Mutagenetix > Incidental Mutation

Incidental Mutation 'R2072:Upf3a'

227232

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

040077-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2072 (G1)

Quality Score

107

Status

Not validated

Chromosome

Chromosomal Location

13835615-13849193 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 13835850 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Arginine at position 56 (K56R)

Ref Sequence

ENSEMBL: ENSMUSP00000037354 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000043767] [ENSMUST00000043962]

AlphaFold

Q3ULJ3

Predicted Effect

possibly damaging
Transcript: ENSMUST00000043767
AA Change: K56R

PolyPhen 2 Score 0.627 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000037354
Gene: ENSMUSG00000038398
AA Change: K56R

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

probably benign
Transcript: ENSMUST00000043962

SMART Domains

Protein: ENSMUSP00000047950
Gene: ENSMUSG00000038416

Domain	Start	End	E-Value	Type
Pfam:TPR_9	11	63	1.8e-3	PFAM
Pfam:ANAPC3	15	95	3.5e-23	PFAM
TPR	130	163	1.17e1	SMART
Blast:TPR	299	333	2e-8	BLAST
Blast:TPR	334	367	1e-14	BLAST
TPR	368	401	1.48e1	SMART
Blast:TPR	402	435	7e-15	BLAST
TPR	445	478	6.68e-6	SMART
TPR	479	512	1.74e-4	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137360

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000211643

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000211724

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.3%

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. 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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610040J01Rik	G	C	5: 64,056,080 (GRCm39)	R272P	possibly damaging	Het
Ablim3	A	T	18: 61,990,159 (GRCm39)	D83E	possibly damaging	Het
Aco1	G	A	4: 40,183,605 (GRCm39)	G508S	probably damaging	Het
Adamts13	C	A	2: 26,895,437 (GRCm39)	T1176N	probably benign	Het
Adgre5	T	C	8: 84,454,433 (GRCm39)	T357A	probably benign	Het
Akap8l	C	T	17: 32,551,457 (GRCm39)	R511H	probably damaging	Het
Ankrd33	T	C	15: 101,017,517 (GRCm39)	V310A	probably benign	Het
Armh3	A	T	19: 45,953,820 (GRCm39)	I188K	probably damaging	Het
Bnipl	C	T	3: 95,151,522 (GRCm39)	G232E	probably damaging	Het
Btbd17	A	T	11: 114,682,778 (GRCm39)		probably null	Het
Cacna1s	G	A	1: 136,007,242 (GRCm39)	V173I	probably benign	Het
Ccdc122	T	C	14: 77,306,391 (GRCm39)		probably null	Het
Ces1a	T	A	8: 93,774,703 (GRCm39)	N12Y	probably benign	Het
Chrdl1	T	C	X: 142,086,414 (GRCm39)	I231V	probably benign	Het
Ciita	C	T	16: 10,336,217 (GRCm39)	T958I	probably benign	Het
Cnot1	G	T	8: 96,466,461 (GRCm39)	T1592K	possibly damaging	Het
Dcaf15	T	C	8: 84,828,370 (GRCm39)	D240G	probably damaging	Het
Dlgap1	C	T	17: 70,969,765 (GRCm39)	R524C	probably damaging	Het
Dmd	G	C	X: 83,356,089 (GRCm39)	A2257P	probably benign	Het
Dsg1c	A	G	18: 20,408,309 (GRCm39)	M453V	probably benign	Het
Ednrb	G	T	14: 104,054,535 (GRCm39)	N432K	probably benign	Het
Fcgbp	G	A	7: 27,819,814 (GRCm39)	G2514S	probably damaging	Het
Fez1	A	G	9: 36,779,241 (GRCm39)	K306R	probably benign	Het
Fmo4	A	G	1: 162,637,456 (GRCm39)	V12A	probably benign	Het
Fpgt	T	C	3: 154,793,511 (GRCm39)	Y172C	probably damaging	Het
Fsip2	T	A	2: 82,839,159 (GRCm39)	F6976I	possibly damaging	Het
Galnt12	C	T	4: 47,108,477 (GRCm39)	R205*	probably null	Het
Grik5	A	T	7: 24,714,738 (GRCm39)	M752K	possibly damaging	Het
Herc2	A	G	7: 55,876,712 (GRCm39)	N4516S	probably damaging	Het
Ifrd2	A	T	9: 107,469,744 (GRCm39)	D439V	probably damaging	Het
Igsf3	A	G	3: 101,346,831 (GRCm39)	T609A	probably benign	Het
Kif5a	T	C	10: 127,081,238 (GRCm39)	D232G	probably damaging	Het
Lgi2	A	G	5: 52,695,847 (GRCm39)	S371P	probably damaging	Het
Marchf3	A	T	18: 56,944,925 (GRCm39)	V56E	possibly damaging	Het
Mib2	T	C	4: 155,744,158 (GRCm39)	D168G	probably damaging	Het
Nhs	T	A	X: 160,625,717 (GRCm39)	H544L	probably damaging	Het
Nlrp2	A	G	7: 5,328,005 (GRCm39)	S683P	probably damaging	Het
Onecut3	T	G	10: 80,330,848 (GRCm39)	L3V	unknown	Het
Or12j2	T	C	7: 139,916,566 (GRCm39)	S264P	possibly damaging	Het
Or4c35	C	A	2: 89,808,557 (GRCm39)	T145K	probably benign	Het
Or5b102	A	T	19: 13,041,044 (GRCm39)	M90L	probably benign	Het
Otogl	C	T	10: 107,616,904 (GRCm39)	C1791Y	probably damaging	Het
Paip1	T	C	13: 119,566,798 (GRCm39)	V128A	possibly damaging	Het
Pcnx2	A	T	8: 126,488,481 (GRCm39)	C1688S	possibly damaging	Het
Pdzd2	A	G	15: 12,385,905 (GRCm39)	L955P	probably damaging	Het
Phlpp2	T	C	8: 110,655,124 (GRCm39)	S605P	possibly damaging	Het
Pkhd1l1	G	T	15: 44,422,035 (GRCm39)	A3102S	probably damaging	Het
Plxnb2	G	T	15: 89,042,654 (GRCm39)	R1545S	probably damaging	Het
Ppp4c	T	C	7: 126,386,520 (GRCm39)		probably null	Het
Prune1	C	T	3: 95,162,719 (GRCm39)	R318Q	probably benign	Het
Psg27	T	C	7: 18,294,342 (GRCm39)	D355G	probably damaging	Het
Psg27	A	G	7: 18,298,934 (GRCm39)	L129P	probably benign	Het
Psmc6	A	G	14: 45,567,323 (GRCm39)	K7E	possibly damaging	Het
Reln	A	T	5: 22,124,175 (GRCm39)	V2777E	probably damaging	Het
Rigi	A	T	4: 40,224,069 (GRCm39)		probably null	Het
Scn11a	G	T	9: 119,640,274 (GRCm39)	A207E	possibly damaging	Het
Slc5a5	C	T	8: 71,345,083 (GRCm39)	G75R	possibly damaging	Het
Smarcd2	A	T	11: 106,156,133 (GRCm39)	L42*	probably null	Het
Smg1	T	C	7: 117,762,389 (GRCm39)		probably benign	Het
Smurf2	T	A	11: 106,732,595 (GRCm39)	Q335L	probably benign	Het
Sspo	A	T	6: 48,450,451 (GRCm39)	H2580L	probably benign	Het
Stk3	T	C	15: 34,959,195 (GRCm39)	M256V	possibly damaging	Het
Syt1	A	G	10: 108,419,833 (GRCm39)	I276T	probably damaging	Het
Syt10	C	T	15: 89,674,979 (GRCm39)	D456N	probably damaging	Het
Taar9	A	T	10: 23,984,877 (GRCm39)	C186S	probably damaging	Het
Tnrc6b	C	T	15: 80,767,166 (GRCm39)	P977L	possibly damaging	Het
Trp53bp2	A	G	1: 182,286,432 (GRCm39)	T1091A	probably benign	Het
Ttn	G	T	2: 76,768,120 (GRCm39)	T2947N	probably damaging	Het
Ube2q1	T	C	3: 89,686,878 (GRCm39)		probably null	Het
Ube3c	A	G	5: 29,840,638 (GRCm39)	E671G	probably benign	Het
Vmn2r15	A	T	5: 109,434,619 (GRCm39)	M695K	possibly damaging	Het
Vmn2r3	A	T	3: 64,182,493 (GRCm39)	M402K	possibly damaging	Het
Zfp354b	T	A	11: 50,813,279 (GRCm39)	R549*	probably null	Het
Zfp37	A	T	4: 62,109,945 (GRCm39)	M411K	probably damaging	Het
Zfp747	T	A	7: 126,973,142 (GRCm39)	T343S	possibly damaging	Het
Zfp853	T	A	5: 143,275,137 (GRCm39)	Q161L	unknown	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
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'- ACACCGAATTCCAAGGGAGG -3'
(R):5'- ATCCTAGTCCAGACTGCTCG -3'

Sequencing Primer
(F):5'- ATTCCAAGGGAGGGGCTGC -3'
(R):5'- TAGTCCAGACTGCTCGCAACAG -3'

Posted On

2014-09-17