Mutagenetix > Incidental Mutation

Incidental Mutation 'R4505:Upf1'

331974

Institutional Source

Beutler Lab

Gene Symbol

Upf1

Ensembl Gene

ENSMUSG00000058301

Gene Name

UPF1 regulator of nonsense transcripts homolog (yeast)

Synonyms

B430202H16Rik, PNORF-1, Rent1

Accession Numbers

Essential gene?

Probably essential (E-score: 0.973) question?

Stock #

R4505 (G1)

Quality Score

207

Status

Validated

Chromosome

Chromosomal Location

70331525-70353278 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 70337566 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 637 (R637C)

Ref Sequence

ENSEMBL: ENSMUSP00000075089 (fasta)

Gene Model

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

AlphaFold

Q9EPU0

Predicted Effect

probably damaging
Transcript: ENSMUST00000075666
AA Change: R637C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: R637C

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 damaging
Transcript: ENSMUST00000215817
AA Change: R626C

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

Meta Mutation Damage Score

0.8701

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.3%

Validation Efficiency

96% (50/52)

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: 47 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc5	A	T	16: 20,333,695	I1367N	probably damaging	Het
Acbd4	A	G	11: 103,104,779		probably benign	Het
Adarb2	A	T	13: 8,697,691	S428C	probably damaging	Het
Atl3	T	A	19: 7,520,819	D193E	probably benign	Het
Bhlhe22	T	C	3: 18,054,959	S58P	probably benign	Het
Clasrp	C	A	7: 19,585,240		probably benign	Het
Cylc2	C	G	4: 51,229,651	T331R	unknown	Het
Epha10	A	G	4: 124,915,687		probably benign	Het
Farp2	A	T	1: 93,619,010	N917I	probably damaging	Het
Fbxo18	A	G	2: 11,749,017	V838A	possibly damaging	Het
Fras1	T	A	5: 96,781,348	N3870K	probably damaging	Het
Gm6632	C	T	5: 59,054,478		noncoding transcript	Het
Gm8909	A	T	17: 36,161,480		probably benign	Het
Gpr20	T	C	15: 73,696,472	T23A	probably benign	Het
Grb14	A	C	2: 65,022,568	V26G	probably damaging	Het
Itgb4	G	A	11: 115,983,261		silent	Het
Jak1	T	C	4: 101,154,603	T1101A	probably benign	Het
Kcnq3	A	T	15: 65,995,342	Y817*	probably null	Het
Krtcap2	A	G	3: 89,246,256		probably benign	Het
Lhx5	C	A	5: 120,440,008	H298N	possibly damaging	Het
Lrig3	C	T	10: 126,013,347	P979S	probably benign	Het
Map3k13	A	G	16: 21,922,178	S752G	probably benign	Het
Map4	T	C	9: 110,032,185	S206P	probably benign	Het
Mon2	A	G	10: 123,009,589	S1405P	probably damaging	Het
Mvb12a	G	T	8: 71,543,459	A86S	probably benign	Het
Olfr160	C	T	9: 37,711,464	V272I	probably benign	Het
Olfr486	T	C	7: 108,171,968	I259V	probably benign	Het
Pithd1	T	C	4: 135,978,833	N37S	probably benign	Het
Piwil4	T	C	9: 14,725,963	T352A	probably damaging	Het
Prb1	T	A	6: 132,207,570	R367*	probably null	Het
Psmb4	A	C	3: 94,886,145	Y142D	probably damaging	Het
Ptprs	T	C	17: 56,451,678	N181S	possibly damaging	Het
Rcbtb2	T	C	14: 73,173,905	L370P	probably damaging	Het
Ric8a	A	G	7: 140,858,516	I223V	probably benign	Het
Runx1t1	G	T	4: 13,889,676	C535F	probably damaging	Het
Samd4b	A	G	7: 28,407,500	M329T	probably benign	Het
Serpinb9g	T	A	13: 33,486,563	F11L	probably damaging	Het
Slc25a51	C	T	4: 45,399,768	V141M	probably benign	Het
Sp110	T	G	1: 85,589,173	Q201P	probably damaging	Het
Taar3	A	G	10: 23,949,573	I6V	possibly damaging	Het
Tjp2	T	C	19: 24,108,831	T776A	possibly damaging	Het
Tmc1	C	T	19: 20,868,374	V162I	probably benign	Het
Ush2a	A	G	1: 188,728,596	T2685A	possibly damaging	Het
Vmn2r102	C	T	17: 19,660,583	T62I	probably benign	Het
Vps13c	A	T	9: 67,939,034	Q2128L	probably benign	Het
Zfp26	T	C	9: 20,442,265	E76G	probably benign	Het
Zfp28	T	C	7: 6,394,161	S532P	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
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
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'- TCAGTACAGGCTGCCAACAC -3'
(R):5'- ACCCTGTCAGAACAACTTGTG -3'

Sequencing Primer
(F):5'- TGCCAACACCCCAGGAGG -3'
(R):5'- TCAGAACAACTTGTGCGGGC -3'

Posted On

2015-07-21