Mutagenetix > Incidental Mutation

Incidental Mutation 'R8911:Upf1'

678625

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

Accession Numbers

Essential gene?

Probably essential (E-score: 0.970) question?

Stock #

R8911 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

70331525-70353278 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 70338437 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 563 (S563T)

Ref Sequence

ENSEMBL: ENSMUSP00000075089 (fasta)

Gene Model

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

AlphaFold

Q9EPU0

Predicted Effect

possibly damaging
Transcript: ENSMUST00000075666
AA Change: S563T

PolyPhen 2 Score 0.527 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: S563T

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: S552T

PolyPhen 2 Score 0.147 (Sensitivity: 0.92; Specificity: 0.87)

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

100% (76/76)

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210408I21Rik	A	T	13: 77,281,115	I774F	probably benign	Het
3425401B19Rik	A	T	14: 32,661,669	C780S	possibly damaging	Het
Abca12	T	C	1: 71,341,531	D306G	probably benign	Het
Adgrl2	T	C	3: 148,852,527		probably benign	Het
Agt	T	C	8: 124,564,445	Y41C	probably benign	Het
Alx3	G	T	3: 107,604,287	R204L	probably damaging	Het
Arih2	C	G	9: 108,611,739	R260P	probably damaging	Het
Bcl11a	C	T	11: 24,164,763	P702L	probably damaging	Het
Bpifa2	A	G	2: 154,009,170	N17S	probably benign	Het
Cabcoco1	T	C	10: 68,541,754	D35G	probably benign	Het
Cd69	T	C	6: 129,275,224	K21R	probably benign	Het
Cntn4	T	C	6: 106,353,782		probably null	Het
Cntnap5c	A	C	17: 58,199,048	N689T	probably damaging	Het
Cog5	A	G	12: 31,833,239	Y389C	probably damaging	Het
Col5a1	T	C	2: 27,997,618		probably null	Het
Coro1b	G	A	19: 4,150,804	R245Q	probably damaging	Het
Csmd1	T	C	8: 16,698,003	D244G	probably damaging	Het
Ctcfl	C	T	2: 173,095,328		probably null	Het
Dpy19l4	G	A	4: 11,317,078	P40L	possibly damaging	Het
Dsg4	C	A	18: 20,451,872	Y214*	probably null	Het
Eapp	A	T	12: 54,692,655		probably benign	Het
Fmo6	T	C	1: 162,920,545	T317A	possibly damaging	Het
Gm11595	A	G	11: 99,772,738	C39R	unknown	Het
Gm281	T	C	14: 13,823,796		probably null	Het
Golim4	T	C	3: 75,906,396		probably benign	Het
Greb1	G	A	12: 16,690,902	S1393L	possibly damaging	Het
Guca1b	A	G	17: 47,389,119	I73V	probably benign	Het
Hdac7	C	T	15: 97,796,908	V796I	possibly damaging	Het
Hectd1	A	G	12: 51,748,833	I2271T	probably damaging	Het
Heg1	T	G	16: 33,738,257	Y1066*	probably null	Het
Helz2	C	A	2: 181,238,380	K514N		Het
Ice1	C	T	13: 70,592,668	R70Q		Het
Il18rap	C	T	1: 40,543,017	T366M	probably benign	Het
Itgae	A	G	11: 73,113,621	T245A	probably damaging	Het
Jhy	G	A	9: 40,911,157	Q562*	probably null	Het
Khnyn	A	G	14: 55,887,278	R330G	probably benign	Het
Lamc2	A	T	1: 153,152,127	C184S	probably damaging	Het
Lhx5	T	A	5: 120,436,444	L271*	probably null	Het
Magel2	G	A	7: 62,379,789	V814M	unknown	Het
Manf	A	G	9: 106,890,262	I85T	possibly damaging	Het
Mgmt	A	G	7: 137,128,065	T203A	probably benign	Het
Mmp9	C	T	2: 164,952,648	S520F	possibly damaging	Het
Myrip	A	G	9: 120,441,418	E578G	possibly damaging	Het
Naaladl2	A	G	3: 23,846,593	M691T	probably damaging	Het
Ncln	C	T	10: 81,487,685	V51I	probably benign	Het
Olfr1217	T	C	2: 89,023,950	N18D	probably benign	Het
Olfr1222	T	C	2: 89,125,264	I156V	probably benign	Het
Olfr136	A	T	17: 38,335,429	T91S	possibly damaging	Het
Pcdhga12	A	T	18: 37,767,065	M317L	possibly damaging	Het
Pcnt	T	G	10: 76,387,525	K1941T	probably damaging	Het
Pde4dip	A	T	3: 97,743,601	M896K	probably benign	Het
Pfkfb3	A	T	2: 11,482,443		probably null	Het
Pik3cb	A	G	9: 99,064,148	S542P	probably benign	Het
Pik3cg	A	G	12: 32,197,258	V822A	probably benign	Het
Plcl2	G	T	17: 50,608,113	G717C	probably damaging	Het
Ptprs	C	T	17: 56,423,320	A1185T	probably benign	Het
Ptpru	T	A	4: 131,776,249	I1157F	probably damaging	Het
Rbbp6	A	G	7: 122,992,045	T457A	possibly damaging	Het
Rdh16f2	A	G	10: 127,876,943	E270G	probably damaging	Het
Rrp15	C	T	1: 186,721,444	E269K	unknown	Het
Sec23b	T	C	2: 144,559,396	V59A	probably benign	Het
Slc22a21	A	T	11: 53,955,983		probably null	Het
Sp5	C	A	2: 70,476,618	P216T	probably benign	Het
Synj1	A	T	16: 90,978,734	D385E	probably damaging	Het
Trim37	C	T	11: 87,206,803	S808F	possibly damaging	Het
Tsks	A	T	7: 44,943,270		probably benign	Het
Upf2	A	G	2: 5,983,082	D580G	unknown	Het
Usp14	A	G	18: 9,996,194	I462T	probably damaging	Het
Usp48	G	A	4: 137,613,685	G332E	probably benign	Het
Vmn1r184	C	G	7: 26,266,885	Q19E	possibly damaging	Het
Vps50	C	A	6: 3,516,710	A64E	probably benign	Het
Zc3h11a	T	A	1: 133,638,601	N211I	probably damaging	Het
Zfp518a	A	C	19: 40,913,426	K600Q	possibly damaging	Het
Zfp729a	A	T	13: 67,619,942	S723T	probably benign	Het
Zmynd12	A	T	4: 119,437,089	I88F	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
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
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
R9163:Upf1	UTSW	8	70340024	missense	probably benign
R9425:Upf1	UTSW	8	70339353	missense	probably benign	0.06

Predicted Primers

PCR Primer
(F):5'- ATCTGCAGATGACAGCTCGC -3'
(R):5'- CATGGCTGTACCTGCCTATTACAG -3'

Sequencing Primer
(F):5'- AGCTCGCCTGTCTCATCCTTTAG -3'
(R):5'- TGCCTATTACAGCTGTGCAG -3'

Posted On

2021-08-02