Mutagenetix > Incidental Mutation

Incidental Mutation 'R0755:Upf1'

70429

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

038935-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.972) question?

Stock #

R0755 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

70784175-70805928 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 70786779 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Serine at position 902 (R902S)

Ref Sequence

ENSEMBL: ENSMUSP00000148927 (fasta)

Gene Model

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

AlphaFold

Q9EPU0

Predicted Effect

probably benign
Transcript: ENSMUST00000075666
AA Change: R913S

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: R913S

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 benign
Transcript: ENSMUST00000215817
AA Change: R902S

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 93.8%

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: 94 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A730061H03Rik	A	T	14: 55,797,638 (GRCm39)		probably benign	Het
Acin1	A	G	14: 54,889,292 (GRCm39)	M1T	probably null	Het
Akp3	G	A	1: 87,055,593 (GRCm39)	G547R	unknown	Het
Aldh1a1	A	G	19: 20,595,358 (GRCm39)	M96V	probably benign	Het
Ankfn1	T	A	11: 89,282,913 (GRCm39)	M245L	probably benign	Het
Arhgap19	T	C	19: 41,769,614 (GRCm39)	K54E	probably damaging	Het
Atp1a2	T	C	1: 172,116,948 (GRCm39)	Q223R	probably benign	Het
Atp8a2	C	T	14: 60,247,330 (GRCm39)	V557I	possibly damaging	Het
AU041133	A	T	10: 81,986,724 (GRCm39)	K126*	probably null	Het
Axin1	T	A	17: 26,401,480 (GRCm39)	Y351N	possibly damaging	Het
Baiap2l1	T	C	5: 144,221,367 (GRCm39)	K176E	probably damaging	Het
Baz2a	C	T	10: 127,955,560 (GRCm39)	T848I	possibly damaging	Het
Bbs2	A	C	8: 94,808,708 (GRCm39)	V333G	probably benign	Het
BC051019	G	A	7: 109,315,302 (GRCm39)	Q318*	probably null	Het
Bltp1	T	C	3: 37,000,513 (GRCm39)	S1231P	probably damaging	Het
Cdc37	C	T	9: 21,051,160 (GRCm39)	D362N	probably damaging	Het
Cep170	A	T	1: 176,583,319 (GRCm39)	V1020E	probably damaging	Het
Chrm4	T	C	2: 91,758,747 (GRCm39)	V385A	probably benign	Het
Cntrl	G	A	2: 35,035,151 (GRCm39)	S373N	probably damaging	Het
Col23a1	G	A	11: 51,467,706 (GRCm39)	G19D	probably damaging	Het
Cyb5r4	G	T	9: 86,911,625 (GRCm39)	A100S	probably damaging	Het
Dctn1	C	T	6: 83,166,059 (GRCm39)	P115S	probably damaging	Het
Dhrs2	C	T	14: 55,472,247 (GRCm39)	T46M	probably damaging	Het
Disp2	T	C	2: 118,620,243 (GRCm39)	F325S	probably benign	Het
Dnah11	T	G	12: 117,918,564 (GRCm39)	T3456P	possibly damaging	Het
Dnah11	C	A	12: 118,162,360 (GRCm39)	V70F	probably benign	Het
Duoxa1	T	A	2: 122,135,161 (GRCm39)	T195S	probably benign	Het
Dync2i1	T	C	12: 116,175,412 (GRCm39)	I922V	probably benign	Het
Eif2ak1	T	A	5: 143,821,742 (GRCm39)	F353I	possibly damaging	Het
Esam	A	G	9: 37,447,998 (GRCm39)	T211A	probably damaging	Het
Faf1	A	G	4: 109,819,036 (GRCm39)	N636S	probably benign	Het
Fbxo25	A	G	8: 13,985,219 (GRCm39)	Y305C	probably benign	Het
Fchsd1	C	T	18: 38,101,803 (GRCm39)		probably null	Het
Fdxacb1	T	A	9: 50,683,025 (GRCm39)	D329E	possibly damaging	Het
Gvin2	A	T	7: 105,545,892 (GRCm39)	F2387I	possibly damaging	Het
Hbq1b	A	T	11: 32,237,104 (GRCm39)		probably null	Het
Hmcn2	T	A	2: 31,343,172 (GRCm39)	V4566E	probably damaging	Het
Igkv6-29	G	A	6: 70,116,053 (GRCm39)	T5I	probably benign	Het
Itfg1	A	T	8: 86,452,834 (GRCm39)	D511E	possibly damaging	Het
Jmjd1c	C	T	10: 66,932,378 (GRCm39)		probably benign	Het
Kat6b	T	A	14: 21,687,661 (GRCm39)	M570K	probably damaging	Het
Kdm4d	T	A	9: 14,375,591 (GRCm39)	K89M	probably damaging	Het
Krt19	A	T	11: 100,032,965 (GRCm39)	D194E	possibly damaging	Het
Lamc1	A	T	1: 153,123,196 (GRCm39)	Y665N	possibly damaging	Het
Lct	A	T	1: 128,221,872 (GRCm39)	S1556T	possibly damaging	Het
Macf1	A	G	4: 123,263,719 (GRCm39)	L4924P	probably damaging	Het
Mef2c	G	A	13: 83,804,472 (GRCm39)		probably null	Het
Mff	G	A	1: 82,728,326 (GRCm39)		probably null	Het
Mycbp2	A	T	14: 103,412,230 (GRCm39)	L2581Q	probably damaging	Het
Mylk	G	C	16: 34,699,845 (GRCm39)	E403Q	possibly damaging	Het
Nos3	T	A	5: 24,572,295 (GRCm39)	L123M	probably damaging	Het
Ntn5	C	T	7: 45,335,952 (GRCm39)	P128S	probably benign	Het
Nudt9	T	C	5: 104,212,920 (GRCm39)	V331A	probably damaging	Het
Or2y3	A	T	17: 38,393,085 (GRCm39)	Y261*	probably null	Het
Or7g34	T	C	9: 19,478,415 (GRCm39)	I88M	possibly damaging	Het
Pcdh7	A	T	5: 57,877,664 (GRCm39)	K406N	possibly damaging	Het
Pkdrej	T	A	15: 85,700,336 (GRCm39)	I1867L	probably benign	Het
Plppr4	C	T	3: 117,116,319 (GRCm39)	G455R	possibly damaging	Het
Pramel11	A	G	4: 143,624,299 (GRCm39)	V66A	probably damaging	Het
Prkag2	G	C	5: 25,152,629 (GRCm39)	S158R	probably benign	Het
Ptprq	T	G	10: 107,418,400 (GRCm39)	T1659P	probably benign	Het
Rasl12	A	G	9: 65,318,241 (GRCm39)	K202E	probably benign	Het
Rb1	A	C	14: 73,434,653 (GRCm39)	*922G	probably null	Het
Rsf1	C	T	7: 97,229,174 (GRCm39)	P22S	probably damaging	Het
Scn1a	T	G	2: 66,151,379 (GRCm39)	T797P	probably damaging	Het
Sgsm2	A	G	11: 74,756,323 (GRCm39)	V342A	probably damaging	Het
Slc22a7	T	G	17: 46,749,113 (GRCm39)	H68P	possibly damaging	Het
Slc4a2	G	A	5: 24,640,575 (GRCm39)	A652T	probably benign	Het
Slc5a1	T	A	5: 33,290,733 (GRCm39)	L106M	probably benign	Het
Slco1c1	C	T	6: 141,477,258 (GRCm39)	P19S	probably damaging	Het
Snx1	A	G	9: 66,005,738 (GRCm39)	F127S	probably damaging	Het
Snx31	A	T	15: 36,534,576 (GRCm39)	I199N	probably damaging	Het
Snx33	T	C	9: 56,832,741 (GRCm39)	I443V	possibly damaging	Het
Sptbn1	A	G	11: 30,089,016 (GRCm39)	F749L	probably damaging	Het
Stoml3	T	A	3: 53,405,559 (GRCm39)	Y53*	probably null	Het
Stxbp2	A	G	8: 3,692,019 (GRCm39)	T554A	probably benign	Het
Tal1	T	C	4: 114,925,573 (GRCm39)	I214T	probably damaging	Het
Tas2r140	T	A	6: 40,468,344 (GRCm39)	I58N	probably damaging	Het
Thap1	A	G	8: 26,648,501 (GRCm39)	Y8C	probably damaging	Het
Thsd7a	A	T	6: 12,555,368 (GRCm39)	L172Q	probably damaging	Het
Ube3c	T	A	5: 29,842,740 (GRCm39)	D735E	probably damaging	Het
Unc80	G	A	1: 66,544,082 (GRCm39)	D402N	probably damaging	Het
Urb1	A	G	16: 90,570,982 (GRCm39)	Y1276H	probably damaging	Het
Urb1	A	T	16: 90,576,026 (GRCm39)	F843L	probably benign	Het
Vmn1r198	C	T	13: 22,539,402 (GRCm39)	T296I	probably benign	Het
Vmn1r33	A	T	6: 66,588,892 (GRCm39)	S221T	probably damaging	Het
Vmn2r103	A	G	17: 19,993,830 (GRCm39)	D69G	probably benign	Het
Vmn2r14	T	G	5: 109,364,226 (GRCm39)	L563F	possibly damaging	Het
Vmn2r60	G	A	7: 41,844,869 (GRCm39)	G744D	probably damaging	Het
Vstm4	T	C	14: 32,614,601 (GRCm39)	V181A	probably damaging	Het
Wdr72	G	A	9: 74,052,376 (GRCm39)	V136I	probably benign	Het
Zfp236	T	A	18: 82,638,457 (GRCm39)	N1388Y	probably damaging	Het
Zfp53	T	A	17: 21,728,839 (GRCm39)	F291I	probably damaging	Het
Zfp944	A	T	17: 22,558,889 (GRCm39)	H119Q	possibly damaging	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
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
R3032: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'- TACATGGCAGTAGTCATGAAGCGGG -3'
(R):5'- AGAGGCATTTAGAGAGCTGCGAATC -3'

Sequencing Primer
(F):5'- ATGTGTCAGTCAACAGCAGC -3'
(R):5'- CTAACCCTAGACAGTGGAGTTCAG -3'

Posted On

2013-09-30