Mutagenetix > Incidental Mutation

Incidental Mutation 'R4838:Upf1'

371545

Institutional Source

Beutler Lab

Gene Symbol

Upf1

Ensembl Gene

ENSMUSG00000058301

Gene Name

UPF1 regulator of nonsense transcripts homolog (yeast)

Synonyms

B430202H16Rik, PNORF-1, Rent1

Accession Numbers

Essential gene?

Probably essential (E-score: 0.970) question?

Stock #

R4838 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

70331525-70353278 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to C at 70339368 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Glutamine at position 402 (H402Q)

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: H413Q

PolyPhen 2 Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: H413Q

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: H402Q

PolyPhen 2 Score 0.032 (Sensitivity: 0.95; Specificity: 0.82)

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.0%

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: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9530077C05Rik	A	T	9: 22,424,377	D97V	probably damaging	Het
Abca15	T	C	7: 120,345,300	V386A	probably benign	Het
Adk	G	A	14: 21,369,086	A247T	probably damaging	Het
Ankrd27	T	A	7: 35,591,806	L9Q	possibly damaging	Het
Atad2	A	G	15: 58,103,283	L638P	probably damaging	Het
Atf7ip	T	A	6: 136,596,491	D1009E	probably benign	Het
Bend7	A	T	2: 4,744,322	K83N	probably damaging	Het
Bicc1	C	T	10: 70,945,316	D562N	possibly damaging	Het
Calcrl	T	A	2: 84,351,205	N200Y	probably damaging	Het
Ccdc125	C	A	13: 100,677,945	A11E	possibly damaging	Het
Cd5l	A	G	3: 87,365,951	T76A	probably benign	Het
Cdhr5	A	T	7: 141,273,731	I2N	probably damaging	Het
Cdk10	C	T	8: 123,230,614	A230V	probably damaging	Het
Cep128	T	C	12: 90,999,545		probably benign	Het
Cep131	T	C	11: 120,076,156	N186D	probably damaging	Het
Cog7	G	T	7: 121,971,381	P168Q	probably damaging	Het
Col28a1	T	A	6: 8,014,559	M949L	probably benign	Het
Coq8b	T	A	7: 27,250,591	M365K	probably damaging	Het
Cpa1	A	G	6: 30,639,516	E18G	possibly damaging	Het
Csmd2	A	G	4: 128,517,749	H2520R	probably benign	Het
Cyp2c69	T	C	19: 39,877,594	N185S	probably benign	Het
Dpm1	G	A	2: 168,210,536	T260I	probably damaging	Het
Dtx3	A	T	10: 127,191,307		probably null	Het
Eepd1	T	C	9: 25,589,460	V401A	possibly damaging	Het
Ehhadh	A	G	16: 21,763,202	S347P	possibly damaging	Het
Elp3	A	G	14: 65,547,864		probably null	Het
Enam	C	T	5: 88,493,108	Q210*	probably null	Het
Epha1	C	T	6: 42,363,816	R607H	probably benign	Het
Erich6	A	G	3: 58,636,830	I112T	probably benign	Het
F830045P16Rik	A	G	2: 129,460,550	V374A	possibly damaging	Het
Fam171a2	C	A	11: 102,438,685	R416L	possibly damaging	Het
Fam35a	A	G	14: 34,268,625	V108A	probably benign	Het
Fbn1	T	C	2: 125,372,399	N764S	probably benign	Het
Fip1l1	C	T	5: 74,591,939	T469I	probably damaging	Het
Flad1	G	A	3: 89,405,910	R342C	probably damaging	Het
Fzd3	A	G	14: 65,239,820	V95A	probably benign	Het
Garem1	T	C	18: 21,147,893	T469A	probably benign	Het
Gm13084	G	A	4: 143,810,805	Q319*	probably null	Het
Gm17093	A	G	14: 44,518,348	Y24C	unknown	Het
Gm4788	T	A	1: 139,733,443	D556V	probably damaging	Het
Gm7534	A	G	4: 134,193,099	V585A	probably benign	Het
Grap2	T	C	15: 80,638,561	V96A	possibly damaging	Het
Greb1	A	T	12: 16,684,360		probably null	Het
Grid2ip	A	T	5: 143,388,775	K913*	probably null	Het
Gzmk	T	C	13: 113,173,021	D126G	probably damaging	Het
Hibch	A	G	1: 52,885,178	I171V	possibly damaging	Het
Hipk2	G	T	6: 38,818,404	T310K	possibly damaging	Het
Hk3	T	C	13: 55,006,418	Y815C	probably damaging	Het
Hps5	A	T	7: 46,788,354	V99E	probably damaging	Het
Hspg2	A	G	4: 137,541,666	H2203R	possibly damaging	Het
Il12rb2	A	G	6: 67,309,137	V108A	probably damaging	Het
Il6st	C	T	13: 112,490,510	R279*	probably null	Het
Kdm2a	A	C	19: 4,325,026	S692R	probably benign	Het
Kif13a	T	C	13: 46,826,748	K176R	probably damaging	Het
Kif5b	T	C	18: 6,216,869	K485E	probably damaging	Het
Ktn1	C	T	14: 47,725,956	R1111*	probably null	Het
Lrrc23	A	T	6: 124,778,189	N128K	probably benign	Het
Mad1l1	G	A	5: 140,300,262	Q293*	probably null	Het
Man1b1	A	T	2: 25,345,475	I338F	possibly damaging	Het
March1	G	T	8: 66,468,363	V225L	probably damaging	Het
Mrpl3	A	G	9: 105,057,032	D118G	probably damaging	Het
Nomo1	A	T	7: 46,083,715	Q1209L	unknown	Het
Nrcam	A	G	12: 44,574,019	E949G	probably damaging	Het
Olfm5	T	G	7: 104,154,365	N297T	probably damaging	Het
Olfr573-ps1	T	A	7: 102,942,246	L110F	probably damaging	Het
Pcdh7	A	T	5: 57,720,804	N567I	probably damaging	Het
Pkn1	A	G	8: 83,677,966	L495P	probably damaging	Het
Pkp1	T	C	1: 135,882,588	S415G	probably damaging	Het
Pou2f1	T	A	1: 165,916,923	Q53L	probably null	Het
Prkce	A	G	17: 86,630,083	K648R	probably benign	Het
Ptprh	G	A	7: 4,573,430	T277I	possibly damaging	Het
Rpl31	C	T	1: 39,370,967	R83C	probably benign	Het
Rpusd3	G	A	6: 113,416,876	Q194*	probably null	Het
Sgsm1	T	A	5: 113,282,626	N298Y	probably damaging	Het
She	G	A	3: 89,851,639	G355D	probably benign	Het
Snx11	C	T	11: 96,774,458	E9K	possibly damaging	Het
Soat1	C	A	1: 156,432,937	A444S	probably benign	Het
Sox6	T	C	7: 115,486,662	Y690C	probably damaging	Het
Spata13	T	A	14: 60,733,179	F10I	probably benign	Het
St18	C	A	1: 6,802,905	T288K	probably benign	Het
Tifa	C	T	3: 127,796,586	S2F	probably damaging	Het
Tmem232	A	T	17: 65,430,888	S392R	probably benign	Het
Tmtc3	T	C	10: 100,466,220	N289S	probably damaging	Het
Tpo	A	G	12: 30,092,634	F697S	probably damaging	Het
Trp53	A	G	11: 69,587,630	T122A	probably damaging	Het
Trps1	A	C	15: 50,827,316	I10S	probably benign	Het
Tubgcp5	C	T	7: 55,794,185		probably benign	Het
Unc13c	T	G	9: 73,932,072	Y499S	possibly damaging	Het
Unc45a	C	A	7: 80,333,035	D381Y	probably damaging	Het
Uroc1	A	T	6: 90,349,192	I510F	possibly damaging	Het
Usp15	A	G	10: 123,127,757	F589L	probably damaging	Het
Vmn2r76	T	C	7: 86,225,525	Y748C	probably damaging	Het
Wwp1	T	C	4: 19,662,143	N151D	probably benign	Het
Zbtb40	A	T	4: 137,001,216	S439T	probably benign	Het
Zbtb6	A	T	2: 37,428,716	L400*	probably null	Het
Zfp125	C	T	12: 20,899,960		noncoding transcript	Het
Zmynd8	A	C	2: 165,840,034	Y183*	probably null	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
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'- CCCAGCAGCTTGTGGTAAATATAC -3'
(R):5'- GTGAGTGAAACAGCCTGGAGTC -3'

Sequencing Primer
(F):5'- TATACCCTGACACAGAGGTCTCGTC -3'
(R):5'- AAACAGCCTGGAGTCTGTCTG -3'

Posted On

2016-03-01