Mutagenetix > Incidental Mutation

Incidental Mutation 'R8826:Upf1'

673459

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

068729-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.973) question?

Stock #

R8826 (G1)

Quality Score

222.009

Status

Validated

Chromosome

Chromosomal Location

70331525-70353278 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 70338280 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 590 (T590A)

Ref Sequence

ENSEMBL: ENSMUSP00000075089 (fasta)

Gene Model

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

AlphaFold

Q9EPU0

Predicted Effect

probably benign
Transcript: ENSMUST00000075666
AA Change: T590A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: T590A

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: T579A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

Validation Efficiency

100% (91/91)

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: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acta1	T	C	8: 123,893,239	M121V	probably damaging	Het
AF529169	T	A	9: 89,601,181	E721V	probably damaging	Het
AI987944	A	T	7: 41,375,203	H120Q	possibly damaging	Het
Aldh9a1	C	G	1: 167,356,550	P205A	probably damaging	Het
Ank2	A	T	3: 126,947,302	N1644K	unknown	Het
Arfgef2	A	T	2: 166,835,466		probably benign	Het
Bpifb4	G	T	2: 153,941,897	V54L	probably benign	Het
Cacna1c	T	A	6: 118,734,875	M456L		Het
Cbln1	T	C	8: 87,471,792	N95S	probably benign	Het
Ccl11	G	T	11: 82,062,218	R67S	possibly damaging	Het
Cd200	G	A	16: 45,394,794	R165C	probably benign	Het
Cd2bp2	A	T	7: 127,194,085	M283K	probably damaging	Het
Cd86	G	T	16: 36,615,288	L256I	possibly damaging	Het
Ces2f	T	A	8: 104,953,102	F409Y	probably benign	Het
Cisd3	A	T	11: 97,688,332	Q100L	probably damaging	Het
Cntnap1	C	T	11: 101,186,829	R1106C	probably damaging	Het
Col6a2	A	T	10: 76,603,599	M777K	probably damaging	Het
Cp	A	G	3: 19,985,575	Y852C	probably damaging	Het
D3Ertd254e	T	C	3: 36,164,106	Y93H	possibly damaging	Het
Ddx1	T	C	12: 13,227,331	E523G	probably damaging	Het
Ddx60	T	A	8: 61,945,956	D236E	probably benign	Het
Dgcr14	A	T	16: 17,905,090	M320K	probably damaging	Het
Dnah9	A	T	11: 65,849,916	F4148Y	probably benign	Het
Dusp6	G	T	10: 99,263,607		probably benign	Het
Eif2a	C	A	3: 58,548,628	Y349*	probably null	Het
Enpep	G	A	3: 129,271,418	T874I	probably damaging	Het
Eps15	A	G	4: 109,312,308	D105G	possibly damaging	Het
Exosc10	G	A	4: 148,568,702		probably null	Het
Fam13b	A	T	18: 34,498,017	N36K	probably damaging	Het
Fanca	T	C	8: 123,268,470	D1431G	probably benign	Het
Fgg	A	G	3: 83,014,318	D436G	probably benign	Het
Fip1l1	C	T	5: 74,564,527	T251I	probably benign	Het
Galnt2	A	G	8: 124,305,608	N104S	probably damaging	Het
Gm4869	A	G	5: 140,469,679	M347V	probably damaging	Het
Gmip	T	C	8: 69,816,098	S458P	possibly damaging	Het
Herc2	A	G	7: 56,106,396	D728G	probably benign	Het
Hif3a	A	G	7: 17,054,746	L100P	probably damaging	Het
Hmox2	C	G	16: 4,766,002	P282R	possibly damaging	Het
Hook1	A	T	4: 95,992,195	H90L	probably benign	Het
Igf2bp2	C	A	16: 22,065,116	G473C	probably damaging	Het
Ip6k2	T	C	9: 108,798,180		probably null	Het
Ipo5	G	T	14: 120,919,954	R68L	probably damaging	Het
Klhdc1	G	T	12: 69,258,618	W234L	probably damaging	Het
Krt8	A	G	15: 102,001,435	V178A	possibly damaging	Het
Lgi3	T	A	14: 70,531,272		probably null	Het
Litaf	T	G	16: 10,966,557	N30H	probably benign	Het
Lman2	C	A	13: 55,362,555	W12L	unknown	Het
Macf1	A	G	4: 123,382,229	L6182P	probably damaging	Het
Magi3	A	T	3: 104,085,346	M270K	probably benign	Het
Mapre2	A	T	18: 23,753,831		probably benign	Het
Mllt10	T	A	2: 18,162,542	V426D	probably benign	Het
Mrgprf	A	G	7: 145,308,309	I203V	probably benign	Het
Mrnip	G	A	11: 50,176,861	C27Y	probably damaging	Het
Mrpl24	C	T	3: 87,922,394	R96*	probably null	Het
Nbas	T	A	12: 13,352,874		probably benign	Het
Nipal4	G	A	11: 46,154,643	T131M	possibly damaging	Het
Nlrp12	T	C	7: 3,240,991	D297G	possibly damaging	Het
Nol6	A	C	4: 41,121,823	M237R	probably benign	Het
Olfr348	T	A	2: 36,786,843	L106*	probably null	Het
Olig1	A	G	16: 91,270,139	E88G	probably benign	Het
Parg	A	G	14: 32,209,218	D265G	possibly damaging	Het
Pcdhgb8	A	T	18: 37,762,248	I124L	probably damaging	Het
Pign	A	G	1: 105,554,102	F822L	probably damaging	Het
Plch2	T	C	4: 154,986,683	T1080A	probably benign	Het
Pld4	A	T	12: 112,766,776	Y262F	possibly damaging	Het
Ppp1r12b	A	G	1: 134,765,992	V977A	probably benign	Het
Ppp6r3	C	T	19: 3,471,984	E565K		Het
Psmg2	A	G	18: 67,654,088		probably benign	Het
Ptcd3	C	T	6: 71,908,661	G27D	probably benign	Het
Retreg2	G	T	1: 75,142,881	G7C	unknown	Het
Rlbp1	A	T	7: 79,377,366	F182Y	probably benign	Het
Rnf148	G	C	6: 23,654,379	S206C	probably benign	Het
Sash1	A	G	10: 8,762,105	M1T	probably null	Het
Shank3	A	T	15: 89,549,395	T1448S	probably damaging	Het
Sipa1l1	A	G	12: 82,342,433	K478E	probably damaging	Het
Slitrk6	A	G	14: 110,751,369	I302T	probably benign	Het
Smc1b	A	G	15: 85,066,328	V1165A	probably damaging	Het
Sncaip	A	T	18: 52,915,309	H939L	probably benign	Het
Stn1	T	C	19: 47,536,270	D27G	probably damaging	Het
Sugct	T	G	13: 17,252,595		probably null	Het
Tmem259	A	G	10: 79,979,149	S214P	probably damaging	Het
Trdv4	G	A	14: 54,075,489	G107S	probably damaging	Het
Ttc3	C	T	16: 94,431,970	L957F	possibly damaging	Het
Ttn	A	G	2: 76,881,127	Y8357H	unknown	Het
Twnk	T	C	19: 45,007,995	V289A	probably benign	Het
Umodl1	A	G	17: 30,983,984	D437G	possibly damaging	Het
Vmn2r63	A	T	7: 42,927,017	D457E	probably benign	Het
Wdr82	A	T	9: 106,184,776	T213S	probably benign	Het
Zfp672	A	T	11: 58,329,764	M3K	unknown	Het
Zfyve26	A	G	12: 79,238,968	V2345A	probably benign	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
R1511:Upf1	UTSW	8	70338505	missense	probably damaging	0.99
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
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'- AGACATGCTACCAGGCTTCTG -3'
(R):5'- ATCCACCAGACAGGACTGAAGG -3'

Sequencing Primer
(F):5'- GGCTTCTGACTCGAACAGAC -3'
(R):5'- ACTGAAGGTCGTACGCCTCTG -3'

Posted On

2021-07-15