Mutagenetix > Incidental Mutation

Incidental Mutation 'R4424:Upf3a'

327264

Institutional Source

Beutler Lab

Gene Symbol

Upf3a

Ensembl Gene

ENSMUSG00000038398

Gene Name

UPF3 regulator of nonsense transcripts homolog A (yeast)

Synonyms

RENT3A, 2600001C03Rik, 4930546M19Rik, UPF3

MMRRC Submission

041696-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4424 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

13835615-13849193 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 13846573 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Threonine at position 318 (P318T)

Ref Sequence

ENSEMBL: ENSMUSP00000037354 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000043767]

AlphaFold

Q3ULJ3

Predicted Effect

probably benign
Transcript: ENSMUST00000043767
AA Change: P318T

PolyPhen 2 Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000037354
Gene: ENSMUSG00000038398
AA Change: P318T

Domain	Start	End	E-Value	Type
low complexity region	6	18	N/A	INTRINSIC
Pfam:Smg4_UPF3	63	224	1.4e-54	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000211724

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.3%

Validation Efficiency

95% (69/73)

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. The encoded protein is one of two functional homologs to yeast Upf3p. 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 binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. It forms with Y14 a complex that binds specifically 20 nt upstream of exon-exon junctions. This gene is located on the long arm of chromosome 13. Two splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: The gene product protects against mRNA transcript degradation. Homozygous constitutive KO is embryonic lethal. Homozygous conditional KO in testes leads to reduced male fertility. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933409G03Rik	A	T	2: 68,445,491 (GRCm39)		probably benign	Het
Aimp1	A	T	3: 132,373,253 (GRCm39)	L229Q	probably benign	Het
Ankrd16	T	A	2: 11,789,215 (GRCm39)	D267E	possibly damaging	Het
Apol11b	A	G	15: 77,522,133 (GRCm39)		probably null	Het
Arfgap1	C	A	2: 180,622,869 (GRCm39)	D327E	probably benign	Het
Arid3b	A	T	9: 57,741,151 (GRCm39)	D98E	probably benign	Het
Art2b	T	A	7: 101,229,129 (GRCm39)	I257F	probably benign	Het
Atp5f1a	T	A	18: 77,867,766 (GRCm39)		probably benign	Het
Carmil3	A	G	14: 55,738,928 (GRCm39)	T861A	probably benign	Het
Cep164	A	T	9: 45,691,002 (GRCm39)	F1259L	possibly damaging	Het
Cfap91	G	T	16: 38,140,727 (GRCm39)	P409T	probably damaging	Het
Chrnd	T	C	1: 87,123,512 (GRCm39)	V350A	probably benign	Het
Clcn7	T	C	17: 25,379,150 (GRCm39)	L744P	probably damaging	Het
Csl	T	A	10: 99,594,453 (GRCm39)	D204V	possibly damaging	Het
Cstdc3	A	G	16: 36,132,951 (GRCm39)	D76G	probably null	Het
Cyp2c29	G	T	19: 39,275,620 (GRCm39)	W20L	probably damaging	Het
Dhrs13	G	T	11: 77,927,951 (GRCm39)	G266*	probably null	Het
Dll3	T	C	7: 27,995,716 (GRCm39)	N362D	probably damaging	Het
Efcab3	T	G	11: 104,626,940 (GRCm39)		probably null	Het
Fanca	A	G	8: 124,015,532 (GRCm39)	V715A	probably benign	Het
Fhod1	T	C	8: 106,063,983 (GRCm39)		probably benign	Het
Fpr2	C	T	17: 18,113,394 (GRCm39)	P130L	probably damaging	Het
Glce	A	G	9: 61,967,535 (GRCm39)	Y539H	probably damaging	Het
Hfe	A	T	13: 23,890,866 (GRCm39)	V91E	probably benign	Het
Hoxd13	A	T	2: 74,500,301 (GRCm39)	K281*	probably null	Het
Ighv1-66	A	T	12: 115,557,157 (GRCm39)	W3R	probably damaging	Het
Impg2	G	A	16: 56,080,388 (GRCm39)	V622I	possibly damaging	Het
Jun	A	G	4: 94,939,084 (GRCm39)	M142T	probably benign	Het
Krt78	T	C	15: 101,856,375 (GRCm39)	T479A	probably benign	Het
Lama3	T	A	18: 12,652,929 (GRCm39)	C216*	probably null	Het
Lin54	G	T	5: 100,594,419 (GRCm39)	T582K	probably damaging	Het
Mapk11	A	G	15: 89,029,576 (GRCm39)		probably null	Het
Mindy3	A	G	2: 12,353,010 (GRCm39)	M397T	probably benign	Het
Mrpl41	T	C	2: 24,864,418 (GRCm39)	T85A	possibly damaging	Het
Msh6	T	A	17: 88,298,217 (GRCm39)	L1354*	probably null	Het
Mtmr12	T	C	15: 12,230,400 (GRCm39)	V41A	probably damaging	Het
Myh2	A	T	11: 67,083,551 (GRCm39)	Q1478L	probably benign	Het
Myo6	A	G	9: 80,195,320 (GRCm39)	K897E	probably benign	Het
Naprt	G	T	15: 75,764,605 (GRCm39)		probably null	Het
Nrl	G	A	14: 55,759,675 (GRCm39)	S84L	probably benign	Het
Nxf1	A	G	19: 8,744,128 (GRCm39)		probably benign	Het
Or8g2b	A	T	9: 39,751,652 (GRCm39)	R307S	possibly damaging	Het
Panx2	G	T	15: 88,952,423 (GRCm39)	V305F	probably benign	Het
Pcdhga1	T	C	18: 37,795,632 (GRCm39)	L212P	probably damaging	Het
Pik3ap1	G	A	19: 41,364,320 (GRCm39)	T133I	probably benign	Het
Ppat	A	G	5: 77,063,061 (GRCm39)	W517R	probably damaging	Het
Ppp1r16b	C	T	2: 158,599,174 (GRCm39)	T382I	probably benign	Het
Prkdc	G	A	16: 15,653,946 (GRCm39)	R3901H	probably damaging	Het
Prkdc	A	G	16: 15,591,603 (GRCm39)	K2694E	probably damaging	Het
Psma8	A	G	18: 14,854,247 (GRCm39)	I42M	probably damaging	Het
Ptprd	A	T	4: 76,021,200 (GRCm39)	M599K	probably benign	Het
Rnmt	A	G	18: 68,444,742 (GRCm39)	D237G	probably null	Het
Rpl31-ps17	C	T	12: 54,748,397 (GRCm39)		noncoding transcript	Het
Scaf11	G	A	15: 96,316,309 (GRCm39)	T1085I	possibly damaging	Het
Sec14l3	G	A	11: 4,016,210 (GRCm39)	R43Q	probably damaging	Het
Shc4	G	T	2: 125,494,442 (GRCm39)	T131K	probably benign	Het
Snx27	A	G	3: 94,469,330 (GRCm39)	F4L	probably benign	Het
Sorcs1	T	C	19: 50,367,379 (GRCm39)	T228A	probably damaging	Het
Spmap2l	T	C	5: 77,202,383 (GRCm39)	I268T	possibly damaging	Het
Sptan1	C	T	2: 29,919,721 (GRCm39)		probably benign	Het
Syvn1	C	T	19: 6,099,951 (GRCm39)		probably benign	Het
Tex47	G	T	5: 7,355,364 (GRCm39)	A182S	probably benign	Het
Tpcn1	T	C	5: 120,680,583 (GRCm39)	K549R	probably damaging	Het
Zbtb40	A	T	4: 136,726,005 (GRCm39)	M518K	probably damaging	Het
Zcchc14	G	A	8: 122,378,680 (GRCm39)		probably benign	Het
Zfp687	G	A	3: 94,916,439 (GRCm39)	P861L	probably damaging	Het

Other mutations in Upf3a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01398:Upf3a	APN	8	13,836,221 (GRCm39)	missense	probably damaging	0.98
IGL01678:Upf3a	APN	8	13,841,930 (GRCm39)	missense	probably benign	0.21
IGL02072:Upf3a	APN	8	13,848,368 (GRCm39)	missense	probably damaging	0.99
R0309:Upf3a	UTSW	8	13,845,500 (GRCm39)	splice site	probably null
R0564:Upf3a	UTSW	8	13,845,656 (GRCm39)	missense	probably benign	0.42
R0571:Upf3a	UTSW	8	13,842,184 (GRCm39)	missense	probably damaging	0.98
R0826:Upf3a	UTSW	8	13,848,338 (GRCm39)	missense	possibly damaging	0.65
R1387:Upf3a	UTSW	8	13,842,118 (GRCm39)	missense	probably damaging	1.00
R1913:Upf3a	UTSW	8	13,842,108 (GRCm39)	missense	probably damaging	1.00
R2072:Upf3a	UTSW	8	13,835,850 (GRCm39)	missense	possibly damaging	0.63
R2520:Upf3a	UTSW	8	13,846,443 (GRCm39)	splice site	probably null
R3845:Upf3a	UTSW	8	13,848,238 (GRCm39)	missense	probably benign	0.16
R4239:Upf3a	UTSW	8	13,846,591 (GRCm39)	missense	probably benign	0.28
R5522:Upf3a	UTSW	8	13,845,497 (GRCm39)	critical splice donor site	probably null
R6321:Upf3a	UTSW	8	13,837,466 (GRCm39)	missense	possibly damaging	0.53
R6922:Upf3a	UTSW	8	13,841,911 (GRCm39)	missense	probably damaging	1.00
R7583:Upf3a	UTSW	8	13,835,889 (GRCm39)	splice site	probably null
R7585:Upf3a	UTSW	8	13,837,418 (GRCm39)	missense	probably damaging	1.00
R7695:Upf3a	UTSW	8	13,848,279 (GRCm39)	missense	probably benign	0.01
R7991:Upf3a	UTSW	8	13,842,166 (GRCm39)	missense	probably damaging	1.00
R8913:Upf3a	UTSW	8	13,845,728 (GRCm39)	missense	possibly damaging	0.94
R9638:Upf3a	UTSW	8	13,848,343 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- TACGTACGGGCCATATCCATG -3'
(R):5'- TAAGCTGATACTGGGGCTCTGG -3'

Sequencing Primer
(F):5'- TAGCAAAGTCTGTATGTATGTGCCCC -3'
(R):5'- CTCTGGGTCAGGGCTCACTATG -3'

Posted On

2015-07-07