Mutagenetix > Incidental Mutation

Incidental Mutation 'R0564:Upf3a'

46070

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

038755-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0564 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

13835615-13849193 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 13845656 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Glutamic Acid at position 252 (K252E)

Ref Sequence

ENSEMBL: ENSMUSP00000037354 (fasta)

Gene Model

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

AlphaFold

Q3ULJ3

Predicted Effect

probably benign
Transcript: ENSMUST00000043767
AA Change: K252E

PolyPhen 2 Score 0.416 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000037354
Gene: ENSMUSG00000038398
AA Change: K252E

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

0.0771

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.7%

Validation Efficiency

98% (52/53)

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: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamtsl5	A	G	10: 80,180,681 (GRCm39)	V127A	probably damaging	Het
Alox12	T	A	11: 70,143,662 (GRCm39)	D202V	probably damaging	Het
Ankib1	A	G	5: 3,779,655 (GRCm39)	Y405H	probably damaging	Het
Apbb2	A	T	5: 66,609,593 (GRCm39)	M18K	probably damaging	Het
Atad2	C	A	15: 57,989,229 (GRCm39)		probably benign	Het
Birc6	T	A	17: 74,932,238 (GRCm39)		probably benign	Het
Ccdc126	T	C	6: 49,311,076 (GRCm39)	M28T	possibly damaging	Het
Cdc16	A	T	8: 13,831,618 (GRCm39)	D617V	probably damaging	Het
Cep135	G	A	5: 76,763,557 (GRCm39)	E516K	probably damaging	Het
Cep135	G	T	5: 76,786,796 (GRCm39)	M1081I	probably benign	Het
Col6a3	A	C	1: 90,735,456 (GRCm39)	V731G	probably damaging	Het
Cstdc6	A	T	16: 36,143,346 (GRCm39)	Y34*	probably null	Het
Cwc27	C	A	13: 104,797,865 (GRCm39)	E365*	probably null	Het
Dip2b	C	A	15: 100,060,600 (GRCm39)	Y258*	probably null	Het
Dnah17	A	G	11: 117,973,807 (GRCm39)	V1900A	probably damaging	Het
Dpysl2	A	T	14: 67,042,895 (GRCm39)		probably benign	Het
Dync2h1	A	T	9: 7,139,432 (GRCm39)	L1401Q	probably damaging	Het
Esf1	A	T	2: 140,000,506 (GRCm39)	Y427N	possibly damaging	Het
Fbln1	T	A	15: 85,111,308 (GRCm39)	V154D	probably benign	Het
Frem2	A	G	3: 53,563,530 (GRCm39)	F326L	probably damaging	Het
Gm4922	T	A	10: 18,659,813 (GRCm39)	N303I	possibly damaging	Het
H1f6	G	T	13: 23,880,307 (GRCm39)	K153N	possibly damaging	Het
Iigp1	G	A	18: 60,523,523 (GRCm39)	V214M	probably damaging	Het
Luzp2	A	G	7: 54,485,710 (GRCm39)	K2E	probably damaging	Het
Mcc	A	G	18: 44,601,574 (GRCm39)	L410P	probably damaging	Het
Mfn2	A	G	4: 147,967,712 (GRCm39)	F452S	probably damaging	Het
Mib2	C	T	4: 155,743,917 (GRCm39)	G42S	probably damaging	Het
Micu2	A	G	14: 58,156,831 (GRCm39)	F335L	possibly damaging	Het
Mpp3	T	G	11: 101,896,173 (GRCm39)	K450T	possibly damaging	Het
Mtmr4	T	A	11: 87,489,714 (GRCm39)	V79E	probably damaging	Het
Nlrp4b	A	G	7: 10,448,585 (GRCm39)	I263V	probably benign	Het
Or52p2	T	C	7: 102,237,738 (GRCm39)	I71V	probably benign	Het
Or6c76	T	G	10: 129,612,005 (GRCm39)	V74G	probably damaging	Het
Pdk1	G	A	2: 71,710,383 (GRCm39)	W113*	probably null	Het
Phaf1	T	A	8: 105,966,603 (GRCm39)		probably benign	Het
Phxr4	A	T	9: 13,342,993 (GRCm39)		probably benign	Het
Rad51ap2	T	A	12: 11,507,897 (GRCm39)	H606Q	probably benign	Het
Ralgapa1	A	T	12: 55,829,670 (GRCm39)	I187K	possibly damaging	Het
Rps27	A	G	3: 90,120,230 (GRCm39)		probably benign	Het
Sema3e	T	A	5: 14,286,099 (GRCm39)		probably null	Het
Sh2d3c	G	A	2: 32,643,064 (GRCm39)	C749Y	probably damaging	Het
Siah2	T	C	3: 58,583,656 (GRCm39)	D210G	probably benign	Het
Smap2	G	A	4: 120,834,174 (GRCm39)	P155S	probably benign	Het
Snrk	C	T	9: 121,995,610 (GRCm39)	T463M	possibly damaging	Het
Tm9sf3	A	G	19: 41,233,964 (GRCm39)		probably benign	Het
Tmem132d	C	T	5: 127,861,842 (GRCm39)	E760K	probably damaging	Het
Tmem184c	A	T	8: 78,332,789 (GRCm39)		probably null	Het
Tmem235	A	T	11: 117,751,674 (GRCm39)	I33F	possibly damaging	Het
Tmem267	A	T	13: 119,629,175 (GRCm39)		probably null	Het
Top1	G	A	2: 160,556,185 (GRCm39)	R548Q	probably damaging	Het
Trio	T	C	15: 27,805,908 (GRCm39)	N527D	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
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
R4424:Upf3a	UTSW	8	13,846,573 (GRCm39)	missense	probably benign	0.09
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'- ATATGAATGTCCCCAGGTGCGGTG -3'
(R):5'- ACCGACAACGGTCGATGAATTACAG -3'

Sequencing Primer
(F):5'- AGAAGGACCACCCCTCTTTTG -3'
(R):5'- TTACAGAGCTACGCTACTTCAG -3'

Posted On

2013-06-11