Mutagenetix > Incidental Mutation

Incidental Mutation 'R4239:Upf3a'

371109

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

041056-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4239 (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 13846591 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glycine at position 324 (R324G)

Ref Sequence

ENSEMBL: ENSMUSP00000037354 (fasta)

Gene Model

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

AlphaFold

Q3ULJ3

Predicted Effect

probably benign
Transcript: ENSMUST00000043767
AA Change: R324G

PolyPhen 2 Score 0.280 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000037354
Gene: ENSMUSG00000038398
AA Change: R324G

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: 99.3%
3x: 98.7%
10x: 97.5%
20x: 95.8%

Validation Efficiency

95% (55/58)

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: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930563M21Rik	T	C	9: 55,888,126 (GRCm39)	D397G	probably benign	Het
Alpk2	T	A	18: 65,433,212 (GRCm39)	I1765F	probably damaging	Het
Ano5	T	A	7: 51,237,414 (GRCm39)	I696N	probably damaging	Het
Areg	A	T	5: 91,291,375 (GRCm39)	N106I	probably damaging	Het
Atad2b	A	G	12: 5,035,710 (GRCm39)	N759D	probably benign	Het
B4galnt4	T	C	7: 140,641,239 (GRCm39)	L18P	probably damaging	Het
Boc	T	C	16: 44,312,247 (GRCm39)	D605G	probably damaging	Het
Cfap46	G	T	7: 139,246,203 (GRCm39)	Q387K	possibly damaging	Het
Cfap74	C	A	4: 155,547,529 (GRCm39)	H1238Q	probably benign	Het
Clip2	A	G	5: 134,564,051 (GRCm39)		probably benign	Het
Cog4	T	C	8: 111,585,244 (GRCm39)	I303T	probably damaging	Het
Col18a1	C	T	10: 76,932,001 (GRCm39)	V363I	unknown	Het
Crip3	A	T	17: 46,742,156 (GRCm39)	K184*	probably null	Het
Ddi1	A	G	9: 6,265,799 (GRCm39)	M190T	probably benign	Het
Dnah3	G	A	7: 119,628,248 (GRCm39)	Q1459*	probably null	Het
Dpp8	A	G	9: 64,962,205 (GRCm39)	D415G	probably benign	Het
Ehhadh	T	G	16: 21,581,438 (GRCm39)	D518A	probably damaging	Het
Erbb2	A	G	11: 98,318,869 (GRCm39)	K549R	probably benign	Het
Fbxl3	G	A	14: 103,326,854 (GRCm39)	S176L	probably damaging	Het
Gm1979	T	C	5: 26,206,119 (GRCm39)	T154A	probably benign	Het
Gm6871	G	T	7: 41,195,204 (GRCm39)	T511K	probably damaging	Het
Gtf2h1	C	T	7: 46,454,489 (GRCm39)	A157V	probably benign	Het
Hexb	T	C	13: 97,313,259 (GRCm39)		probably benign	Het
Ifi214	A	T	1: 173,352,509 (GRCm39)	S307T	possibly damaging	Het
Ighv3-4	A	T	12: 114,217,533 (GRCm39)	D19E	probably benign	Het
Klk6	A	G	7: 43,478,597 (GRCm39)	H168R	probably benign	Het
Large2	A	G	2: 92,196,950 (GRCm39)		probably benign	Het
Myo5c	T	C	9: 75,191,224 (GRCm39)	I1086T	probably benign	Het
Nes	C	A	3: 87,886,666 (GRCm39)	P1598T	probably damaging	Het
Or13a25	A	G	7: 140,247,496 (GRCm39)	N99D	probably benign	Het
Or51f1d	T	C	7: 102,701,003 (GRCm39)	V166A	probably benign	Het
Or5g25	T	A	2: 85,478,647 (GRCm39)	Q6L	probably damaging	Het
Otud7a	A	G	7: 63,300,702 (GRCm39)	D47G	probably damaging	Het
Phactr1	T	A	13: 43,248,363 (GRCm39)	N437K	possibly damaging	Het
Plcb1	A	T	2: 135,186,078 (GRCm39)	I682F	probably damaging	Het
Plcz1	T	A	6: 139,986,344 (GRCm39)		probably null	Het
Prl7a1	T	A	13: 27,821,549 (GRCm39)	Q129L	possibly damaging	Het
Prrt4	T	C	6: 29,170,163 (GRCm39)	Y763C	probably damaging	Het
Psma7	T	C	2: 179,681,304 (GRCm39)		probably benign	Het
Serpinb6b	G	C	13: 33,156,246 (GRCm39)	C112S	probably damaging	Het
Slc14a2	G	A	18: 78,250,283 (GRCm39)	R62C	probably damaging	Het
Slc35f5	G	A	1: 125,500,211 (GRCm39)	A242T	possibly damaging	Het
Speer4b	T	C	5: 27,706,311 (GRCm39)	R19G	probably benign	Het
Trank1	A	G	9: 111,196,103 (GRCm39)	I1376V	probably benign	Het
Trbv12-2	A	G	6: 41,095,831 (GRCm39)	N12D	probably benign	Het
Uba7	T	C	9: 107,854,001 (GRCm39)		probably null	Het
Usp46	T	G	5: 74,192,928 (GRCm39)		probably benign	Het
Vmn2r14	T	G	5: 109,364,277 (GRCm39)		probably null	Het
Wbp2	G	A	11: 115,971,373 (GRCm39)		probably benign	Het
Wdpcp	T	A	11: 21,645,269 (GRCm39)	N232K	probably damaging	Het
Wdpcp	T	A	11: 21,645,271 (GRCm39)	M233K	probably benign	Het
Zfp157	A	G	5: 138,445,803 (GRCm39)	I53V	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
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'- ACAGTAGCAGTAATAATAACCGTGG -3'
(R):5'- TAAGCCCAGGAAGGAGGTCTTAC -3'

Sequencing Primer
(F):5'- CCGTGGTAATGTTACAATTTCTCAGC -3'
(R):5'- TCTTACAAGGCAAGGGAGATGC -3'

Posted On

2016-02-17