Mutagenetix > Incidental Mutation

Incidental Mutation 'R7464:Upf1'

578641

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

045538-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.972) question?

Stock #

R7464 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

70784175-70805928 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 70786073 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Leucine at position 962 (S962L)

Ref Sequence

ENSEMBL: ENSMUSP00000075089 (fasta)

Gene Model

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

AlphaFold

Q9EPU0

Predicted Effect

probably benign
Transcript: ENSMUST00000075666
AA Change: S962L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: S962L

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: S951L

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 98.9%

Validation Efficiency

96% (79/82)

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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aass	C	T	6: 23,077,152 (GRCm39)	G736R	possibly damaging	Het
Acta2	G	A	19: 34,229,931 (GRCm39)	T8I	probably benign	Het
Ankar	A	T	1: 72,738,053 (GRCm39)	V43E	possibly damaging	Het
Apof	A	G	10: 128,105,505 (GRCm39)	I220V	probably benign	Het
Asxl1	G	T	2: 153,239,705 (GRCm39)	A499S	probably benign	Het
Baz2a	T	A	10: 127,957,942 (GRCm39)	D1069E	possibly damaging	Het
Baz2b	T	C	2: 59,807,792 (GRCm39)	T156A	possibly damaging	Het
Bbc3	A	T	7: 16,051,082 (GRCm39)	R169W	unknown	Het
C5ar1	T	A	7: 15,982,691 (GRCm39)	I110L	probably benign	Het
Cd19	C	A	7: 126,010,975 (GRCm39)	R323L	probably damaging	Het
Cdc14b	A	T	13: 64,344,489 (GRCm39)	C113*	probably null	Het
Cngb1	C	A	8: 95,980,811 (GRCm39)	W914L	possibly damaging	Het
Colgalt2	A	G	1: 152,379,895 (GRCm39)	K445E	probably damaging	Het
Crebrf	A	G	17: 26,982,461 (GRCm39)	M608V	unknown	Het
Csf1	T	A	3: 107,656,191 (GRCm39)	H280L	probably benign	Het
Cyp2j11	C	A	4: 96,233,357 (GRCm39)	R113L	probably damaging	Het
D5Ertd579e	G	A	5: 36,771,129 (GRCm39)	H1089Y	probably damaging	Het
Ddx60	C	T	8: 62,393,708 (GRCm39)	T48M	possibly damaging	Het
Defa40	T	A	8: 21,739,910 (GRCm39)	S45T	probably damaging	Het
Dock10	T	C	1: 80,518,032 (GRCm39)	D1315G	probably damaging	Het
Dock2	T	G	11: 34,586,105 (GRCm39)	N526H	probably damaging	Het
Dram2	T	C	3: 106,480,999 (GRCm39)	*268Q	probably null	Het
Emc8	A	G	8: 121,394,657 (GRCm39)	Y21H	possibly damaging	Het
Fam162a	A	G	16: 35,891,863 (GRCm39)	L4P	probably damaging	Het
Fan1	T	A	7: 64,022,234 (GRCm39)	N340Y	probably damaging	Het
Fbxw10	T	A	11: 62,744,124 (GRCm39)	I307N	probably benign	Het
Fbxw16	A	G	9: 109,268,619 (GRCm39)	V257A	possibly damaging	Het
Fer1l6	T	A	15: 58,445,096 (GRCm39)		probably null	Het
Galnt7	A	G	8: 58,037,054 (GRCm39)	Y112H	possibly damaging	Het
Gigyf2	T	C	1: 87,356,326 (GRCm39)	I803T	unknown	Het
Gm28729	A	G	9: 96,403,288 (GRCm39)	I44T	possibly damaging	Het
Gm5447	A	G	13: 31,158,377 (GRCm39)	I34V	not run	Het
H2-M9	A	T	17: 36,953,303 (GRCm39)		probably null	Het
Helz	G	A	11: 107,527,104 (GRCm39)	C864Y	probably damaging	Het
Il25	A	G	14: 55,170,679 (GRCm39)	Y84C	probably null	Het
Itga10	T	A	3: 96,555,471 (GRCm39)	C142S	probably damaging	Het
Kcna10	A	T	3: 107,101,395 (GRCm39)	M9L	probably damaging	Het
Klhl6	G	T	16: 19,775,863 (GRCm39)	Q232K	possibly damaging	Het
Mb21d2	T	G	16: 28,748,298 (GRCm39)	I40L	possibly damaging	Het
Mdm1	T	C	10: 117,988,171 (GRCm39)	S334P	probably benign	Het
Mllt10	T	A	2: 18,175,090 (GRCm39)	D549E	probably benign	Het
Mlxipl	T	C	5: 135,162,482 (GRCm39)	V648A	probably benign	Het
Nars2	A	G	7: 96,689,137 (GRCm39)	K353R	probably benign	Het
Nav1	T	A	1: 135,512,647 (GRCm39)	M138L	probably benign	Het
Neb	T	C	2: 52,083,902 (GRCm39)	T5635A	probably benign	Het
Nktr	A	C	9: 121,579,393 (GRCm39)	I1154L	unknown	Het
Or14j8	A	T	17: 38,263,171 (GRCm39)	V248D	probably damaging	Het
Or2a57	T	G	6: 43,213,228 (GRCm39)	S229A	probably damaging	Het
Or4g17	T	A	2: 111,209,543 (GRCm39)	L66Q	probably damaging	Het
Oxld1	T	C	11: 120,347,963 (GRCm39)	D78G	probably benign	Het
Pde1b	T	C	15: 103,433,256 (GRCm39)	I255T	probably benign	Het
Pkp4	T	A	2: 59,138,481 (GRCm39)	F244I	probably benign	Het
Polg2	C	A	11: 106,664,540 (GRCm39)	V305L	probably benign	Het
Pramel34	C	T	5: 93,784,099 (GRCm39)	C455Y	probably damaging	Het
Ptpn18	G	A	1: 34,512,445 (GRCm39)	D417N	possibly damaging	Het
Sash1	T	C	10: 8,632,509 (GRCm39)	D242G	possibly damaging	Het
Six4	T	C	12: 73,159,304 (GRCm39)	T219A	possibly damaging	Het
Slc28a3	A	C	13: 58,710,835 (GRCm39)	Y562*	probably null	Het
Soat1	A	T	1: 156,266,887 (GRCm39)	W310R	probably damaging	Het
Son	CATGGACTCCCAGATGTTAGCAACTAGCTCTATGGACTCCCAGATGTTAGCAACTAGCTCTATGGACTCCCAGATGTTAGCAACCAGCAGTATGGACTCCCAGATGTTAGCAACCAGCAGTATGGACTCCCAGATGTTAGCAACCAGCTCCATGGACTCCCAGATGTTAGCAAC	CATGGACTCCCAGATGTTAGCAACTAGCTCTATGGACTCCCAGATGTTAGCAACCAGCAGTATGGACTCCCAGATGTTAGCAACCAGCAGTATGGACTCCCAGATGTTAGCAACCAGCTCCATGGACTCCCAGATGTTAGCAAC	16: 91,453,579 (GRCm39)		probably benign	Het
Spef2	T	C	15: 9,740,671 (GRCm39)	N30D	probably benign	Het
Spopfm2	A	T	3: 94,083,411 (GRCm39)	N133K	probably benign	Het
Srebf2	T	A	15: 82,057,075 (GRCm39)	I270N	probably damaging	Het
St8sia3	T	C	18: 64,404,589 (GRCm39)	W289R	probably damaging	Het
Stx5a	T	A	19: 8,720,868 (GRCm39)		probably benign	Het
Tacc1	T	C	8: 25,654,480 (GRCm39)	D689G	probably damaging	Het
Tacc3	A	G	5: 33,818,628 (GRCm39)	D21G	probably benign	Het
Tapt1	G	A	5: 44,346,030 (GRCm39)	R307*	probably null	Het
Tbc1d9b	T	A	11: 50,022,312 (GRCm39)	V16E	probably damaging	Het
Tchhl1	G	A	3: 93,377,971 (GRCm39)	R225K	probably benign	Het
Thumpd3	G	A	6: 113,032,730 (GRCm39)	G156D	probably benign	Het
Tmem178	C	T	17: 81,252,331 (GRCm39)	P72S	probably benign	Het
Tmem52	C	T	4: 155,553,926 (GRCm39)	P46S	probably benign	Het
Tmem94	G	T	11: 115,677,082 (GRCm39)	R118L	possibly damaging	Het
Tulp3	A	T	6: 128,303,792 (GRCm39)	V269D	probably benign	Het
Ubr1	A	G	2: 120,720,255 (GRCm39)		probably null	Het
Vcpip1	C	T	1: 9,816,745 (GRCm39)	R546Q	probably damaging	Het
Vmn2r49	A	C	7: 9,722,820 (GRCm39)	S151R	probably benign	Het
Wac	T	C	18: 7,871,746 (GRCm39)		probably null	Het
Wrn	C	T	8: 33,826,024 (GRCm39)		probably null	Het
Zfp286	C	A	11: 62,671,627 (GRCm39)	D149Y	probably benign	Het
Zfp748	A	G	13: 67,690,091 (GRCm39)	C390R	probably damaging	Het
Zfp873	A	G	10: 81,896,210 (GRCm39)	T314A	possibly damaging	Het
Zfyve1	C	T	12: 83,598,261 (GRCm39)	D656N	probably benign	Het
Zmym1	T	A	4: 126,952,728 (GRCm39)	K18*	probably null	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
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
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'- GCAGTGAAATATGGCAAGGTCTAC -3'
(R):5'- AGTTCCATCGTGGCCAGATC -3'

Sequencing Primer
(F):5'- GCCTGGGCAGTAGAGATAAAACC -3'
(R):5'- ATCGTGGCCAGATCTCACC -3'

Posted On

2019-10-07