Mutagenetix > Incidental Mutation

Incidental Mutation 'R3032:Upf1'

264753

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

040548-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.972) question?

Stock #

R3032 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

70784175-70805928 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 70791110 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Histidine at position 544 (R544H)

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: R555H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: R555H

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: R544H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

Meta Mutation Damage Score

0.8963

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.1%

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: 15 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acox2	A	T	14: 8,253,466 (GRCm38)	L227Q	probably damaging	Het
Ddx41	G	A	13: 55,682,293 (GRCm39)	R205W	possibly damaging	Het
Dpysl4	A	G	7: 138,676,152 (GRCm39)	N315D	probably benign	Het
Eps8	A	T	6: 137,489,175 (GRCm39)	S408T	probably damaging	Het
F13b	A	C	1: 139,445,071 (GRCm39)	T574P	probably damaging	Het
Fgfrl1	A	G	5: 108,853,926 (GRCm39)	I344M	probably benign	Het
Or5b21	G	A	19: 12,839,282 (GRCm39)	V48I	probably benign	Het
Park7	T	C	4: 150,985,509 (GRCm39)	K122R	probably benign	Het
Psg18	G	A	7: 18,084,904 (GRCm39)	S64L	probably benign	Het
Rhbdf1	T	C	11: 32,159,985 (GRCm39)	D172G	probably damaging	Het
Serpinb6b	G	A	13: 33,152,551 (GRCm39)	G20D	possibly damaging	Het
Sorcs1	G	A	19: 50,213,613 (GRCm39)	R705C	probably damaging	Het
Syt14	A	T	1: 192,669,059 (GRCm39)	Y65N	possibly damaging	Het
Tll1	T	C	8: 64,551,526 (GRCm39)	N285S	probably damaging	Het
Umodl1	G	A	17: 31,208,502 (GRCm39)	R849Q	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
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'- ATCTGCAGATGACAGCTCGC -3'
(R):5'- CATGGCTGTACCTGCCTATTAC -3'

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

Posted On

2015-02-05