194:Copa	UTSW	1	172119944	missense	probably damaging	0.99
R7348:Copa	UTSW	1	172102223	missense	possibly damaging	0.96
R7710:Copa	UTSW	1	172109844	missense	possibly damaging	0.50
R7745:Copa	UTSW	1	172111942	missense	probably damaging	1.00
R7893:Copa	UTSW	1	172119565	nonsense	probably null
R8168:Copa	UTSW	1	172099672	missense	probably damaging	1.00
R8273:Copa	UTSW	1	172118979	critical splice donor site	probably null
R8704:Copa	UTSW	1	172104126	missense	probably benign	0.01
R8754:Copa	UTSW	1	172108359	missense	probably damaging	1.00
R8757:Copa	UTSW	1	172119514	missense	probably benign	0.04
R8759:Copa	UTSW	1	172119514	missense	probably benign	0.04
R8885:Copa	UTSW	1	172097745	missense	probably damaging	1.00
R8891:Copa	UTSW	1	172119251	missense	probably damaging	1.00
R8927:Copa	UTSW	1	172104170	missense	probably null	0.03
R8928:Copa	UTSW	1	172104170	missense	probably null	0.03
R8956:Copa	UTSW	1	172109913	missense	possibly damaging	0.65
R9063:Copa	UTSW	1	172116962	missense	probably benign	0.00
R9295:Copa	UTSW	1	172112256	missense	probably damaging	0.99
R9364:Copa	UTSW	1	172117264	missense	probably benign	0.00
R9437:Copa	UTSW	1	172104145	missense	possibly damaging	0.93
T0722:Copa	UTSW	1	172111948	missense	possibly damaging	0.87
Z1177:Copa	UTSW	1	172106123	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- TGCCTGTTCACATTGCTCGG -3'
(R):5'- GAAGACCTACTGCCCAGATC -3'

Sequencing Primer
(F):5'- ACTACATAGTGAGACCCTGTCTG -3'
(R):5'- AAAAGCCTACTTACATGCCTTTC -3'

Posted On

2015-03-25