Mutagenetix > Incidental Mutation

Incidental Mutation 'R0270:Upf1'

35227

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

038496-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.970) question?

Stock #

R0270 (G1)

Quality Score

126

Status

Validated

Chromosome

Chromosomal Location

70331525-70353278 bp(-) (GRCm38)

Type of Mutation

splice site

DNA Base Change (assembly)

G to A at 70335645 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000148927 (fasta)

Gene Model

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

AlphaFold

Q9EPU0

Predicted Effect

probably benign
Transcript: ENSMUST00000075666

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301

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 benign
Transcript: ENSMUST00000215817

Coding Region Coverage

1x: 98.7%
3x: 97.7%
10x: 96.0%
20x: 93.2%

Validation Efficiency

99% (113/114)

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: 109 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110009E18Rik	T	A	1: 120,166,176 (GRCm38)		probably benign	Het
4922502D21Rik	A	T	6: 129,325,608 (GRCm38)	L152*	probably null	Het
Abcf3	T	A	16: 20,560,168 (GRCm38)		probably null	Het
Acadm	C	T	3: 153,936,324 (GRCm38)	M190I	possibly damaging	Het
Adamtsl3	G	A	7: 82,556,824 (GRCm38)	R739Q	probably damaging	Het
Ank1	T	A	8: 23,088,925 (GRCm38)		probably benign	Het
Ap3b1	T	A	13: 94,404,118 (GRCm38)		probably benign	Het
Arhgdib	A	G	6: 136,926,734 (GRCm38)	V31A	probably damaging	Het
Arid4a	A	G	12: 71,072,632 (GRCm38)	R342G	probably damaging	Het
Asic3	C	T	5: 24,417,702 (GRCm38)	L517F	probably benign	Het
Atxn7l1	C	T	12: 33,342,151 (GRCm38)	P242L	possibly damaging	Het
AY761185	T	A	8: 20,944,600 (GRCm38)	E37D	possibly damaging	Het
Babam1	T	A	8: 71,398,406 (GRCm38)	D104E	probably damaging	Het
Batf	A	T	12: 85,708,672 (GRCm38)	T100S	probably benign	Het
Blcap	A	T	2: 157,557,977 (GRCm38)	Y59*	probably null	Het
Cacnb3	G	A	15: 98,642,559 (GRCm38)	A350T	probably damaging	Het
Cdk15	T	A	1: 59,310,806 (GRCm38)	V319D	probably damaging	Het
Cenpf	T	C	1: 189,650,714 (GRCm38)	H2661R	probably benign	Het
Cenpq	T	C	17: 40,930,050 (GRCm38)	E106G	probably damaging	Het
Cfap43	A	G	19: 47,797,203 (GRCm38)		probably benign	Het
Cfb	G	A	17: 34,860,386 (GRCm38)	S778L	possibly damaging	Het
Clspn	T	A	4: 126,573,236 (GRCm38)	N631K	probably damaging	Het
Cntn2	T	A	1: 132,521,724 (GRCm38)	T660S	probably damaging	Het
Cntrob	T	A	11: 69,311,341 (GRCm38)	H475L	possibly damaging	Het
Ddx46	T	C	13: 55,674,104 (GRCm38)	I863T	probably benign	Het
Dnah11	G	A	12: 118,041,013 (GRCm38)	T2191I	probably damaging	Het
Dock9	T	C	14: 121,575,999 (GRCm38)	T1703A	probably benign	Het
Fam13c	C	T	10: 70,544,513 (GRCm38)	P424S	probably benign	Het
Fan1	T	C	7: 64,348,871 (GRCm38)	N968D	probably benign	Het
Fbxl20	A	T	11: 98,098,503 (GRCm38)		probably benign	Het
Fkbp1b	A	T	12: 4,838,229 (GRCm38)		probably benign	Het
G930045G22Rik	T	A	6: 50,847,059 (GRCm38)		noncoding transcript	Het
Gm28042	C	A	2: 120,041,592 (GRCm38)	R1008S	probably benign	Het
Gm6614	T	A	6: 141,972,411 (GRCm38)	I580F	possibly damaging	Het
Gm8298	T	A	3: 59,877,019 (GRCm38)	N304K	probably benign	Het
Gon4l	G	A	3: 88,858,400 (GRCm38)	S376N	probably damaging	Het
Gstt3	C	A	10: 75,780,915 (GRCm38)	R15L	probably damaging	Het
Gtdc1	A	T	2: 44,752,174 (GRCm38)	S73T	possibly damaging	Het
H2afy	G	A	13: 56,096,114 (GRCm38)		probably benign	Het
Hhatl	A	G	9: 121,784,720 (GRCm38)	S419P	probably benign	Het
Hirip3	T	G	7: 126,863,191 (GRCm38)	S46R	probably damaging	Het
Hsf2	A	G	10: 57,502,639 (GRCm38)	T204A	probably benign	Het
Impg2	G	A	16: 56,269,015 (GRCm38)	E1108K	possibly damaging	Het
Itgb2l	G	T	16: 96,422,930 (GRCm38)		probably benign	Het
Itih5	A	T	2: 10,251,264 (GRCm38)	N847I	probably benign	Het
Kif1a	T	C	1: 93,054,442 (GRCm38)		probably benign	Het
Klhl1	T	A	14: 96,518,344 (GRCm38)		probably benign	Het
Ktn1	T	A	14: 47,714,662 (GRCm38)	D963E	probably benign	Het
Lclat1	T	A	17: 73,240,027 (GRCm38)	V313E	probably benign	Het
Lrrn4	T	C	2: 132,870,719 (GRCm38)	S395G	probably benign	Het
Mbtps1	G	A	8: 119,538,117 (GRCm38)		probably benign	Het
Me1	A	G	9: 86,596,204 (GRCm38)		probably benign	Het
Mov10	C	A	3: 104,795,405 (GRCm38)	C948F	probably benign	Het
Mterf1a	G	A	5: 3,890,990 (GRCm38)	Q293*	probably null	Het
Nfkb2	A	T	19: 46,311,626 (GRCm38)	M838L	possibly damaging	Het
Nhlrc2	T	A	19: 56,551,870 (GRCm38)	L97Q	probably damaging	Het
Nr6a1	A	T	2: 38,739,020 (GRCm38)	Y331N	possibly damaging	Het
Nup214	C	T	2: 32,034,814 (GRCm38)	A1785V	probably damaging	Het
Ogg1	C	T	6: 113,329,256 (GRCm38)	T138I	probably benign	Het
Olfr1461	A	G	19: 13,165,887 (GRCm38)	Y291C	probably damaging	Het
Olfr1489	A	G	19: 13,633,684 (GRCm38)	Y191C	probably damaging	Het
Olfr202	A	G	16: 59,283,753 (GRCm38)	V248A	probably damaging	Het
Olfr829	T	A	9: 18,856,831 (GRCm38)	Y60N	probably damaging	Het
Plod2	G	T	9: 92,584,521 (GRCm38)	R178L	probably benign	Het
Polr3b	T	A	10: 84,718,475 (GRCm38)	L1017Q	probably benign	Het
Postn	C	A	3: 54,384,550 (GRCm38)	T724N	probably damaging	Het
Ppm1l	T	G	3: 69,317,976 (GRCm38)		probably benign	Het
Prpf8	T	G	11: 75,505,249 (GRCm38)	L1983R	probably damaging	Het
Psma7	A	G	2: 180,039,400 (GRCm38)	V59A	probably benign	Het
Qser1	T	A	2: 104,788,961 (GRCm38)	Y502F	probably benign	Het
Rad50	T	C	11: 53,668,025 (GRCm38)	D1129G	probably damaging	Het
Rasal1	C	A	5: 120,674,729 (GRCm38)	P606Q	probably damaging	Het
Rgs6	A	G	12: 83,133,689 (GRCm38)	Y438C	probably damaging	Het
Rnf180	A	G	13: 105,252,266 (GRCm38)	C73R	probably benign	Het
Rnf216	T	A	5: 143,080,241 (GRCm38)	I474F	possibly damaging	Het
Sdha	A	T	13: 74,332,247 (GRCm38)	L371Q	probably damaging	Het
Sdk1	T	G	5: 142,084,566 (GRCm38)	L1162R	possibly damaging	Het
Sh3rf2	T	C	18: 42,104,081 (GRCm38)	I223T	probably damaging	Het
Sirpb1a	A	G	3: 15,410,527 (GRCm38)	V316A	probably damaging	Het
Slc12a4	A	T	8: 105,945,389 (GRCm38)	I897N	probably benign	Het
Slc35d1	A	T	4: 103,190,838 (GRCm38)	V243E	probably damaging	Het
Slc4a11	T	A	2: 130,690,932 (GRCm38)	K200N	possibly damaging	Het
Slc9a8	T	A	2: 167,451,296 (GRCm38)	M188K	probably damaging	Het
Snrnp200	T	C	2: 127,232,982 (GRCm38)	S1492P	probably damaging	Het
Sphk2	T	C	7: 45,710,725 (GRCm38)	*618W	probably null	Het
Sytl2	T	C	7: 90,403,020 (GRCm38)		probably benign	Het
Tdpoz3	A	G	3: 93,826,924 (GRCm38)	N302S	probably benign	Het
Tdrd6	T	C	17: 43,624,308 (GRCm38)	M1950V	probably benign	Het
Tmem39a	A	G	16: 38,564,313 (GRCm38)		probably benign	Het
Trip4	A	T	9: 65,858,358 (GRCm38)	I353K	probably damaging	Het
Trip6	A	T	5: 137,312,841 (GRCm38)	F204L	probably benign	Het
Trpm4	T	A	7: 45,319,253 (GRCm38)	I419F	possibly damaging	Het
Ttn	C	A	2: 76,944,796 (GRCm38)	E1967D	probably damaging	Het
Uba2	C	T	7: 34,150,856 (GRCm38)	V391M	possibly damaging	Het
Ubr4	T	G	4: 139,479,435 (GRCm38)		probably benign	Het
Vmn1r228	A	C	17: 20,776,596 (GRCm38)	V220G	possibly damaging	Het
Vmn2r79	A	G	7: 87,003,386 (GRCm38)	M429V	probably benign	Het
Vps36	C	T	8: 22,210,456 (GRCm38)	T210I	possibly damaging	Het
Wdr17	C	T	8: 54,693,096 (GRCm38)	A90T	possibly damaging	Het
Ybx1	C	T	4: 119,281,591 (GRCm38)	G126D	probably benign	Het
Yipf5	C	A	18: 40,206,407 (GRCm38)		probably benign	Het
Zdhhc5	A	C	2: 84,690,115 (GRCm38)	S573A	probably benign	Het
Zfp457	A	T	13: 67,293,927 (GRCm38)	C99S	probably damaging	Het
Zfp52	T	A	17: 21,561,302 (GRCm38)	C471S	probably damaging	Het
Zfp558	C	T	9: 18,467,956 (GRCm38)	V71I	probably damaging	Het
Zfp651	A	G	9: 121,767,575 (GRCm38)	T666A	probably benign	Het
Zfp655	A	G	5: 145,244,457 (GRCm38)	Y375C	probably damaging	Het
Zfp882	A	T	8: 71,914,615 (GRCm38)	T429S	probably benign	Het
Zmym2	T	C	14: 56,949,684 (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
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
R6056:Upf1	UTSW	8	70,333,037 (GRCm38)	missense	probably damaging	0.98
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'- TGAAAAGGCTCCTCACAGGTTCCC -3'
(R):5'- CTTGAATAGTGTTGACCCAGGCCC -3'

Sequencing Primer
(F):5'- TGGCAGACCTCCAGTAACC -3'
(R):5'- TTGATTGAGCCCCTGAGC -3'

Posted On

2013-05-09