Mutagenetix > Incidental Mutation

Incidental Mutation 'R1511:Upf1'

168320

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

039558-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.973) question?

Stock #

R1511 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

70331525-70353278 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 70338505 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 529 (I529T)

Ref Sequence

ENSEMBL: ENSMUSP00000148927 (fasta)

Gene Model

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

AlphaFold

Q9EPU0

Predicted Effect

probably damaging
Transcript: ENSMUST00000075666
AA Change: I540T

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: I540T

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: I529T

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

Coding Region Coverage

1x: 99.0%
3x: 98.0%
10x: 95.4%
20x: 89.7%

Validation Efficiency

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: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aacs	C	A	5: 125,514,977	N576K	probably benign	Het
Abca5	G	T	11: 110,299,978	L769M	probably damaging	Het
Abca5	T	A	11: 110,299,986	H766L	possibly damaging	Het
Acvr1c	A	G	2: 58,287,884	I191T	probably damaging	Het
Agps	A	T	2: 75,866,779	E314D	probably damaging	Het
Agxt	G	A	1: 93,135,768	G131R	probably damaging	Het
Ak8	A	G	2: 28,742,746	T326A	probably benign	Het
Aldoart2	T	A	12: 55,566,277	I329N	probably benign	Het
Apaf1	T	C	10: 91,060,185	I342V	possibly damaging	Het
Arhgap40	T	C	2: 158,527,161	S68P	probably benign	Het
Arsi	G	A	18: 60,916,651	G202E	probably benign	Het
AU022252	C	T	4: 119,228,097	R71Q	possibly damaging	Het
Baz1b	T	C	5: 135,217,782	L695P	probably damaging	Het
Baz2b	A	T	2: 59,962,024	S587T	probably benign	Het
Cep76	T	C	18: 67,624,958	M421V	probably benign	Het
Clk2	A	G	3: 89,168,703	D60G	probably damaging	Het
Clstn3	G	T	6: 124,462,169	T6K	probably damaging	Het
Cluap1	T	A	16: 3,919,558	D180E	probably benign	Het
Col12a1	T	C	9: 79,699,552	I530V	probably benign	Het
Cpt1a	T	C	19: 3,365,788		probably benign	Het
Cr2	T	G	1: 195,155,272	K797Q	possibly damaging	Het
Crybg3	C	A	16: 59,554,112	V2260L	probably benign	Het
Csnk1a1	T	A	18: 61,585,250		probably benign	Het
Cxcr1	T	C	1: 74,192,770	D31G	probably benign	Het
Cyp2a5	G	T	7: 26,835,936	D108Y	probably damaging	Het
Dnajc1	A	G	2: 18,222,727	V376A	possibly damaging	Het
Eif4enif1	T	C	11: 3,236,278	V462A	probably benign	Het
Elmo1	A	G	13: 20,290,477	K357R	possibly damaging	Het
Eml6	T	A	11: 29,818,374	H771L	probably damaging	Het
Epb41l4a	A	G	18: 33,832,664	I370T	probably benign	Het
Esp36	A	T	17: 38,417,281	N79K	possibly damaging	Het
Fam229b	A	G	10: 39,118,919	*81Q	probably null	Het
Fat4	T	C	3: 38,983,076	Y3626H	probably damaging	Het
Fbn1	A	T	2: 125,306,285	F2681Y	probably benign	Het
Gad1-ps	A	G	10: 99,445,469		noncoding transcript	Het
Galm	C	A	17: 80,183,267	N284K	probably damaging	Het
Gtf3c2	A	T	5: 31,159,102	S735T	probably benign	Het
Hsph1	A	T	5: 149,630,383	S207T	probably benign	Het
Il33	C	T	19: 29,955,215	R159C	probably damaging	Het
Invs	A	G	4: 48,382,148	N106S	possibly damaging	Het
Kif21b	G	T	1: 136,169,324		probably null	Het
Kirrel2	A	G	7: 30,456,498	C42R	probably damaging	Het
Letm1	A	C	5: 33,752,555	C378W	probably damaging	Het
Lrrc71	T	A	3: 87,745,484	K160N	probably benign	Het
Lrrtm3	A	G	10: 64,089,025	I121T	probably damaging	Het
Lztr1	T	A	16: 17,509,670	V79E	probably damaging	Het
Mmp8	T	G	9: 7,566,278	D378E	probably damaging	Het
Mpzl3	A	G	9: 45,066,529	E145G	probably damaging	Het
Mrps2	C	T	2: 28,469,664	L178F	probably damaging	Het
Mzb1	A	G	18: 35,647,822		probably null	Het
Nckap1	T	C	2: 80,553,415	D135G	probably damaging	Het
Ndst1	A	G	18: 60,697,170	F623L	possibly damaging	Het
Nlrp5	A	T	7: 23,413,347	D143V	probably damaging	Het
Olfr1225	A	G	2: 89,170,937	S92P	probably damaging	Het
Olfr1241	T	C	2: 89,482,248	M296V	probably null	Het
Olfr1311	A	G	2: 112,021,404	V150A	probably benign	Het
Olfr146	T	C	9: 39,019,025	D172G	probably benign	Het
Olfr307	T	C	7: 86,336,345	D17G	possibly damaging	Het
Olfr32	A	G	2: 90,138,404	V245A	probably benign	Het
Olfr548-ps1	T	C	7: 102,542,125	L63P	probably damaging	Het
Olfr907	A	G	9: 38,498,818	I50V	probably benign	Het
Parp14	T	G	16: 35,857,224	E791D	probably benign	Het
Pcdh8	C	T	14: 79,769,389	R578H	possibly damaging	Het
Phrf1	T	A	7: 141,259,801		probably benign	Het
Polr3b	C	A	10: 84,680,385	H626N	probably benign	Het
Ppp1r12a	A	G	10: 108,251,859	T58A	probably benign	Het
Ppp4r3b	T	A	11: 29,182,460	V33D	probably damaging	Het
Ppp5c	A	G	7: 17,009,982	Y176H	probably damaging	Het
R3hdm1	A	G	1: 128,197,005	Y343C	probably damaging	Het
Rabac1	C	T	7: 24,972,130	V122M	probably damaging	Het
Rasef	G	T	4: 73,735,748	Q561K	probably damaging	Het
Rbl1	A	G	2: 157,195,634	S198P	probably damaging	Het
Rbm12	A	T	2: 156,097,536	M272K	probably damaging	Het
Rexo1	T	G	10: 80,550,050	K391N	possibly damaging	Het
Rnf43	T	C	11: 87,731,347	S384P	probably benign	Het
Rpsa	A	T	9: 120,131,000	I210F	possibly damaging	Het
Rslcan18	A	G	13: 67,098,952	Y75H	possibly damaging	Het
Scn9a	T	A	2: 66,526,813	D1048V	probably benign	Het
Sec11a	T	C	7: 80,927,734		probably null	Het
Sidt2	A	G	9: 45,950,089	V19A	probably damaging	Het
Snx14	G	A	9: 88,398,364	Q522*	probably null	Het
Stx1b	A	G	7: 127,814,972	L74S	probably damaging	Het
Tm7sf3	A	T	6: 146,609,878	M371K	probably benign	Het
Tmem115	T	C	9: 107,534,975	V166A	probably benign	Het
Traf5	T	A	1: 191,999,951	T310S	probably benign	Het
Trdn	A	G	10: 33,466,452	K619E	probably benign	Het
Trmt10a	T	A	3: 138,152,184		probably null	Het
Txk	A	C	5: 72,707,671	I287R	probably damaging	Het
Txndc16	T	C	14: 45,151,887	D452G	probably damaging	Het
Ube2f	G	A	1: 91,262,301		probably null	Het
Ubtfl1	T	G	9: 18,410,193	I339R	probably benign	Het
Vmn1r197	A	G	13: 22,328,653	D248G	possibly damaging	Het
Vmn1r5	A	T	6: 56,985,786	T149S	probably benign	Het
Vmn1r83	C	T	7: 12,321,270	V287I	possibly damaging	Het
Vmn2r118	G	A	17: 55,608,496	R485*	probably null	Het
Vmn2r-ps130	A	G	17: 23,063,801	T152A	probably benign	Het
Vps13b	T	C	15: 35,839,975	F2448L	probably damaging	Het
Vps13b	A	G	15: 35,841,573	N2583S	probably benign	Het
Wscd1	C	T	11: 71,788,675	P458L	probably damaging	Het
Xylt2	T	A	11: 94,670,433	D168V	probably damaging	Het
Zdhhc2	A	G	8: 40,467,972	T306A	probably benign	Het
Zfp804b	A	T	5: 6,769,771	D1097E	possibly damaging	Het
Zfp93	T	A	7: 24,275,731	C380*	probably null	Het
Zfp960	T	A	17: 17,088,256	C411S	probably damaging	Het
Zmynd15	T	A	11: 70,464,793	V430E	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
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
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'- TGCTACCAGGCTTCTGACTCGAAC -3'
(R):5'- GGCATGGCTGTACCTGCCTATTAC -3'

Sequencing Primer
(F):5'- ACCATGAGAAGTTCTCTCTCAG -3'
(R):5'- ATGCTGACAGCCTATTCCAC -3'

Posted On

2014-04-13