Mutagenetix > Incidental Mutation

Incidental Mutation 'R6056:Upf1'

484404

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

044223-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.970) question?

Stock #

R6056 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

70331525-70353278 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 70333037 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 1053 (Y1053C)

Ref Sequence

ENSEMBL: ENSMUSP00000148927 (fasta)

Gene Model

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

AlphaFold

Q9EPU0

Predicted Effect

probably damaging
Transcript: ENSMUST00000075666
AA Change: Y1064C

PolyPhen 2 Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: Y1064C

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 damaging
Transcript: ENSMUST00000215817
AA Change: Y1053C

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)

Meta Mutation Damage Score

0.0637

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.4%
20x: 95.4%

Validation Efficiency

96% (99/103)

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: 101 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310002L09Rik	A	T	4: 73,942,878 (GRCm38)	W162R	probably benign	Het
2610507B11Rik	C	A	11: 78,271,384 (GRCm38)	L691I	possibly damaging	Het
4930438A08Rik	C	A	11: 58,293,638 (GRCm38)	P394H	probably damaging	Het
Aggf1	C	T	13: 95,371,615 (GRCm38)	C81Y	probably benign	Het
Agxt2	A	T	15: 10,378,877 (GRCm38)	D188V	probably damaging	Het
Angpt2	T	C	8: 18,698,116 (GRCm38)	K376R	probably benign	Het
Anxa5	A	G	3: 36,450,691 (GRCm38)	S241P	probably damaging	Het
Aox3	A	T	1: 58,169,859 (GRCm38)	K850N	probably damaging	Het
Arid5a	T	C	1: 36,319,392 (GRCm38)	M415T	probably benign	Het
Aspa	T	A	11: 73,308,752 (GRCm38)	N233I	probably damaging	Het
Atp4b	C	T	8: 13,388,782 (GRCm38)	R198Q	probably damaging	Het
Atp8b2	A	T	3: 89,946,221 (GRCm38)	V719E	possibly damaging	Het
Cacna1s	T	G	1: 136,105,836 (GRCm38)	V1017G	probably damaging	Het
Chrna4	G	T	2: 181,029,442 (GRCm38)	Q174K	probably damaging	Het
Chrnb1	A	T	11: 69,786,939 (GRCm38)	V329D	probably damaging	Het
Chst14	T	C	2: 118,927,733 (GRCm38)	L336P	probably damaging	Het
Clec2e	T	C	6: 129,100,809 (GRCm38)	D22G	probably benign	Het
Csrnp2	A	C	15: 100,482,382 (GRCm38)	S343A	probably benign	Het
Dapl1	C	A	2: 59,484,713 (GRCm38)	A2E	probably damaging	Het
Dlec1	G	T	9: 119,121,923 (GRCm38)	R519L	probably damaging	Het
Dmgdh	T	A	13: 93,708,743 (GRCm38)	F415I	possibly damaging	Het
Dmgdh	T	C	13: 93,752,326 (GRCm38)	V824A	probably damaging	Het
Dnah11	T	G	12: 117,928,456 (GRCm38)	T3661P	probably benign	Het
Dnah3	A	G	7: 120,030,031 (GRCm38)	F1434L	probably damaging	Het
Dnajc11	C	A	4: 151,978,126 (GRCm38)		probably benign	Het
Dot1l	A	G	10: 80,786,095 (GRCm38)	E527G	probably damaging	Het
Drc7	T	C	8: 95,075,051 (GRCm38)	L680P	probably damaging	Het
Dysf	T	C	6: 84,106,862 (GRCm38)	Y742H	probably benign	Het
Ece1	A	G	4: 137,961,647 (GRCm38)	Y665C	probably damaging	Het
Emc1	A	G	4: 139,354,222 (GRCm38)	K54E	possibly damaging	Het
Enoph1	C	T	5: 100,067,901 (GRCm38)	T247M	probably damaging	Het
Exoc2	T	C	13: 30,900,829 (GRCm38)	K383R	probably benign	Het
Fam227b	A	T	2: 126,121,052 (GRCm38)	H181Q	probably damaging	Het
Fsip2	A	T	2: 82,985,673 (GRCm38)	M3917L	probably benign	Het
Gtf3a	T	A	5: 146,955,528 (GRCm38)		probably benign	Het
Hgfac	T	A	5: 35,041,629 (GRCm38)	C11*	probably null	Het
Hmcn1	C	A	1: 150,663,909 (GRCm38)	A2944S	probably damaging	Het
Hps5	T	A	7: 46,767,097 (GRCm38)	Y947F	probably benign	Het
Ighv2-5	A	T	12: 113,685,500 (GRCm38)	I111K	probably benign	Het
Inpp5e	A	T	2: 26,407,848 (GRCm38)	L247*	probably null	Het
Kbtbd11	T	C	8: 15,027,577 (GRCm38)	S59P	probably benign	Het
Kctd19	G	A	8: 105,396,450 (GRCm38)	H111Y	probably damaging	Het
Kif1a	T	C	1: 93,024,648 (GRCm38)	D1303G	probably damaging	Het
Kif7	A	G	7: 79,714,094 (GRCm38)	V22A	possibly damaging	Het
Lrit3	A	T	3: 129,789,355 (GRCm38)	C328S	probably damaging	Het
Lrrc37a	G	T	11: 103,497,658 (GRCm38)	Q2314K	unknown	Het
Lurap1	G	T	4: 116,137,402 (GRCm38)	P211T	possibly damaging	Het
Mbd2	T	A	18: 70,580,803 (GRCm38)	N5K	possibly damaging	Het
Mbtps1	A	C	8: 119,515,602 (GRCm38)	L894V	probably benign	Het
Mefv	G	A	16: 3,708,042 (GRCm38)	S787F	possibly damaging	Het
Miip	T	A	4: 147,862,335 (GRCm38)	I289F	probably damaging	Het
Mogat2	T	A	7: 99,223,513 (GRCm38)	I155F	possibly damaging	Het
Mpp3	C	A	11: 102,011,689 (GRCm38)		probably null	Het
Mrrf	A	G	2: 36,177,221 (GRCm38)	K220E	probably damaging	Het
Mtmr6	C	T	14: 60,298,170 (GRCm38)	P485L	probably damaging	Het
Mtor	G	A	4: 148,537,435 (GRCm38)	R1896K	probably benign	Het
Myh3	C	T	11: 67,087,545 (GRCm38)	P453S	probably benign	Het
Nebl	A	G	2: 17,450,234 (GRCm38)	V112A	probably benign	Het
Nmnat2	G	A	1: 153,074,734 (GRCm38)	W55*	probably null	Het
Nprl3	A	G	11: 32,267,432 (GRCm38)	S37P	probably damaging	Het
Olfr1246	T	C	2: 89,591,101 (GRCm38)	N5D	possibly damaging	Het
Oraov1	G	T	7: 144,915,286 (GRCm38)	V17L	possibly damaging	Het
Pcdhga4	T	G	18: 37,686,330 (GRCm38)	S311A	probably benign	Het
Pcdhgb6	T	C	18: 37,743,112 (GRCm38)	V291A	probably benign	Het
Peg10	GAT	GATCAT	6: 4,756,449 (GRCm38)		probably benign	Het
Peg3	T	C	7: 6,709,571 (GRCm38)	E884G	probably damaging	Het
Pgpep1	G	A	8: 70,652,451 (GRCm38)	T53M	probably damaging	Het
Phf12	A	G	11: 78,009,515 (GRCm38)	T146A	probably benign	Het
Polr3k	C	G	2: 181,864,488 (GRCm38)	N10K	probably damaging	Het
Prickle4	C	A	17: 47,690,210 (GRCm38)	G144C	probably damaging	Het
Ptpn6	T	C	6: 124,732,435 (GRCm38)	Y25C	probably damaging	Het
Rad1	A	G	15: 10,488,074 (GRCm38)	I95V	probably damaging	Het
Rad23b	A	G	4: 55,382,540 (GRCm38)	T248A	probably benign	Het
Rapgef3	T	C	15: 97,758,861 (GRCm38)	D299G	probably damaging	Het
Rcc2	T	G	4: 140,717,024 (GRCm38)	V342G	possibly damaging	Het
Rgs3	G	T	4: 62,625,906 (GRCm38)	R136L	probably damaging	Het
Scube2	A	T	7: 109,833,013 (GRCm38)	C399*	probably null	Het
Serpinb3d	T	C	1: 107,079,722 (GRCm38)	Y178C	probably damaging	Het
Slc1a7	A	G	4: 108,012,261 (GRCm38)	T508A	probably benign	Het
Slc29a4	C	T	5: 142,720,077 (GRCm38)	R439C	probably damaging	Het
Sntg2	A	G	12: 30,312,561 (GRCm38)	I62T	probably benign	Het
Sowaha	G	A	11: 53,479,087 (GRCm38)	P274L	probably damaging	Het
Sptan1	A	G	2: 29,996,782 (GRCm38)	N869S	probably benign	Het
Stx18	C	A	5: 38,106,564 (GRCm38)	A64D	probably damaging	Het
Stxbp5	A	G	10: 9,770,686 (GRCm38)	V94A	probably benign	Het
Sult1a1	T	A	7: 126,676,452 (GRCm38)		probably null	Het
Susd1	G	T	4: 59,379,687 (GRCm38)	H313Q	possibly damaging	Het
Tdrd9	A	T	12: 111,985,041 (GRCm38)	K88N	probably damaging	Het
Tlr5	A	C	1: 182,974,038 (GRCm38)	R302S	possibly damaging	Het
Tnr	C	T	1: 159,886,909 (GRCm38)	T786I	probably damaging	Het
Tprgl	A	G	4: 154,160,095 (GRCm38)	S148P	probably damaging	Het
Trpc4ap	T	A	2: 155,671,074 (GRCm38)	N127I	probably damaging	Het
Tulp2	T	A	7: 45,490,373 (GRCm38)		probably null	Het
Uggt2	C	T	14: 119,035,969 (GRCm38)		probably null	Het
Ulk4	T	A	9: 121,272,955 (GRCm38)	Y19F	probably damaging	Het
Vars2	A	T	17: 35,665,788 (GRCm38)	H223Q	probably benign	Het
Vmn2r106	T	A	17: 20,267,544 (GRCm38)		probably null	Het
Ythdc2	T	A	18: 44,840,210 (GRCm38)	F305I	probably damaging	Het
Zfp281	T	C	1: 136,625,440 (GRCm38)	F52S	possibly damaging	Het
Zfp292	A	T	4: 34,809,784 (GRCm38)	C1087S	probably damaging	Het
Zfp335	A	T	2: 164,895,098 (GRCm38)		probably null	Het

Other mutations in Upf1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01113:Upf1	APN	8	70,338,284 (GRCm38)	missense	probably benign
IGL01890:Upf1	APN	8	70,334,230 (GRCm38)	missense	possibly damaging	0.94
IGL02534:Upf1	APN	8	70,335,652 (GRCm38)	critical splice donor site	probably null
IGL03142:Upf1	APN	8	70,333,327 (GRCm38)	missense	probably benign	0.04
IGL03151:Upf1	APN	8	70,335,387 (GRCm38)	missense	probably damaging	0.98
Nanosphere	UTSW	8	70,344,262 (GRCm38)	missense	probably benign	0.01
Particulate	UTSW	8	70,337,025 (GRCm38)	missense	probably damaging	0.96
R0270:Upf1	UTSW	8	70,335,645 (GRCm38)	splice site	probably benign
R0477:Upf1	UTSW	8	70,334,080 (GRCm38)	missense	probably benign
R0755:Upf1	UTSW	8	70,334,129 (GRCm38)	missense	probably benign	0.01
R1018:Upf1	UTSW	8	70,338,906 (GRCm38)	missense	possibly damaging	0.85
R1067:Upf1	UTSW	8	70,338,403 (GRCm38)	missense	probably damaging	0.98
R1445:Upf1	UTSW	8	70,341,524 (GRCm38)	missense	probably benign	0.00
R1458:Upf1	UTSW	8	70,344,254 (GRCm38)	missense	probably benign	0.00
R1511:Upf1	UTSW	8	70,338,505 (GRCm38)	missense	probably damaging	0.99
R1552:Upf1	UTSW	8	70,333,059 (GRCm38)	nonsense	probably null
R1560:Upf1	UTSW	8	70,338,442 (GRCm38)	missense	probably damaging	1.00
R1562:Upf1	UTSW	8	70,343,367 (GRCm38)	nonsense	probably null
R2082:Upf1	UTSW	8	70,341,572 (GRCm38)	missense	probably damaging	1.00
R2143:Upf1	UTSW	8	70,339,354 (GRCm38)	missense	probably null	1.00
R2423:Upf1	UTSW	8	70,338,460 (GRCm38)	missense	probably damaging	1.00
R2425:Upf1	UTSW	8	70,338,460 (GRCm38)	missense	probably damaging	1.00
R3031:Upf1	UTSW	8	70,338,460 (GRCm38)	missense	probably damaging	1.00
R3032:Upf1	UTSW	8	70,338,460 (GRCm38)	missense	probably damaging	1.00
R3123:Upf1	UTSW	8	70,337,483 (GRCm38)	splice site	probably benign
R3508:Upf1	UTSW	8	70,338,460 (GRCm38)	missense	probably damaging	1.00
R3747:Upf1	UTSW	8	70,333,350 (GRCm38)	missense	possibly damaging	0.75
R3748:Upf1	UTSW	8	70,333,350 (GRCm38)	missense	possibly damaging	0.75
R3750:Upf1	UTSW	8	70,333,350 (GRCm38)	missense	possibly damaging	0.75
R3754:Upf1	UTSW	8	70,339,814 (GRCm38)	missense	probably benign	0.30
R3964:Upf1	UTSW	8	70,338,460 (GRCm38)	missense	probably damaging	1.00
R3965:Upf1	UTSW	8	70,338,460 (GRCm38)	missense	probably damaging	1.00
R4152:Upf1	UTSW	8	70,338,460 (GRCm38)	missense	probably damaging	1.00
R4505:Upf1	UTSW	8	70,337,566 (GRCm38)	missense	probably damaging	1.00
R4506:Upf1	UTSW	8	70,337,566 (GRCm38)	missense	probably damaging	1.00
R4838:Upf1	UTSW	8	70,339,368 (GRCm38)	missense	probably benign	0.03
R5001:Upf1	UTSW	8	70,334,700 (GRCm38)	missense	probably damaging	1.00
R5715:Upf1	UTSW	8	70,352,978 (GRCm38)	missense	probably damaging	0.96
R5748:Upf1	UTSW	8	70,338,517 (GRCm38)	missense	probably damaging	1.00
R5856:Upf1	UTSW	8	70,334,762 (GRCm38)	critical splice acceptor site	probably null
R5930:Upf1	UTSW	8	70,344,262 (GRCm38)	missense	probably benign	0.01
R6010:Upf1	UTSW	8	70,337,025 (GRCm38)	missense	probably damaging	0.96
R6870:Upf1	UTSW	8	70,341,561 (GRCm38)	missense	probably benign	0.11
R7205:Upf1	UTSW	8	70,340,045 (GRCm38)	missense	possibly damaging	0.94
R7385:Upf1	UTSW	8	70,340,618 (GRCm38)	missense	probably damaging	1.00
R7464:Upf1	UTSW	8	70,333,423 (GRCm38)	missense	probably benign
R7759:Upf1	UTSW	8	70,334,080 (GRCm38)	missense	probably benign
R7783:Upf1	UTSW	8	70,352,858 (GRCm38)	missense	probably benign	0.11
R8079:Upf1	UTSW	8	70,338,884 (GRCm38)	critical splice donor site	probably null
R8192:Upf1	UTSW	8	70,340,644 (GRCm38)	missense	probably benign	0.03
R8544:Upf1	UTSW	8	70,337,052 (GRCm38)	missense	probably damaging	1.00
R8738:Upf1	UTSW	8	70,333,323 (GRCm38)	missense	probably benign	0.06
R8738:Upf1	UTSW	8	70,333,322 (GRCm38)	missense	probably benign	0.01
R8826:Upf1	UTSW	8	70,338,280 (GRCm38)	missense	probably benign
R8876:Upf1	UTSW	8	70,344,268 (GRCm38)	missense	possibly damaging	0.92
R8906:Upf1	UTSW	8	70,334,165 (GRCm38)	nonsense	probably null
R8911:Upf1	UTSW	8	70,338,437 (GRCm38)	missense	possibly damaging	0.53
R9163:Upf1	UTSW	8	70,340,024 (GRCm38)	missense	probably benign
R9425:Upf1	UTSW	8	70,339,353 (GRCm38)	missense	probably benign	0.06

Predicted Primers

PCR Primer
(F):5'- GGGAAGAAACCCCATACTGC -3'
(R):5'- CCTAGCTTTAGGTAGACCTTGC -3'

Posted On

2017-07-14