Mutagenetix > Incidental Mutation

Incidental Mutation 'R7205:Upf1'

560534

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 #

R7205 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

70331525-70353278 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 70340045 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 338 (A338T)

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: A338T

PolyPhen 2 Score 0.935 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: A338T

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: A338T

PolyPhen 2 Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)

Meta Mutation Damage Score

0.1270

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

97% (99/102)

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: 101 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932415D10Rik	A	T	10: 82,289,327	D2616E	probably benign	Het
5430419D17Rik	T	C	7: 131,277,623		probably null	Het
Abca15	A	T	7: 120,394,364	K1269M	possibly damaging	Het
Adgrl2	A	T	3: 148,858,949	Y332N	probably damaging	Het
Adgrv1	C	T	13: 81,479,658	V3695I	probably benign	Het
Aldh1l1	A	T	6: 90,598,275	Y848F	probably damaging	Het
Ambra1	T	C	2: 91,767,758	V88A	possibly damaging	Het
Ankrd12	C	T	17: 65,985,165	R1091Q	probably damaging	Het
Apob	T	G	12: 8,005,087	V1362G	probably damaging	Het
Arhgap17	A	G	7: 123,306,438	L328P	probably damaging	Het
Arhgap27	A	C	11: 103,344,541	V9G	probably benign	Het
Arhgap33	A	T	7: 30,533,009	D34E	probably damaging	Het
Ash1l	A	G	3: 88,965,952	D14G	probably benign	Het
Atf6b	T	C	17: 34,653,729	Y575H	probably damaging	Het
BC100530	T	C	16: 36,367,447	I19V	probably benign	Het
Bcl2l2	T	G	14: 54,884,601	S74A	probably benign	Het
Begain	T	C	12: 109,038,868	T73A	possibly damaging	Het
Bicdl1	C	T	5: 115,670,281	R264Q	probably damaging	Het
Ccdc180	A	G	4: 45,914,588	D701G	probably benign	Het
Cd200r4	G	T	16: 44,833,166	V146L	probably damaging	Het
Cd226	G	A	18: 89,247,198	C200Y	probably damaging	Het
Cdk12	A	G	11: 98,224,625	N864S	unknown	Het
Clcnkb	A	T	4: 141,408,635	L413Q	probably damaging	Het
Cldn10	T	C	14: 118,861,843	V123A	possibly damaging	Het
Cnn1	T	A	9: 22,105,782		probably null	Het
Cpa5	C	A	6: 30,630,830	Q364K	probably benign	Het
Ddx11	A	G	17: 66,130,771	E164G	probably benign	Het
Dnah12	G	A	14: 26,778,912		probably null	Het
Drc7	T	A	8: 95,077,921	Y855N	probably damaging	Het
Fam20b	C	A	1: 156,702,398		probably null	Het
Fip1l1	T	A	5: 74,588,075		probably null	Het
Flt4	A	G	11: 49,634,298	D657G	probably null	Het
Fmo3	T	A	1: 162,954,288	T499S	possibly damaging	Het
Fyco1	C	T	9: 123,822,426	G1190S	probably benign	Het
Galnt17	C	A	5: 131,306,752		probably benign	Het
Ggcx	T	C	6: 72,428,004	I465T	probably damaging	Het
Gm11238	A	G	4: 73,654,920	Y132C	probably damaging	Het
Gm281	T	C	14: 13,866,032	T286A		Het
Gm4788	A	T	1: 139,753,050	Y243*	probably null	Het
Gm7361	T	A	5: 26,261,118	N159K	probably damaging	Het
Golgb1	A	G	16: 36,875,301	N54S	unknown	Het
Grin2c	G	A	11: 115,251,050	P848S	probably damaging	Het
Grina	T	C	15: 76,249,087	V285A	probably damaging	Het
Gtpbp6	A	G	5: 110,104,612	L381P	probably damaging	Het
Herc2	G	T	7: 56,182,640	G3028V	probably damaging	Het
Ibsp	A	T	5: 104,310,431	Y278F	probably damaging	Het
Ints4	T	A	7: 97,535,226	L846*	probably null	Het
Kif17	A	G	4: 138,293,766	K849E	probably benign	Het
Krt77	G	A	15: 101,869,371	P83L	probably benign	Het
Ky	T	G	9: 102,542,292	D499E	probably damaging	Het
Lrp3	A	T	7: 35,202,626	M610K	probably damaging	Het
Lrrfip1	T	A	1: 91,091,616	D156E	probably benign	Het
Map6	C	A	7: 99,269,050	H343Q	probably benign	Het
Micu2	G	T	14: 57,954,149	D148E	probably benign	Het
Mks1	T	A	11: 87,856,602	S153T	probably benign	Het
Muc6	AGGCGCAGAAACCCTGGC	AGGC	7: 141,634,450		probably null	Het
Myh9	T	C	15: 77,783,472	K587R	probably benign	Het
Neb	T	C	2: 52,196,356	Y5478C	probably damaging	Het
Nelfe	G	A	17: 34,850,936		probably null	Het
Nps	T	A	7: 135,268,781	L11I	probably damaging	Het
Nsd1	A	T	13: 55,246,470	D731V	probably damaging	Het
Nup50	A	G	15: 84,933,658	T93A	probably benign	Het
Nup98	A	T	7: 102,195,041	F29Y	unknown	Het
Olfr1195	T	C	2: 88,683,423	H103R	possibly damaging	Het
Olfr1414	A	T	1: 92,511,851	M59K	probably benign	Het
Olfr212	A	G	6: 116,515,975	Y66C	probably damaging	Het
Olfr469	T	C	7: 107,822,575	N298S	probably benign	Het
Oprd1	A	G	4: 132,113,801	I282T	probably damaging	Het
Osbp2	T	C	11: 3,712,134	I240V	probably damaging	Het
Otub2	C	A	12: 103,392,904	P84Q	probably benign	Het
Parp9	A	T	16: 35,956,990	I435F	probably benign	Het
Pcdh18	C	T	3: 49,755,474	R464H	probably benign	Het
Pcsk6	G	T	7: 66,025,408		probably null	Het
Ptgs2	G	A	1: 150,102,761	R208Q	probably benign	Het
Rab11b	G	A	17: 33,749,867	R51C	probably damaging	Het
Rad1	A	G	15: 10,493,257	I257V	probably benign	Het
Rbms3	C	T	9: 116,586,017		probably null	Het
Rxfp2	A	T	5: 150,059,899	I300L	probably benign	Het
Rxfp2	C	A	5: 150,059,903	T301K	probably benign	Het
Sars2	G	T	7: 28,744,308	A112S	probably benign	Het
Scn10a	T	C	9: 119,613,550	D1543G	probably damaging	Het
Serpinb1b	A	G	13: 33,087,423	H59R	probably benign	Het
Sgsm2	T	A	11: 74,854,493	D661V	possibly damaging	Het
Smad6	C	A	9: 64,020,406	V207L	probably damaging	Het
Son	TCCCCCAGCCGCAGGAGCCGAACCCCCAGCCGCAGGAGCAGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCG	TCCCCCAGCCGCAGGAGCCGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCG	16: 91,660,295		probably benign	Het
Tenm2	C	T	11: 36,049,129	R1390Q	probably damaging	Het
Tmem132a	T	A	19: 10,866,931	Q101L	probably damaging	Het
Tmem151a	A	G	19: 5,082,773	V135A	probably damaging	Het
Trappc10	T	C	10: 78,210,428	K443E	probably damaging	Het
Trrap	A	T	5: 144,842,707	N3161I	possibly damaging	Het
Tspan32	G	T	7: 143,005,126	R6L	possibly damaging	Het
Ugt2a2	T	C	5: 87,460,609	D457G	possibly damaging	Het
Ulk2	A	T	11: 61,834,831	S140T	possibly damaging	Het
Usp43	C	T	11: 67,883,284	R460Q	probably null	Het
Uxs1	A	G	1: 43,816,958		probably benign	Het
Vmn1r59	A	G	7: 5,454,726	C12R	probably damaging	Het
Wdr64	A	G	1: 175,789,933	D693G	probably benign	Het
Wnk1	A	T	6: 119,943,878		probably null	Het
Wnt2	G	T	6: 18,028,047	R63S	probably benign	Het
Zcchc6	C	G	13: 59,788,550	D1246H	probably damaging	Het
Zfp418	A	T	7: 7,181,563	Q175L	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
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
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'- AGTTAGCACTTTCAAGAGGGC -3'
(R):5'- GGCTCTCTACAAAGCTTGCTG -3'

Sequencing Primer
(F):5'- ACTTTCAAGAGGGCGTGGC -3'
(R):5'- CAGATGCTGGAGTTCCTGGC -3'

Posted On

2019-06-26