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, Rent1, PNORF-1

MMRRC Submission

038496-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.972) question?

Stock #

R0270 (G1)

Quality Score

126

Status

Validated

Chromosome

Chromosomal Location

70784175-70805928 bp(-) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

G to A at 70788295 bp (GRCm39)

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: 120,093,906 (GRCm39)		probably benign	Het
Aadacl2fm3	T	A	3: 59,784,440 (GRCm39)	N304K	probably benign	Het
Abcf3	T	A	16: 20,378,918 (GRCm39)		probably null	Het
Acadm	C	T	3: 153,641,961 (GRCm39)	M190I	possibly damaging	Het
Adamtsl3	G	A	7: 82,206,032 (GRCm39)	R739Q	probably damaging	Het
Ank1	T	A	8: 23,578,941 (GRCm39)		probably benign	Het
Ap3b1	T	A	13: 94,540,626 (GRCm39)		probably benign	Het
Arhgdib	A	G	6: 136,903,732 (GRCm39)	V31A	probably damaging	Het
Arid4a	A	G	12: 71,119,406 (GRCm39)	R342G	probably damaging	Het
Asic3	C	T	5: 24,622,700 (GRCm39)	L517F	probably benign	Het
Atxn7l1	C	T	12: 33,392,150 (GRCm39)	P242L	possibly damaging	Het
AY761185	T	A	8: 21,434,616 (GRCm39)	E37D	possibly damaging	Het
Babam1	T	A	8: 71,851,050 (GRCm39)	D104E	probably damaging	Het
Batf	A	T	12: 85,755,446 (GRCm39)	T100S	probably benign	Het
Blcap	A	T	2: 157,399,897 (GRCm39)	Y59*	probably null	Het
Cacnb3	G	A	15: 98,540,440 (GRCm39)	A350T	probably damaging	Het
Cdk15	T	A	1: 59,349,965 (GRCm39)	V319D	probably damaging	Het
Cenpf	T	C	1: 189,382,911 (GRCm39)	H2661R	probably benign	Het
Cenpq	T	C	17: 41,240,941 (GRCm39)	E106G	probably damaging	Het
Cfap43	A	G	19: 47,785,642 (GRCm39)		probably benign	Het
Cfb	G	A	17: 35,079,362 (GRCm39)	S778L	possibly damaging	Het
Clec2m	A	T	6: 129,302,571 (GRCm39)	L152*	probably null	Het
Clspn	T	A	4: 126,467,029 (GRCm39)	N631K	probably damaging	Het
Cntn2	T	A	1: 132,449,462 (GRCm39)	T660S	probably damaging	Het
Cntrob	T	A	11: 69,202,167 (GRCm39)	H475L	possibly damaging	Het
Ddx46	T	C	13: 55,821,917 (GRCm39)	I863T	probably benign	Het
Dnah11	G	A	12: 118,004,748 (GRCm39)	T2191I	probably damaging	Het
Dock9	T	C	14: 121,813,411 (GRCm39)	T1703A	probably benign	Het
Fam13c	C	T	10: 70,380,343 (GRCm39)	P424S	probably benign	Het
Fan1	T	C	7: 63,998,619 (GRCm39)	N968D	probably benign	Het
Fbxl20	A	T	11: 97,989,329 (GRCm39)		probably benign	Het
Fkbp1b	A	T	12: 4,888,229 (GRCm39)		probably benign	Het
G930045G22Rik	T	A	6: 50,824,039 (GRCm39)		noncoding transcript	Het
Gm28042	C	A	2: 119,872,073 (GRCm39)	R1008S	probably benign	Het
Gon4l	G	A	3: 88,765,707 (GRCm39)	S376N	probably damaging	Het
Gstt3	C	A	10: 75,616,749 (GRCm39)	R15L	probably damaging	Het
Gtdc1	A	T	2: 44,642,186 (GRCm39)	S73T	possibly damaging	Het
Hhatl	A	G	9: 121,613,786 (GRCm39)	S419P	probably benign	Het
Hirip3	T	G	7: 126,462,363 (GRCm39)	S46R	probably damaging	Het
Hsf2	A	G	10: 57,378,735 (GRCm39)	T204A	probably benign	Het
Impg2	G	A	16: 56,089,378 (GRCm39)	E1108K	possibly damaging	Het
Itgb2l	G	T	16: 96,224,130 (GRCm39)		probably benign	Het
Itih5	A	T	2: 10,256,075 (GRCm39)	N847I	probably benign	Het
Kif1a	T	C	1: 92,982,164 (GRCm39)		probably benign	Het
Klhl1	T	A	14: 96,755,780 (GRCm39)		probably benign	Het
Ktn1	T	A	14: 47,952,119 (GRCm39)	D963E	probably benign	Het
Lclat1	T	A	17: 73,547,022 (GRCm39)	V313E	probably benign	Het
Lrrn4	T	C	2: 132,712,639 (GRCm39)	S395G	probably benign	Het
Macroh2a1	G	A	13: 56,243,927 (GRCm39)		probably benign	Het
Mbtps1	G	A	8: 120,264,856 (GRCm39)		probably benign	Het
Me1	A	G	9: 86,478,257 (GRCm39)		probably benign	Het
Mov10	C	A	3: 104,702,721 (GRCm39)	C948F	probably benign	Het
Mterf1a	G	A	5: 3,940,990 (GRCm39)	Q293*	probably null	Het
Nfkb2	A	T	19: 46,300,065 (GRCm39)	M838L	possibly damaging	Het
Nhlrc2	T	A	19: 56,540,302 (GRCm39)	L97Q	probably damaging	Het
Nr6a1	A	T	2: 38,629,032 (GRCm39)	Y331N	possibly damaging	Het
Nup214	C	T	2: 31,924,826 (GRCm39)	A1785V	probably damaging	Het
Ogg1	C	T	6: 113,306,217 (GRCm39)	T138I	probably benign	Het
Or5ac20	A	G	16: 59,104,116 (GRCm39)	V248A	probably damaging	Het
Or5b107	A	G	19: 13,143,251 (GRCm39)	Y291C	probably damaging	Het
Or5b124	A	G	19: 13,611,048 (GRCm39)	Y191C	probably damaging	Het
Or7g17	T	A	9: 18,768,127 (GRCm39)	Y60N	probably damaging	Het
Plod2	G	T	9: 92,466,574 (GRCm39)	R178L	probably benign	Het
Polr3b	T	A	10: 84,554,339 (GRCm39)	L1017Q	probably benign	Het
Postn	C	A	3: 54,291,971 (GRCm39)	T724N	probably damaging	Het
Ppm1l	T	G	3: 69,225,309 (GRCm39)		probably benign	Het
Prpf8	T	G	11: 75,396,075 (GRCm39)	L1983R	probably damaging	Het
Psma7	A	G	2: 179,681,193 (GRCm39)	V59A	probably benign	Het
Qser1	T	A	2: 104,619,306 (GRCm39)	Y502F	probably benign	Het
Rad50	T	C	11: 53,558,852 (GRCm39)	D1129G	probably damaging	Het
Rasal1	C	A	5: 120,812,794 (GRCm39)	P606Q	probably damaging	Het
Rgs6	A	G	12: 83,180,463 (GRCm39)	Y438C	probably damaging	Het
Rnf180	A	G	13: 105,388,774 (GRCm39)	C73R	probably benign	Het
Rnf216	T	A	5: 143,065,996 (GRCm39)	I474F	possibly damaging	Het
Sdha	A	T	13: 74,480,366 (GRCm39)	L371Q	probably damaging	Het
Sdk1	T	G	5: 142,070,321 (GRCm39)	L1162R	possibly damaging	Het
Sh3rf2	T	C	18: 42,237,146 (GRCm39)	I223T	probably damaging	Het
Sirpb1a	A	G	3: 15,475,587 (GRCm39)	V316A	probably damaging	Het
Slc12a4	A	T	8: 106,672,021 (GRCm39)	I897N	probably benign	Het
Slc35d1	A	T	4: 103,048,035 (GRCm39)	V243E	probably damaging	Het
Slc4a11	T	A	2: 130,532,852 (GRCm39)	K200N	possibly damaging	Het
Slc9a8	T	A	2: 167,293,216 (GRCm39)	M188K	probably damaging	Het
Slco1a8	T	A	6: 141,918,137 (GRCm39)	I580F	possibly damaging	Het
Snrnp200	T	C	2: 127,074,902 (GRCm39)	S1492P	probably damaging	Het
Sphk2	T	C	7: 45,360,149 (GRCm39)	*618W	probably null	Het
Sytl2	T	C	7: 90,052,228 (GRCm39)		probably benign	Het
Tdpoz3	A	G	3: 93,734,231 (GRCm39)	N302S	probably benign	Het
Tdrd6	T	C	17: 43,935,199 (GRCm39)	M1950V	probably benign	Het
Tmem39a	A	G	16: 38,384,675 (GRCm39)		probably benign	Het
Trip4	A	T	9: 65,765,640 (GRCm39)	I353K	probably damaging	Het
Trip6	A	T	5: 137,311,103 (GRCm39)	F204L	probably benign	Het
Trpm4	T	A	7: 44,968,677 (GRCm39)	I419F	possibly damaging	Het
Ttn	C	A	2: 76,775,140 (GRCm39)	E1967D	probably damaging	Het
Uba2	C	T	7: 33,850,281 (GRCm39)	V391M	possibly damaging	Het
Ubr4	T	G	4: 139,206,746 (GRCm39)		probably benign	Het
Vmn1r228	A	C	17: 20,996,858 (GRCm39)	V220G	possibly damaging	Het
Vmn2r79	A	G	7: 86,652,594 (GRCm39)	M429V	probably benign	Het
Vps36	C	T	8: 22,700,472 (GRCm39)	T210I	possibly damaging	Het
Wdr17	C	T	8: 55,146,131 (GRCm39)	A90T	possibly damaging	Het
Ybx1	C	T	4: 119,138,788 (GRCm39)	G126D	probably benign	Het
Yipf5	C	A	18: 40,339,460 (GRCm39)		probably benign	Het
Zbtb47	A	G	9: 121,596,641 (GRCm39)	T666A	probably benign	Het
Zdhhc5	A	C	2: 84,520,459 (GRCm39)	S573A	probably benign	Het
Zfp457	A	T	13: 67,441,991 (GRCm39)	C99S	probably damaging	Het
Zfp52	T	A	17: 21,781,564 (GRCm39)	C471S	probably damaging	Het
Zfp558	C	T	9: 18,379,252 (GRCm39)	V71I	probably damaging	Het
Zfp655	A	G	5: 145,181,267 (GRCm39)	Y375C	probably damaging	Het
Zfp882	A	T	8: 72,668,459 (GRCm39)	T429S	probably benign	Het
Zmym2	T	C	14: 57,187,141 (GRCm39)		probably null	Het

Other mutations in Upf1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01113:Upf1	APN	8	70,790,934 (GRCm39)	missense	probably benign
IGL01890:Upf1	APN	8	70,786,880 (GRCm39)	missense	possibly damaging	0.94
IGL02534:Upf1	APN	8	70,788,302 (GRCm39)	critical splice donor site	probably null
IGL03142:Upf1	APN	8	70,785,977 (GRCm39)	missense	probably benign	0.04
IGL03151:Upf1	APN	8	70,788,037 (GRCm39)	missense	probably damaging	0.98
Nanosphere	UTSW	8	70,796,912 (GRCm39)	missense	probably benign	0.01
Particulate	UTSW	8	70,789,675 (GRCm39)	missense	probably damaging	0.96
R0477:Upf1	UTSW	8	70,786,730 (GRCm39)	missense	probably benign
R0755:Upf1	UTSW	8	70,786,779 (GRCm39)	missense	probably benign	0.01
R1018:Upf1	UTSW	8	70,791,556 (GRCm39)	missense	possibly damaging	0.85
R1067:Upf1	UTSW	8	70,791,053 (GRCm39)	missense	probably damaging	0.98
R1445:Upf1	UTSW	8	70,794,174 (GRCm39)	missense	probably benign	0.00
R1458:Upf1	UTSW	8	70,796,904 (GRCm39)	missense	probably benign	0.00
R1511:Upf1	UTSW	8	70,791,155 (GRCm39)	missense	probably damaging	0.99
R1552:Upf1	UTSW	8	70,785,709 (GRCm39)	nonsense	probably null
R1560:Upf1	UTSW	8	70,791,092 (GRCm39)	missense	probably damaging	1.00
R1562:Upf1	UTSW	8	70,796,017 (GRCm39)	nonsense	probably null
R2082:Upf1	UTSW	8	70,794,222 (GRCm39)	missense	probably damaging	1.00
R2143:Upf1	UTSW	8	70,792,004 (GRCm39)	missense	probably null	1.00
R2423:Upf1	UTSW	8	70,791,110 (GRCm39)	missense	probably damaging	1.00
R2425:Upf1	UTSW	8	70,791,110 (GRCm39)	missense	probably damaging	1.00
R3031:Upf1	UTSW	8	70,791,110 (GRCm39)	missense	probably damaging	1.00
R3032:Upf1	UTSW	8	70,791,110 (GRCm39)	missense	probably damaging	1.00
R3123:Upf1	UTSW	8	70,790,133 (GRCm39)	splice site	probably benign
R3508:Upf1	UTSW	8	70,791,110 (GRCm39)	missense	probably damaging	1.00
R3747:Upf1	UTSW	8	70,786,000 (GRCm39)	missense	possibly damaging	0.75
R3748:Upf1	UTSW	8	70,786,000 (GRCm39)	missense	possibly damaging	0.75
R3750:Upf1	UTSW	8	70,786,000 (GRCm39)	missense	possibly damaging	0.75
R3754:Upf1	UTSW	8	70,792,464 (GRCm39)	missense	probably benign	0.30
R3964:Upf1	UTSW	8	70,791,110 (GRCm39)	missense	probably damaging	1.00
R3965:Upf1	UTSW	8	70,791,110 (GRCm39)	missense	probably damaging	1.00
R4152:Upf1	UTSW	8	70,791,110 (GRCm39)	missense	probably damaging	1.00
R4505:Upf1	UTSW	8	70,790,216 (GRCm39)	missense	probably damaging	1.00
R4506:Upf1	UTSW	8	70,790,216 (GRCm39)	missense	probably damaging	1.00
R4838:Upf1	UTSW	8	70,792,018 (GRCm39)	missense	probably benign	0.03
R5001:Upf1	UTSW	8	70,787,350 (GRCm39)	missense	probably damaging	1.00
R5715:Upf1	UTSW	8	70,805,628 (GRCm39)	missense	probably damaging	0.96
R5748:Upf1	UTSW	8	70,791,167 (GRCm39)	missense	probably damaging	1.00
R5856:Upf1	UTSW	8	70,787,412 (GRCm39)	critical splice acceptor site	probably null
R5930:Upf1	UTSW	8	70,796,912 (GRCm39)	missense	probably benign	0.01
R6010:Upf1	UTSW	8	70,789,675 (GRCm39)	missense	probably damaging	0.96
R6056:Upf1	UTSW	8	70,785,687 (GRCm39)	missense	probably damaging	0.98
R6870:Upf1	UTSW	8	70,794,211 (GRCm39)	missense	probably benign	0.11
R7205:Upf1	UTSW	8	70,792,695 (GRCm39)	missense	possibly damaging	0.94
R7385:Upf1	UTSW	8	70,793,268 (GRCm39)	missense	probably damaging	1.00
R7464:Upf1	UTSW	8	70,786,073 (GRCm39)	missense	probably benign
R7759:Upf1	UTSW	8	70,786,730 (GRCm39)	missense	probably benign
R7783:Upf1	UTSW	8	70,805,508 (GRCm39)	missense	probably benign	0.11
R8079:Upf1	UTSW	8	70,791,534 (GRCm39)	critical splice donor site	probably null
R8192:Upf1	UTSW	8	70,793,294 (GRCm39)	missense	probably benign	0.03
R8544:Upf1	UTSW	8	70,789,702 (GRCm39)	missense	probably damaging	1.00
R8738:Upf1	UTSW	8	70,785,973 (GRCm39)	missense	probably benign	0.06
R8738:Upf1	UTSW	8	70,785,972 (GRCm39)	missense	probably benign	0.01
R8826:Upf1	UTSW	8	70,790,930 (GRCm39)	missense	probably benign
R8876:Upf1	UTSW	8	70,796,918 (GRCm39)	missense	possibly damaging	0.92
R8906:Upf1	UTSW	8	70,786,815 (GRCm39)	nonsense	probably null
R8911:Upf1	UTSW	8	70,791,087 (GRCm39)	missense	possibly damaging	0.53
R9163:Upf1	UTSW	8	70,792,674 (GRCm39)	missense	probably benign
R9425:Upf1	UTSW	8	70,792,003 (GRCm39)	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