Mutagenetix > Incidental Mutation

Incidental Mutation 'R5001:Upf1'

389916

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

042595-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.970) question?

Stock #

R5001 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

70331525-70353278 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 70334700 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 835 (S835P)

Ref Sequence

ENSEMBL: ENSMUSP00000148927 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000075666] [ENSMUST00000140239] [ENSMUST00000165819] [ENSMUST00000207684] [ENSMUST00000215817]

AlphaFold

Q9EPU0

Predicted Effect

probably damaging
Transcript: ENSMUST00000075666
AA Change: S846P

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

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: S846P

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: ENSMUST00000140239

SMART Domains

Protein: ENSMUSP00000120598
Gene: ENSMUSG00000087408

Domain	Start	End	E-Value	Type
low complexity region	49	68	N/A	INTRINSIC
TLC	97	311	1.24e-57	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000165819

SMART Domains

Protein: ENSMUSP00000128325
Gene: ENSMUSG00000087408

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
Pfam:TGFb_propeptide	33	169	7e-16	PFAM
low complexity region	225	237	N/A	INTRINSIC
TGFB	251	357	6.22e-56	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000207684

Predicted Effect

probably damaging
Transcript: ENSMUST00000215817
AA Change: S835P

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

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.4%
20x: 92.7%

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: 99 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adcy3	G	A	12: 4,198,434	V499M	possibly damaging	Het
Aff4	T	C	11: 53,404,357	S795P	probably damaging	Het
Ank	G	A	15: 27,562,733	V176I	probably damaging	Het
Ankfn1	A	G	11: 89,441,442	I446T	possibly damaging	Het
Arhgap33	C	A	7: 30,533,016	S32I	possibly damaging	Het
Ascc3	T	A	10: 50,823,648	Y1856N	probably damaging	Het
Atf3	T	C	1: 191,177,275	T66A	probably benign	Het
Atf7ip	T	C	6: 136,561,388	C548R	probably damaging	Het
Bag6	A	G	17: 35,145,176	T841A	probably damaging	Het
Bbof1	A	T	12: 84,426,856	Q320L	possibly damaging	Het
Bmp2k	A	T	5: 97,053,142	Q307L	probably damaging	Het
Btaf1	T	A	19: 36,986,652	N874K	possibly damaging	Het
Calr4	G	A	4: 109,238,982		probably null	Het
Camk1d	T	C	2: 5,313,101	I248V	possibly damaging	Het
Ccdc130	G	A	8: 84,258,675	P322S	probably benign	Het
Ccdc177	G	A	12: 80,757,386	R705C	unknown	Het
Cdk18	C	T	1: 132,118,849		probably null	Het
Cers4	A	G	8: 4,515,565	S4G	probably benign	Het
Cfap54	A	G	10: 92,964,534	V1604A	probably benign	Het
Chd8	C	T	14: 52,203,915	G907S	probably benign	Het
Cnksr3	G	A	10: 7,126,746	Q149*	probably null	Het
Cntd1	T	C	11: 101,285,731	V218A	possibly damaging	Het
Cog7	A	T	7: 121,949,886	V384E	probably damaging	Het
Col5a2	A	G	1: 45,502,898	V6A	unknown	Het
Col7a1	T	C	9: 108,965,078		probably null	Het
Cpsf6	T	A	10: 117,367,961	I29L	possibly damaging	Het
Cyp3a13	T	C	5: 137,898,916	T379A	probably benign	Het
Ddx46	T	C	13: 55,652,919	S296P	probably damaging	Het
Dmbt1	A	G	7: 131,050,012	D328G	probably damaging	Het
Dnah8	T	G	17: 30,787,185	L3692W	probably damaging	Het
Dnmt3l	A	C	10: 78,059,731	S368R	probably null	Het
Egfr	A	G	11: 16,904,434	K869E	probably damaging	Het
Ehd1	G	A	19: 6,297,694	M359I	probably benign	Het
F5	A	T	1: 164,195,570	T1566S	probably benign	Het
Fam207a	A	G	10: 77,490,016	V154A	probably benign	Het
Flrt2	T	C	12: 95,778,951	I21T	probably benign	Het
Galnt1	T	A	18: 24,271,755	I383K	probably benign	Het
Ghdc	G	T	11: 100,766,834	A523D	probably damaging	Het
Gm24022	A	G	12: 113,429,779		probably benign	Het
Golga3	T	C	5: 110,205,777	S934P	probably damaging	Het
Gpr135	T	A	12: 72,070,508	T162S	probably benign	Het
Gucd1	G	A	10: 75,517,202		probably null	Het
Hcrtr2	T	A	9: 76,230,604	I410F	probably benign	Het
Ick	T	C	9: 78,131,519	S17P	probably damaging	Het
Igkv6-15	T	C	6: 70,406,649	Y56C	probably damaging	Het
Il22ra1	A	T	4: 135,733,104	Y57F	probably damaging	Het
Irak4	A	G	15: 94,558,273	E247G	possibly damaging	Het
Kank3	T	C	17: 33,821,772	V13A	possibly damaging	Het
Klhl1	A	T	14: 96,136,610	S667T	probably damaging	Het
Klhl6	T	G	16: 19,946,991	*620C	probably null	Het
Lct	A	G	1: 128,308,241	L343P	probably damaging	Het
Lgr6	G	T	1: 134,990,632	P264T	probably benign	Het
Lilrb4a	T	A	10: 51,491,420		probably null	Het
Lin7a	G	T	10: 107,382,669	G25*	probably null	Het
Lmnb2	G	A	10: 80,918,112	T36M	probably damaging	Het
Manba	T	C	3: 135,567,630	F775S	probably benign	Het
March6	A	G	15: 31,465,322	V812A	probably damaging	Het
Megf6	T	A	4: 154,268,060	L1292H	probably damaging	Het
Myo18b	T	G	5: 112,761,340	Q1979P	probably damaging	Het
Myoz1	T	C	14: 20,653,701	M59V	probably damaging	Het
Naa35	T	C	13: 59,625,531	I100T	possibly damaging	Het
Nox4	A	T	7: 87,360,803	Y404F	probably damaging	Het
Ntn1	T	C	11: 68,260,532	Y441C	probably damaging	Het
Olfr1329	C	A	4: 118,917,243	V75F	probably damaging	Het
Olfr351	T	C	2: 36,860,070	T93A	probably benign	Het
Olfr984	G	A	9: 40,101,227	H88Y	probably benign	Het
Onecut3	A	G	10: 80,495,320	T105A	unknown	Het
Pabpc1l	A	G	2: 164,042,518	S392G	probably benign	Het
Pan3	T	A	5: 147,526,682		probably null	Het
Pcdha4	G	A	18: 36,954,948	S728N	probably benign	Het
Pds5a	T	C	5: 65,696,785	D38G	probably damaging	Het
Pgm2l1	A	G	7: 100,272,376	I605V	probably benign	Het
Phip	T	C	9: 82,896,019		probably null	Het
Pilra	T	C	5: 137,835,515	I96M	probably damaging	Het
Ppig	T	A	2: 69,741,486	V183D	unknown	Het
Ppp2r2a	A	T	14: 67,022,308	L313*	probably null	Het
Ppp4c	A	G	7: 126,787,537	F126S	probably damaging	Het
Ptger2	C	A	14: 44,989,367	R135S	probably damaging	Het
Rab11fip5	T	A	6: 85,347,806	E506D	probably damaging	Het
Rdh12	G	A	12: 79,212,742	G133R	probably damaging	Het
Rims2	A	T	15: 39,452,428	D610V	probably benign	Het
Saa1	T	A	7: 46,740,708	Y122F	probably damaging	Het
Sept10	A	T	10: 59,176,989	V269E	probably damaging	Het
Serpina3n	T	A	12: 104,408,739	D23E	probably benign	Het
Serpinb11	A	G	1: 107,376,868	K188E	possibly damaging	Het
Slc18a3	C	T	14: 32,463,779	V216M	possibly damaging	Het
Slc19a3	G	T	1: 83,022,620	N225K	probably benign	Het
Slc4a1	T	A	11: 102,351,503	I797F	probably benign	Het
Spic	A	G	10: 88,675,899	M165T	possibly damaging	Het
Timm44	A	T	8: 4,275,886	M1K	probably null	Het
Tmc6	A	G	11: 117,770,784	L572P	probably benign	Het
Tnc	G	A	4: 63,984,489	T1517I	probably damaging	Het
Tnc	G	A	4: 64,000,062	T1204M	probably benign	Het
Trip11	A	T	12: 101,884,910	L680*	probably null	Het
Trps1	T	A	15: 50,661,307	M887L	possibly damaging	Het
Tulp3	A	C	6: 128,325,068	V330G	probably damaging	Het
Wdr64	A	G	1: 175,792,959		probably null	Het
Zbtb40	A	G	4: 136,996,150	L643P	probably damaging	Het
Zc3h18	A	T	8: 122,383,520	D36V	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
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
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'- TGCACATGTACTCCCAGGAC -3'
(R):5'- TATACCATGGAGCCTACTCAGCC -3'

Sequencing Primer
(F):5'- CATGTACTCCCAGGACAGATATGAG -3'
(R):5'- ATGGAGCCTACTCAGCCTTTGC -3'

Posted On

2016-06-06