Mutagenetix > Incidental Mutation

Incidental Mutation 'R5930:Upf1'

460177

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

044125-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.972) question?

Stock #

R5930 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

70784175-70805928 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 70796912 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 107 (T107I)

Ref Sequence

ENSEMBL: ENSMUSP00000148927 (fasta)

Gene Model

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

AlphaFold

Q9EPU0

Predicted Effect

probably benign
Transcript: ENSMUST00000075666
AA Change: T107I

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: T107I

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: ENSMUST00000215817
AA Change: T107I

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)

Meta Mutation Damage Score

0.0928

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.1%
20x: 94.5%

Validation Efficiency

94% (102/109)

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: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrv1	C	T	13: 81,545,570 (GRCm39)	V5572I	probably benign	Het
Agap1	C	T	1: 89,770,818 (GRCm39)	T656I	probably damaging	Het
Als2cl	C	T	9: 110,716,432 (GRCm39)	R247W	probably damaging	Het
Ankfy1	A	T	11: 72,603,071 (GRCm39)	R33S	probably benign	Het
Ano5	T	C	7: 51,235,079 (GRCm39)	F671L	probably damaging	Het
Arhgap26	A	G	18: 39,283,145 (GRCm39)	M361V	probably damaging	Het
Bckdk	A	G	7: 127,505,145 (GRCm39)	E175G	probably damaging	Het
Bptf	G	T	11: 106,964,022 (GRCm39)	T1724K	probably damaging	Het
Btn2a2	T	A	13: 23,670,398 (GRCm39)	I112F	probably damaging	Het
Cln8	T	A	8: 14,946,621 (GRCm39)	W212R	probably damaging	Het
Cnbd1	T	C	4: 18,886,119 (GRCm39)	E300G	probably benign	Het
Cnksr3	T	C	10: 7,092,993 (GRCm39)	I173V	probably benign	Het
Cntn2	T	A	1: 132,451,170 (GRCm39)	D484V	probably damaging	Het
Cyp4a14	C	A	4: 115,348,607 (GRCm39)	G319V	probably damaging	Het
Cyp4f37	G	A	17: 32,848,957 (GRCm39)	R275Q	possibly damaging	Het
Def8	C	T	8: 124,186,809 (GRCm39)		probably benign	Het
Dnaaf4	T	C	9: 72,879,280 (GRCm39)	V356A	probably damaging	Het
Dnah10	T	C	5: 124,868,855 (GRCm39)		probably null	Het
Dock6	A	G	9: 21,735,712 (GRCm39)	V1012A	probably benign	Het
Dus3l	T	A	17: 57,076,579 (GRCm39)	N586K	probably damaging	Het
Dyrk2	T	A	10: 118,696,173 (GRCm39)	I362F	probably damaging	Het
Eeig2	A	T	3: 108,887,468 (GRCm39)	S265R	probably benign	Het
Erc2	T	A	14: 27,498,815 (GRCm39)	D230E	probably damaging	Het
Fat1	A	G	8: 45,497,073 (GRCm39)	H4186R	probably benign	Het
Fbxo44	A	G	4: 148,241,052 (GRCm39)	F179S	probably damaging	Het
Fech	A	G	18: 64,611,720 (GRCm39)		probably null	Het
Fer1l5	T	A	1: 36,424,254 (GRCm39)	C289*	probably null	Het
Fhl5	T	A	4: 25,214,756 (GRCm39)	D7V	probably benign	Het
Flvcr1	G	T	1: 190,741,748 (GRCm39)	T514K	probably damaging	Het
Fmo1	A	T	1: 162,667,185 (GRCm39)		probably null	Het
Gabra6	G	A	11: 42,198,268 (GRCm39)	T384M	probably benign	Het
Gli3	A	G	13: 15,723,210 (GRCm39)	Y117C	probably damaging	Het
Gnao1	A	G	8: 94,622,873 (GRCm39)	D59G	probably benign	Het
Gria2	T	C	3: 80,614,556 (GRCm39)	I495V	possibly damaging	Het
Hnf1b	C	A	11: 83,754,811 (GRCm39)	H161Q	probably benign	Het
Itga8	T	A	2: 12,235,019 (GRCm39)	D413V	possibly damaging	Het
Itpr3	A	T	17: 27,329,895 (GRCm39)	Q1563L	possibly damaging	Het
Kctd16	A	G	18: 40,663,882 (GRCm39)	N337S	probably benign	Het
Klra4	C	T	6: 130,030,016 (GRCm39)	V190M	possibly damaging	Het
Krtap4-9	T	A	11: 99,676,462 (GRCm39)		probably benign	Het
L3mbtl1	GGCCG	GG	2: 162,809,256 (GRCm39)		probably benign	Het
Mchr1	T	C	15: 81,122,044 (GRCm39)	F265L	probably damaging	Het
Megf8	T	A	7: 25,025,866 (GRCm39)	Y83*	probably null	Het
Mettl18	A	G	1: 163,824,746 (GRCm39)	M356V	probably null	Het
Mrm1	G	A	11: 84,710,018 (GRCm39)	R61W	probably damaging	Het
Muc4	A	T	16: 32,570,523 (GRCm39)	T528S	probably benign	Het
Myef2	A	T	2: 124,937,651 (GRCm39)	L530*	probably null	Het
Nhlrc4	T	C	17: 26,162,693 (GRCm39)	E18G	probably benign	Het
Nisch	C	T	14: 30,895,102 (GRCm39)	V1065I	probably benign	Het
Nlgn2	C	T	11: 69,724,975 (GRCm39)	R97H	probably damaging	Het
Nos2	T	C	11: 78,828,741 (GRCm39)	L321S	probably damaging	Het
Oaz3	T	C	3: 94,343,717 (GRCm39)	M49V	possibly damaging	Het
Olfm5	A	G	7: 103,803,362 (GRCm39)	V367A	probably damaging	Het
Omd	C	T	13: 49,743,112 (GRCm39)	P54L	possibly damaging	Het
Or10ak12	C	T	4: 118,666,575 (GRCm39)	R162H	probably benign	Het
Or11g26	C	A	14: 50,753,249 (GRCm39)	A196D	probably benign	Het
Or2g7	C	A	17: 38,378,641 (GRCm39)	A193D	probably benign	Het
Or51f23	A	T	7: 102,453,481 (GRCm39)	R265S	probably damaging	Het
Or7d10	A	G	9: 19,832,206 (GRCm39)	K234E	probably damaging	Het
Pard3b	T	A	1: 61,807,289 (GRCm39)		probably benign	Het
Pcdhb18	A	C	18: 37,624,988 (GRCm39)	I773L	possibly damaging	Het
Pde11a	T	C	2: 75,970,175 (GRCm39)		probably null	Het
Pfkfb4	A	C	9: 108,859,462 (GRCm39)		probably benign	Het
Phb2	T	G	6: 124,692,612 (GRCm39)	I260S	probably damaging	Het
Pkd1l1	G	A	11: 8,908,969 (GRCm39)	T345I	unknown	Het
Pla2g6	T	C	15: 79,187,728 (GRCm39)		probably benign	Het
Pou4f2	G	A	8: 79,163,020 (GRCm39)	S5F	unknown	Het
Ppp1r9a	A	T	6: 5,157,002 (GRCm39)		probably null	Het
Pramel5	A	G	4: 143,999,553 (GRCm39)	I178T	probably benign	Het
Prom2	C	T	2: 127,372,053 (GRCm39)	W745*	probably null	Het
Pros1	T	A	16: 62,748,424 (GRCm39)	N632K	probably damaging	Het
Rab4b	A	G	7: 26,873,927 (GRCm39)	I117T	probably benign	Het
Rbm25	T	A	12: 83,724,640 (GRCm39)	H796Q	possibly damaging	Het
Rnf151	A	T	17: 24,937,004 (GRCm39)		probably null	Het
Rps6ka1	A	T	4: 133,598,882 (GRCm39)	L97I	probably damaging	Het
Scart1	C	T	7: 139,810,359 (GRCm39)	P984S	probably benign	Het
Semp2l2a	T	A	8: 13,887,263 (GRCm39)	D276V	probably benign	Het
Sergef	T	A	7: 46,092,888 (GRCm39)	T374S	probably benign	Het
Sh3rf3	G	T	10: 58,966,808 (GRCm39)	G717C	probably damaging	Het
Slc29a4	C	T	5: 142,707,157 (GRCm39)	T500I	possibly damaging	Het
Smc1b	T	A	15: 84,970,322 (GRCm39)	D977V	probably damaging	Het
Spata31d1d	C	T	13: 59,874,829 (GRCm39)	C902Y	probably benign	Het
St14	A	T	9: 31,015,056 (GRCm39)	V314D	probably damaging	Het
Stat3	A	T	11: 100,784,496 (GRCm39)	I602N	possibly damaging	Het
Stx4a	T	A	7: 127,445,661 (GRCm39)	I189N	probably damaging	Het
Tacc1	A	G	8: 25,672,215 (GRCm39)	S338P	probably benign	Het
Tcirg1	T	A	19: 3,952,424 (GRCm39)	T315S	possibly damaging	Het
Tenm4	A	T	7: 96,503,926 (GRCm39)	N1295I	probably damaging	Het
Tm7sf3	T	C	6: 146,505,409 (GRCm39)	K516E	possibly damaging	Het
Tmem198b	T	C	10: 128,637,323 (GRCm39)	E272G	possibly damaging	Het
Tnip3	A	G	6: 65,582,937 (GRCm39)	Q237R	probably damaging	Het
Trim15	C	T	17: 37,173,252 (GRCm39)		probably null	Het
Trim30a	T	A	7: 104,070,657 (GRCm39)	N252I	possibly damaging	Het
Ttc39a	A	G	4: 109,288,075 (GRCm39)	E227G	probably benign	Het
Ttll13	A	G	7: 79,902,914 (GRCm39)	E194G	probably damaging	Het
Vac14	A	G	8: 111,436,981 (GRCm39)	I565V	probably damaging	Het
Zcchc14	A	T	8: 122,338,097 (GRCm39)		probably benign	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
R0270:Upf1	UTSW	8	70,788,295 (GRCm39)	splice site	probably benign
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
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'- ATTTAGTCAGGATCCATGCCC -3'
(R):5'- ACGGGATTCAGTAGCATAGACC -3'

Sequencing Primer
(F):5'- AGGATCCATGCCCTGCCTTG -3'
(R):5'- TTCAGTAGCATAGACCTCAGGAGTG -3'

Posted On

2017-02-28