Mutagenetix > Incidental Mutation

Incidental Mutation 'R2143:Upf1'

236507

Institutional Source

Beutler Lab

Gene Symbol

Upf1

Ensembl Gene

ENSMUSG00000058301

Gene Name

UPF1 regulator of nonsense transcripts homolog (yeast)

Synonyms

B430202H16Rik, PNORF-1, Rent1

MMRRC Submission

040146-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.970) question?

Stock #

R2143 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

70331525-70353278 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 70339354 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 418 (D418G)

Ref Sequence

ENSEMBL: ENSMUSP00000075089 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000075666] [ENSMUST00000215817]

AlphaFold

Q9EPU0

Predicted Effect

probably null
Transcript: ENSMUST00000075666
AA Change: D418G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: D418G

Domain	Start	End	E-Value	Type
low complexity region	47	67	N/A	INTRINSIC
low complexity region	101	110	N/A	INTRINSIC
Pfam:UPF1_Zn_bind	116	267	4.1e-78	PFAM
Pfam:ResIII	475	617	1.3e-6	PFAM
Pfam:AAA_11	476	600	4.5e-24	PFAM
Pfam:AAA_30	476	688	5.6e-13	PFAM
Pfam:AAA_19	483	559	3.8e-16	PFAM
Pfam:AAA_11	576	679	7.7e-30	PFAM
Pfam:AAA_12	686	883	3.3e-64	PFAM
low complexity region	995	1001	N/A	INTRINSIC
low complexity region	1013	1028	N/A	INTRINSIC
low complexity region	1066	1081	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000215817
AA Change: D407G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.4%
20x: 95.3%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein is located only in the cytoplasm. When translation ends, it interacts with the protein that is a functional homolog of yeast Upf2p to trigger mRNA decapping. Use of multiple polyadenylation sites has been noted for this gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
PHENOTYPE: Mice homozygous for a targeted null mutation are viable in the pre-implantation period but resorb in the early post-implantation period. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 111 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310034C09Rik	G	C	16: 88,759,165	S89T	probably benign	Het
4930522L14Rik	C	G	5: 109,736,750	C414S	probably damaging	Het
4930553M12Rik	G	A	4: 88,868,174	T69I	unknown	Het
4930553M12Rik	T	A	4: 88,868,175	T69S	unknown	Het
Apobr	G	A	7: 126,587,116	E600K	probably benign	Het
Armc8	C	A	9: 99,505,308	R419L	probably damaging	Het
Ash1l	T	A	3: 88,985,419	M1535K	probably benign	Het
Atf7ip2	A	G	16: 10,240,645	E316G	probably null	Het
Atp2a1	G	A	7: 126,448,725	R638*	probably null	Het
Atp5s	A	G	12: 69,741,054	Q88R	probably damaging	Het
Atp8b4	A	T	2: 126,374,510	I672N	probably damaging	Het
Atrn	T	C	2: 130,957,996	V431A	probably benign	Het
Babam1	T	C	8: 71,398,440	S116P	probably damaging	Het
Ccdc142	T	C	6: 83,102,222	L180P	probably damaging	Het
Cd52	T	C	4: 134,093,737		probably benign	Het
Cdk17	T	C	10: 93,218,019	L125P	probably damaging	Het
Ckap5	A	G	2: 91,565,745	D531G	probably benign	Het
Cntn5	G	T	9: 9,748,415	P487Q	probably damaging	Het
Crispld1	C	T	1: 17,749,636	T286I	probably benign	Het
Crtap	T	C	9: 114,379,968	Y336C	probably damaging	Het
Ctu2	T	A	8: 122,479,152	I213K	probably benign	Het
Dsc3	A	G	18: 19,980,686	F393S	possibly damaging	Het
Dsg2	T	A	18: 20,579,161	I118N	probably damaging	Het
Dstyk	T	A	1: 132,463,375	M838K	probably damaging	Het
Elmo3	T	C	8: 105,308,673	V450A	probably damaging	Het
Eml5	A	C	12: 98,810,605	F1417C	probably damaging	Het
Enam	T	A	5: 88,492,920	M147K	probably benign	Het
Entpd1	T	C	19: 40,736,783	Y409H	probably damaging	Het
Extl1	C	A	4: 134,371,044	E225D	probably benign	Het
Fbn2	A	G	18: 58,052,993	V1761A	possibly damaging	Het
Fsip2	A	T	2: 82,990,271	L5449F	possibly damaging	Het
Gabra5	G	A	7: 57,489,015	T95I	probably damaging	Het
Gal3st2c	C	T	1: 94,009,451	Q373*	probably null	Het
Gbp5	A	C	3: 142,503,832	T180P	probably damaging	Het
Glb1	T	C	9: 114,437,824	L212P	probably damaging	Het
Gm11596	A	T	11: 99,792,963	C110*	probably null	Het
Gpat2	T	C	2: 127,433,762	F487L	probably damaging	Het
Hsph1	A	T	5: 149,631,486	H110Q	probably damaging	Het
Ikbke	C	A	1: 131,273,474	V176L	probably damaging	Het
Ildr2	T	C	1: 166,269,326	V38A	probably damaging	Het
Inpp4a	G	T	1: 37,387,746	C326F	probably damaging	Het
Irak2	T	A	6: 113,672,827	V141D	probably benign	Het
Jade1	G	A	3: 41,604,708	R408Q	probably benign	Het
Jmjd7	C	A	2: 120,030,120		probably null	Het
Kdm7a	C	T	6: 39,168,950	V348I	possibly damaging	Het
Kif20a	A	G	18: 34,625,604	D42G	possibly damaging	Het
Klhl7	A	T	5: 24,100,863	M37L	probably benign	Het
Krt5	A	G	15: 101,712,359	I151T	probably damaging	Het
Krtap1-5	T	C	11: 99,580,818	I50V	probably benign	Het
Letm1	A	AG	5: 33,769,515		probably null	Het
Lrrc71	C	T	3: 87,745,521	W148*	probably null	Het
Lsmem1	GTACATACATACATACATACATACATACA	GTACATACATACATACATACATACATACATACA	12: 40,185,261		probably null	Het
Map1a	T	A	2: 121,301,945	S843T	probably damaging	Het
Map1s	T	A	8: 70,910,964	D48E	probably damaging	Het
Mast4	A	G	13: 102,735,475	F2462L	possibly damaging	Het
Mettl21e	T	A	1: 44,210,238	Y86F	probably benign	Het
Myh6	A	T	14: 54,952,954	D1035E	probably damaging	Het
Naip6	C	T	13: 100,299,859	D719N	probably damaging	Het
Nat8f2	T	G	6: 85,868,257	H41P	probably benign	Het
Ncam1	T	A	9: 49,543,019	Q597L	possibly damaging	Het
Nek1	T	A	8: 61,028,696	I215K	probably damaging	Het
Nol11	A	T	11: 107,181,055	S237R	probably benign	Het
Npr2	T	C	4: 43,648,166	F870S	probably damaging	Het
Nsd1	T	C	13: 55,260,397	Y1285H	probably damaging	Het
Nup93	C	T	8: 94,296,480	Q229*	probably null	Het
Olfr1234	C	T	2: 89,363,103	E109K	probably damaging	Het
Olfr834	G	A	9: 18,988,803	A272T	probably benign	Het
Pappa	T	A	4: 65,180,949	Y568*	probably null	Het
Parva	A	G	7: 112,560,067	D180G	possibly damaging	Het
Pask	C	T	1: 93,321,297	A794T	probably benign	Het
Pax1	T	A	2: 147,365,882	C225S	probably damaging	Het
Pde4dip	T	A	3: 97,888,519	E51V	possibly damaging	Het
Pde6c	A	T	19: 38,162,329	H562L	probably damaging	Het
Pet100	T	G	8: 3,622,355	L14R	probably damaging	Het
Pfkfb2	T	C	1: 130,698,723	T438A	probably benign	Het
Pira2	A	T	7: 3,844,345	L115Q	probably damaging	Het
Polr2d	T	A	18: 31,796,079	L127Q	probably damaging	Het
Prkd1	A	G	12: 50,489,911	V130A	possibly damaging	Het
Psd3	T	C	8: 67,964,351	D45G	probably damaging	Het
Ptpn13	A	G	5: 103,556,133	T1344A	probably benign	Het
Ptpn6	T	A	6: 124,724,984	H406L	probably benign	Het
Ric1	A	T	19: 29,533,252	S78C	probably damaging	Het
Ric1	G	A	19: 29,533,253	S78N	probably damaging	Het
Scgb1b2	G	T	7: 31,291,763		probably benign	Het
Senp7	A	G	16: 56,169,806	H639R	probably benign	Het
Sgtb	A	T	13: 104,124,259	D72V	probably damaging	Het
Slc44a5	T	C	3: 154,258,449	M484T	probably benign	Het
Slc5a1	A	G	5: 33,160,796	K598E	probably benign	Het
Slit3	T	A	11: 35,612,261		probably null	Het
Smc1b	T	C	15: 85,123,802	H258R	probably benign	Het
Smu1	T	C	4: 40,744,073	D318G	probably damaging	Het
Sned1	T	A	1: 93,271,684	F495L	probably damaging	Het
Svs3a	C	A	2: 164,289,884	S124Y	probably damaging	Het
Syngr4	A	G	7: 45,887,040	V186A	probably benign	Het
Tarsl2	G	A	7: 65,655,791	M254I	possibly damaging	Het
Tdpoz1	T	A	3: 93,670,836	R214*	probably null	Het
Tm2d3	A	G	7: 65,695,239	D54G	probably damaging	Het
Trim66	A	T	7: 109,475,113	I647N	probably damaging	Het
Triml2	T	A	8: 43,193,511	W346R	probably damaging	Het
Trp53bp1	A	T	2: 121,216,064	V1085D	probably benign	Het
Trpv2	T	C	11: 62,592,786	V483A	probably benign	Het
Ugp2	G	T	11: 21,328,949	N412K	probably benign	Het
Vmn2r77	C	A	7: 86,811,944	P826Q	probably damaging	Het
Vrtn	T	C	12: 84,650,162	M562T	probably benign	Het
Wdr55	A	G	18: 36,762,366	N132S	possibly damaging	Het
Wipf2	A	T	11: 98,896,214	R356S	possibly damaging	Het
Zdhhc6	T	C	19: 55,298,796	K411E	probably benign	Het
Zfp260	A	G	7: 30,105,340	K222E	probably damaging	Het
Zfp280d	A	G	9: 72,312,729	N237S	probably damaging	Het
Zfp445	T	G	9: 122,853,482	S465R	possibly damaging	Het
Zfp821	A	G	8: 109,724,347	D324G	probably damaging	Het

Other mutations in Upf1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01113:Upf1	APN	8	70338284	missense	probably benign
IGL01890:Upf1	APN	8	70334230	missense	possibly damaging	0.94
IGL02534:Upf1	APN	8	70335652	critical splice donor site	probably null
IGL03142:Upf1	APN	8	70333327	missense	probably benign	0.04
IGL03151:Upf1	APN	8	70335387	missense	probably damaging	0.98
Nanosphere	UTSW	8	70344262	missense	probably benign	0.01
Particulate	UTSW	8	70337025	missense	probably damaging	0.96
R0270:Upf1	UTSW	8	70335645	splice site	probably benign
R0477:Upf1	UTSW	8	70334080	missense	probably benign
R0755:Upf1	UTSW	8	70334129	missense	probably benign	0.01
R1018:Upf1	UTSW	8	70338906	missense	possibly damaging	0.85
R1067:Upf1	UTSW	8	70338403	missense	probably damaging	0.98
R1445:Upf1	UTSW	8	70341524	missense	probably benign	0.00
R1458:Upf1	UTSW	8	70344254	missense	probably benign	0.00
R1511:Upf1	UTSW	8	70338505	missense	probably damaging	0.99
R1552:Upf1	UTSW	8	70333059	nonsense	probably null
R1560:Upf1	UTSW	8	70338442	missense	probably damaging	1.00
R1562:Upf1	UTSW	8	70343367	nonsense	probably null
R2082:Upf1	UTSW	8	70341572	missense	probably damaging	1.00
R2423:Upf1	UTSW	8	70338460	missense	probably damaging	1.00
R2425:Upf1	UTSW	8	70338460	missense	probably damaging	1.00
R3031:Upf1	UTSW	8	70338460	missense	probably damaging	1.00
R3032:Upf1	UTSW	8	70338460	missense	probably damaging	1.00
R3123:Upf1	UTSW	8	70337483	splice site	probably benign
R3508:Upf1	UTSW	8	70338460	missense	probably damaging	1.00
R3747:Upf1	UTSW	8	70333350	missense	possibly damaging	0.75
R3748:Upf1	UTSW	8	70333350	missense	possibly damaging	0.75
R3750:Upf1	UTSW	8	70333350	missense	possibly damaging	0.75
R3754:Upf1	UTSW	8	70339814	missense	probably benign	0.30
R3964:Upf1	UTSW	8	70338460	missense	probably damaging	1.00
R3965:Upf1	UTSW	8	70338460	missense	probably damaging	1.00
R4152:Upf1	UTSW	8	70338460	missense	probably damaging	1.00
R4505:Upf1	UTSW	8	70337566	missense	probably damaging	1.00
R4506:Upf1	UTSW	8	70337566	missense	probably damaging	1.00
R4838:Upf1	UTSW	8	70339368	missense	probably benign	0.03
R5001:Upf1	UTSW	8	70334700	missense	probably damaging	1.00
R5715:Upf1	UTSW	8	70352978	missense	probably damaging	0.96
R5748:Upf1	UTSW	8	70338517	missense	probably damaging	1.00
R5856:Upf1	UTSW	8	70334762	critical splice acceptor site	probably null
R5930:Upf1	UTSW	8	70344262	missense	probably benign	0.01
R6010:Upf1	UTSW	8	70337025	missense	probably damaging	0.96
R6056:Upf1	UTSW	8	70333037	missense	probably damaging	0.98
R6870:Upf1	UTSW	8	70341561	missense	probably benign	0.11
R7205:Upf1	UTSW	8	70340045	missense	possibly damaging	0.94
R7385:Upf1	UTSW	8	70340618	missense	probably damaging	1.00
R7464:Upf1	UTSW	8	70333423	missense	probably benign
R7759:Upf1	UTSW	8	70334080	missense	probably benign
R7783:Upf1	UTSW	8	70352858	missense	probably benign	0.11
R8079:Upf1	UTSW	8	70338884	critical splice donor site	probably null
R8192:Upf1	UTSW	8	70340644	missense	probably benign	0.03
R8544:Upf1	UTSW	8	70337052	missense	probably damaging	1.00
R8738:Upf1	UTSW	8	70333322	missense	probably benign	0.01
R8738:Upf1	UTSW	8	70333323	missense	probably benign	0.06
R8826:Upf1	UTSW	8	70338280	missense	probably benign
R8876:Upf1	UTSW	8	70344268	missense	possibly damaging	0.92
R8906:Upf1	UTSW	8	70334165	nonsense	probably null
R8911:Upf1	UTSW	8	70338437	missense	possibly damaging	0.53
R9163:Upf1	UTSW	8	70340024	missense	probably benign
R9425:Upf1	UTSW	8	70339353	missense	probably benign	0.06

Predicted Primers

PCR Primer
(F):5'- CCCAGCAGCTTGTGGTAAATATAC -3'
(R):5'- ATGTGTGAGTGAAACAGCCTG -3'

Sequencing Primer
(F):5'- TATACCCTGACACAGAGGTCTCGTC -3'
(R):5'- TGAAACAGCCTGGAGTCTGTC -3'

Posted On

2014-10-01