Mutagenetix > Incidental Mutation

Incidental Mutation 'R1552:Upf1'

170012

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

039591-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.970) question?

Stock #

R1552 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

70331525-70353278 bp(-) (GRCm38)

Type of Mutation

nonsense

DNA Base Change (assembly)

G to A at 70333059 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Stop codon at position 1046 (Q1046*)

Ref Sequence

ENSEMBL: ENSMUSP00000148927 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000075666] [ENSMUST00000140239] [ENSMUST00000165819] [ENSMUST00000207684] [ENSMUST00000215817]

AlphaFold

Q9EPU0

Predicted Effect

probably null
Transcript: ENSMUST00000075666
AA Change: Q1057*

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: Q1057*

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 benign
Transcript: ENSMUST00000140239

SMART Domains

Protein: ENSMUSP00000120598
Gene: ENSMUSG00000087408

Domain	Start	End	E-Value	Type
low complexity region	49	68	N/A	INTRINSIC
TLC	97	311	1.24e-57	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000165819

SMART Domains

Protein: ENSMUSP00000128325
Gene: ENSMUSG00000087408

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
Pfam:TGFb_propeptide	33	169	7e-16	PFAM
low complexity region	225	237	N/A	INTRINSIC
TGFB	251	357	6.22e-56	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000207684

Predicted Effect

probably null
Transcript: ENSMUST00000215817
AA Change: Q1046*

Meta Mutation Damage Score

0.9754

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.1%
20x: 91.7%

Validation Efficiency

97% (71/73)

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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1810046K07Rik	T	A	9: 51,291,570	S95C	probably damaging	Het
Abcc5	T	A	16: 20,398,867	I365F	probably damaging	Het
Abhd15	T	C	11: 77,515,407	L70P	probably damaging	Het
Adam18	A	C	8: 24,646,361	H381Q	probably benign	Het
Ankfy1	T	C	11: 72,754,495		probably null	Het
Arcn1	C	T	9: 44,758,994	A112T	probably damaging	Het
Calhm1	C	T	19: 47,141,201	R294H	probably benign	Het
Ccdc121	A	G	1: 181,510,991	L132P	probably damaging	Het
Cdk5rap1	T	C	2: 154,370,695	E81G	probably benign	Het
Cep170	T	C	1: 176,782,494		probably benign	Het
Cep350	C	T	1: 155,910,738	R1454Q	possibly damaging	Het
Chrna3	C	A	9: 55,015,908	E205D	probably benign	Het
Chst5	T	C	8: 111,890,280	D236G	probably damaging	Het
Coro1a	T	C	7: 126,699,952	N367D	probably benign	Het
Cyp3a16	T	C	5: 145,436,536	I474V	probably benign	Het
Cyth3	G	A	5: 143,697,750	V87I	probably benign	Het
Dclk3	C	A	9: 111,488,579	T761K	probably damaging	Het
Dvl2	T	A	11: 70,006,372	M300K	possibly damaging	Het
Eefsec	C	T	6: 88,376,200		probably benign	Het
Exog	T	C	9: 119,445,110	S54P	unknown	Het
Fasn	A	G	11: 120,818,558	S519P	probably damaging	Het
Gas8	G	A	8: 123,520,646	A16T	probably benign	Het
Got2	A	G	8: 95,869,494	S333P	probably benign	Het
Hadhb	T	A	5: 30,176,933	L287Q	probably null	Het
Ift57	A	G	16: 49,759,353	T211A	probably benign	Het
Il1rap	A	G	16: 26,722,434	E475G	possibly damaging	Het
Ilkap	A	T	1: 91,384,594	D11E	probably damaging	Het
Impact	T	C	18: 12,984,280	S137P	probably benign	Het
Jarid2	T	C	13: 44,911,199	V920A	probably damaging	Het
Kcnk18	A	T	19: 59,235,458	H345L	probably damaging	Het
Kdm4d	A	T	9: 14,464,029	Y178N	probably damaging	Het
Klk1b1	A	G	7: 43,969,343	Y48C	probably damaging	Het
Klra5	G	T	6: 129,909,885	T60K	probably damaging	Het
Kng2	A	T	16: 22,987,520	L643H	probably damaging	Het
Lamb3	A	G	1: 193,330,759		probably null	Het
Lingo2	A	G	4: 35,708,315	V555A	probably damaging	Het
Mbd5	T	C	2: 49,272,934	S251P	probably damaging	Het
Mc4r	T	C	18: 66,859,695	S116G	probably benign	Het
Mipol1	T	C	12: 57,306,088	V71A	possibly damaging	Het
Myo15b	A	C	11: 115,866,635	S1104R	probably benign	Het
Nek1	T	A	8: 61,006,737	D26E	probably damaging	Het
Neu1	C	T	17: 34,932,113		probably benign	Het
Npffr2	T	C	5: 89,583,116	S302P	possibly damaging	Het
Olfr912	T	C	9: 38,581,379	M34T	probably benign	Het
Palmd	T	A	3: 116,948,040		probably benign	Het
Pcdh8	A	T	14: 79,770,607	V172E	probably benign	Het
Pnpla6	C	A	8: 3,522,403	Q291K	probably damaging	Het
Prkch	T	C	12: 73,702,546	F357L	probably benign	Het
Ptprj	A	T	2: 90,471,153	Y212N	probably damaging	Het
Reln	G	T	5: 21,960,378	H2061N	probably benign	Het
Rint1	T	A	5: 23,800,658	S113T	probably benign	Het
Rnf38	G	C	4: 44,142,468		probably null	Het
Slc30a4	T	A	2: 122,686,016	I374L	probably benign	Het
Slfn10-ps	T	C	11: 83,029,850		noncoding transcript	Het
Smcp	A	T	3: 92,584,403	C46S	unknown	Het
Smu1	A	C	4: 40,748,570	V240G	probably damaging	Het
Srsf5	A	G	12: 80,949,745		probably benign	Het
Stn1	T	C	19: 47,536,373		probably null	Het
Stx18	A	G	5: 38,104,991	E63G	probably damaging	Het
Tas2r130	A	G	6: 131,630,167	Y222H	probably benign	Het
Tescl	G	T	7: 24,333,333	P189Q	probably benign	Het
Tlr1	A	G	5: 64,926,860	S125P	probably damaging	Het
Ugt2a2	G	T	5: 87,462,021	D566E	possibly damaging	Het
Uhrf1bp1	T	C	17: 27,890,071	F1088S	possibly damaging	Het
Unc13b	A	T	4: 43,237,144	T3405S	probably damaging	Het
Wwox	T	A	8: 114,445,350	Y61*	probably null	Het
Zfhx4	C	T	3: 5,403,110	T2776M	probably damaging	Het
Zranb3	G	A	1: 127,960,751		probably benign	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
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
R2143:Upf1	UTSW	8	70339354	missense	probably null	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'- TCATTCACCCTTCAGAAAGGCAGC -3'
(R):5'- GCCCTCGAACATGTACTTCCAGAC -3'

Sequencing Primer
(F):5'- TTCTCTGCTGTAGGATGCAG -3'
(R):5'- TTAGTATGATCAGCGCAGGC -3'

Posted On

2014-04-13