Mutagenetix > Incidental Mutation

Incidental Mutation 'R7783:Upf1'

599384

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 #

R7783 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

70331525-70353278 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 70352858 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 46 (T46A)

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: T46A

PolyPhen 2 Score 0.107 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: T46A

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: T46A

PolyPhen 2 Score 0.143 (Sensitivity: 0.92; Specificity: 0.86)

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb9	G	T	5: 124,078,812	Y447*	probably null	Het
Abl2	T	C	1: 156,559,071	V8A	probably benign	Het
Adam33	C	T	2: 131,058,337	R103K	unknown	Het
Adamts13	G	T	2: 26,990,585	A727S	not run	Het
Alpk2	A	T	18: 65,306,254	C689*	probably null	Het
Amt	C	T	9: 108,297,215	Q60*	probably null	Het
Ankrd12	A	G	17: 66,027,250		probably null	Het
Ankrd28	A	T	14: 31,706,813	N920K	probably damaging	Het
Ankrd36	T	C	11: 5,635,359	L390P	probably damaging	Het
Arvcf	T	G	16: 18,389,198	H7Q	probably benign	Het
Asns	A	G	6: 7,677,978	S367P	probably damaging	Het
BC005537	C	T	13: 24,803,399	R7W	possibly damaging	Het
C7	T	A	15: 5,007,710	H562L	probably benign	Het
Ccdc77	T	C	6: 120,350,373	D37G	probably damaging	Het
Cdc14a	C	T	3: 116,404,587	A58T	probably damaging	Het
Cdc42bpb	C	T	12: 111,336,025		probably null	Het
Corin	A	T	5: 72,301,624	F1068L	probably benign	Het
Epb42	T	G	2: 121,034,435	K58N	probably benign	Het
Ercc3	T	A	18: 32,248,243	S371T	probably damaging	Het
Fam193a	A	C	5: 34,431,180	K358Q	probably damaging	Het
Fem1a	G	A	17: 56,257,522	C205Y	probably benign	Het
Fh1	G	A	1: 175,612,178	T233M	probably damaging	Het
Ftsj3	CCTTCTTCTTCTTCTTCT	CCTTCTTCTTCTTCT	11: 106,252,551		probably benign	Het
Gabra6	T	C	11: 42,316,462	N265S	probably damaging	Het
Gm10801	C	CGTG	2: 98,663,807		probably null	Het
Gm996	A	T	2: 25,577,808	L697Q	probably damaging	Het
Grm6	T	A	11: 50,863,082	C738S	probably damaging	Het
Gtsf1	C	T	15: 103,428,569		probably benign	Het
Hcrtr2	T	A	9: 76,232,914	Y364F	probably damaging	Het
Ick	G	T	9: 78,135,645	V51F	probably damaging	Het
Ifit1bl1	T	C	19: 34,593,936	I374V	probably benign	Het
Il31ra	A	T	13: 112,541,251	F250L	probably benign	Het
Iqgap1	A	G	7: 80,809,059	V37A	probably benign	Het
Izumo3	A	T	4: 92,145,023	I182K	probably damaging	Het
Kidins220	G	A	12: 24,988,556	A36T	probably damaging	Het
Lrrtm1	G	T	6: 77,244,253	R231L	probably damaging	Het
Micalcl	A	T	7: 112,412,976	S678C	probably damaging	Het
Mme	T	G	3: 63,364,867	F629C	probably damaging	Het
Muc5b	T	A	7: 141,857,341	H1341Q	unknown	Het
Olfr1339	T	A	4: 118,734,902	D124E	probably damaging	Het
Olfr1391	A	G	11: 49,328,202	S264G	probably benign	Het
Olfr495	A	G	7: 108,396,089	H323R	probably benign	Het
Olfr513	A	T	7: 108,755,569	T238S	probably damaging	Het
Olfr61	A	G	7: 140,637,724	T8A	possibly damaging	Het
Parm1	A	T	5: 91,593,865	M31L	probably benign	Het
Pcdhb18	G	A	18: 37,489,821	C68Y	probably benign	Het
Pkn3	A	T	2: 30,079,622	E35V	probably damaging	Het
Pla2g4a	A	T	1: 149,872,744	Y238N	probably damaging	Het
Pld6	T	C	11: 59,787,271	D122G	probably damaging	Het
Prag1	G	T	8: 36,103,255	A331S	possibly damaging	Het
Rbm44	A	G	1: 91,168,829	D970G	probably benign	Het
Rps6kc1	A	G	1: 190,773,654	V1037A	probably benign	Het
Slc12a7	T	C	13: 73,805,469	V766A	probably benign	Het
Spata18	A	G	5: 73,668,610	T87A		Het
St3gal3	T	C	4: 117,940,123	M308V	probably benign	Het
Stx19	T	C	16: 62,822,286	L155S	probably benign	Het
Tespa1	A	T	10: 130,356,883	T145S	probably damaging	Het
Timm21	A	C	18: 84,947,721	F221V	possibly damaging	Het
Tlr1	A	T	5: 64,924,921	F771Y	probably damaging	Het
Tmem150a	C	A	6: 72,358,623	L125I	unknown	Het
Try4	T	C	6: 41,302,295	L4P	possibly damaging	Het
Txlna	C	T	4: 129,632,157	R299H	probably damaging	Het
Txndc16	A	T	14: 45,144,960	N609K	probably benign	Het
Zfp266	T	C	9: 20,500,330	N184D	probably benign	Het
Zfp407	A	G	18: 84,209,922	V1854A	possibly damaging	Het
Zfp626	T	A	7: 27,818,370	C259S	possibly 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
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'- TTGTTAACTGGACCTGAAGCC -3'
(R):5'- AACTCAGAGCTCAGAACCGG -3'

Sequencing Primer
(F):5'- TTAACTGGACCTGAAGCCGGTAG -3'
(R):5'- GCTCTGCTTTCGGAGGC -3'

Posted On

2019-11-26