Mutagenetix > Incidental Mutation

Incidental Mutation 'R1445:Upf1'

158792

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

039500-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.969) question?

Stock #

R1445 (G1)

Quality Score

210

Status

Validated

Chromosome

Chromosomal Location

70331525-70353278 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 70341524 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Leucine at position 244 (Q244L)

Ref Sequence

ENSEMBL: ENSMUSP00000148927 (fasta)

Gene Model

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

AlphaFold

Q9EPU0

Predicted Effect

probably benign
Transcript: ENSMUST00000075666
AA Change: Q244L

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

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: Q244L

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: Q244L

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

Meta Mutation Damage Score

0.1415

Coding Region Coverage

1x: 98.8%
3x: 97.7%
10x: 93.9%
20x: 84.0%

Validation Efficiency

96% (101/105)

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
1700061I17Rik	G	T	3: 117,067,736		noncoding transcript	Het
2300003K06Rik	G	T	11: 99,837,967	Q17K	probably benign	Het
Abca16	T	C	7: 120,520,033	V999A	probably benign	Het
Actn3	C	T	19: 4,865,455		probably benign	Het
Agap2	T	A	10: 127,091,112		probably benign	Het
Ago3	C	A	4: 126,371,787	R278L	probably benign	Het
Aldh1a2	T	C	9: 71,285,210	V449A	possibly damaging	Het
Alkbh2	C	T	5: 114,124,226	E148K	probably damaging	Het
Aplnr	A	G	2: 85,137,009	Y126C	probably damaging	Het
Apob	T	C	12: 8,016,084	I4351T	possibly damaging	Het
Ash1l	T	C	3: 89,007,352	L1763P	probably benign	Het
Aspn	T	C	13: 49,557,373	S165P	possibly damaging	Het
Atg13	A	T	2: 91,679,990	V349E	probably damaging	Het
Atp1b2	T	A	11: 69,602,483		probably null	Het
B3glct	A	T	5: 149,754,139	D411V	probably damaging	Het
Bcar3	A	T	3: 122,523,191	I255F	probably damaging	Het
Cacna1b	G	A	2: 24,718,136		probably benign	Het
Cep164	T	G	9: 45,778,900	E675A	possibly damaging	Het
Chd1l	C	T	3: 97,582,731	E503K	probably benign	Het
Chst8	C	A	7: 34,748,168	M8I	possibly damaging	Het
Clec4n	A	G	6: 123,235,516	E67G	probably benign	Het
Cobll1	A	T	2: 65,099,136	D653E	probably damaging	Het
Col9a1	T	C	1: 24,237,498		probably null	Het
Crip2	T	C	12: 113,143,504	L30P	probably damaging	Het
Ctbp1	C	T	5: 33,261,063	V22I	probably benign	Het
Cwc22	T	C	2: 77,917,177		probably benign	Het
Cyp4a32	C	A	4: 115,602,950	Y119*	probably null	Het
Dido1	G	T	2: 180,671,470	A463E	possibly damaging	Het
Dnah7a	G	A	1: 53,528,797	P1880L	probably benign	Het
Dock2	T	A	11: 34,239,705	T1489S	probably benign	Het
Dsp	A	G	13: 38,191,931	T1231A	probably damaging	Het
Eif2ak1	G	T	5: 143,873,899		probably benign	Het
Epc1	A	T	18: 6,452,360	M233K	probably damaging	Het
Fam189a2	G	A	19: 24,021,634	T140M	probably damaging	Het
Gigyf2	A	G	1: 87,443,638		probably benign	Het
Greb1	T	G	12: 16,707,851	H58P	probably damaging	Het
Gtpbp1	T	C	15: 79,713,448	I348T	possibly damaging	Het
Hck	A	T	2: 153,128,272	N64Y	probably benign	Het
Herc2	T	C	7: 56,168,996	S2812P	probably damaging	Het
Inpp4b	T	A	8: 81,952,834		probably null	Het
Kcnq5	A	C	1: 21,405,024	S473A	probably benign	Het
Lrat	T	G	3: 82,903,369	D115A	probably damaging	Het
Lyst	A	G	13: 13,640,054	I1131M	possibly damaging	Het
Man2a2	T	C	7: 80,368,562	D160G	probably benign	Het
Marf1	C	T	16: 14,115,824	D1567N	probably benign	Het
Mars	T	C	10: 127,297,988	D680G	possibly damaging	Het
Mat1a	T	C	14: 41,121,840	S339P	probably damaging	Het
Megf8	T	C	7: 25,342,656	S1300P	probably damaging	Het
Mga	T	C	2: 119,902,698	L9S	probably damaging	Het
Mllt6	T	C	11: 97,672,451		probably benign	Het
Mrpl37	A	G	4: 107,064,495	L179P	probably benign	Het
Mtnr1a	G	T	8: 45,087,745	V248L	probably benign	Het
Mylk	T	C	16: 34,815,465	S19P	possibly damaging	Het
Olfr738	A	G	14: 50,414,401	T286A	probably damaging	Het
Parp8	A	T	13: 117,025,350		probably null	Het
Pcnx2	T	C	8: 125,752,284	D2075G	probably damaging	Het
Pigo	A	T	4: 43,021,460	I494K	probably benign	Het
Pkd1l1	A	T	11: 8,870,313	D1217E	probably benign	Het
Pkhd1l1	T	C	15: 44,505,644	V895A	probably benign	Het
Plcb4	A	T	2: 136,000,189	H1031L	possibly damaging	Het
Plxnb1	A	G	9: 109,108,921	K1245R	probably null	Het
Pold1	C	T	7: 44,542,757		probably benign	Het
Ptprq	T	C	10: 107,662,562	I885V	probably damaging	Het
Ptprz1	A	G	6: 23,050,474	D1398G	probably damaging	Het
Pygm	G	A	19: 6,389,887	A364T	probably benign	Het
Rbl1	T	C	2: 157,193,098	N354S	probably benign	Het
Scgb2b19	C	T	7: 33,279,612		probably null	Het
Slc26a8	C	T	17: 28,648,213	V545M	possibly damaging	Het
Slc27a1	T	A	8: 71,584,113		probably null	Het
Smpd1	A	G	7: 105,556,674	D416G	possibly damaging	Het
Sorbs3	A	G	14: 70,193,646	V284A	probably benign	Het
Stfa2l1	T	C	16: 36,161,784	V75A	probably damaging	Het
Syndig1	A	G	2: 149,930,921	D166G	probably damaging	Het
Tcp10a	G	A	17: 7,326,007		probably null	Het
Themis2	T	A	4: 132,782,901	I663F	possibly damaging	Het
Thrap3	T	C	4: 126,176,336	Q586R	probably damaging	Het
Tinag	C	A	9: 77,045,516	C62F	probably damaging	Het
Tmem206	A	G	1: 191,348,362		probably benign	Het
Tmod1	T	C	4: 46,090,884	Y146H	probably damaging	Het
Tmprss4	T	A	9: 45,184,385	I54F	possibly damaging	Het
Tnks	A	C	8: 34,834,603		probably benign	Het
Trim43a	GATTTATTTATTTATTTATTTATTTATTTATTTATTTATT	GATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATT	9: 88,582,989		probably benign	Het
Trpc6	A	G	9: 8,680,537	E844G	probably benign	Het
Ubtd2	C	T	11: 32,516,125	R115W	probably damaging	Het
Ubxn6	T	C	17: 56,069,042	D373G	probably benign	Het
Usp33	A	G	3: 152,368,634	I372M	probably damaging	Het
Usp34	A	G	11: 23,351,629	E351G	probably damaging	Het
Utrn	A	G	10: 12,678,574		probably benign	Het
Vmn1r78	A	G	7: 12,152,581	K40E	possibly damaging	Het
Vmn2r7	T	A	3: 64,724,802	M80L	probably benign	Het
Vps13a	G	T	19: 16,701,238	Y1126*	probably null	Het
Wfdc11	T	C	2: 164,664,446	N60S	probably benign	Het
Wnk2	C	T	13: 49,071,110	D992N	probably damaging	Het
Zpbp2	C	A	11: 98,553,844	T66K	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
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
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'- ACCCAAGTGCAAAGAGACTAAGCTG -3'
(R):5'- CTGCTGTGAACTGAGGCCAGAG -3'

Sequencing Primer
(F):5'- GCTCCTTGGAGTAGGAATCTCATAAC -3'
(R):5'- AGATGCTGCTGCTGCCTTC -3'

Posted On

2014-03-14