Mutagenetix > Incidental Mutation

Incidental Mutation 'R6321:Upf3a'

510350

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

044418-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6321 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

13835615-13849193 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 13837466 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Isoleucine at position 137 (N137I)

Ref Sequence

ENSEMBL: ENSMUSP00000037354 (fasta)

Gene Model

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

AlphaFold

Q3ULJ3

Predicted Effect

possibly damaging
Transcript: ENSMUST00000043767
AA Change: N137I

PolyPhen 2 Score 0.527 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000037354
Gene: ENSMUSG00000038398
AA Change: N137I

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: ENSMUST00000211643

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000211724

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.3%
20x: 97.8%

Validation Efficiency

100% (52/52)

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
Actbl2	G	T	13: 111,391,915 (GRCm39)	M83I	probably damaging	Het
Adgra2	T	A	8: 27,604,190 (GRCm39)	M460K	probably benign	Het
Aldh16a1	G	A	7: 44,799,189 (GRCm39)	A31V	probably damaging	Het
Ank2	T	C	3: 126,740,587 (GRCm39)		probably benign	Het
Arrdc4	C	A	7: 68,398,793 (GRCm39)	D8Y	probably benign	Het
Auts2	A	G	5: 131,494,953 (GRCm39)	Y110H	probably damaging	Het
Blnk	A	T	19: 40,922,903 (GRCm39)	Y405N	probably damaging	Het
Capsl	T	C	15: 9,461,855 (GRCm39)	F84L	probably damaging	Het
Cdcp3	T	C	7: 130,858,735 (GRCm39)		probably null	Het
Cenpl	T	C	1: 160,902,465 (GRCm39)	S46P	probably benign	Het
Chd1l	G	A	3: 97,494,483 (GRCm39)	A399V	probably damaging	Het
Chrnd	C	T	1: 87,119,951 (GRCm39)	R90C	probably damaging	Het
Cyfip2	A	T	11: 46,182,347 (GRCm39)	M37K	probably benign	Het
Dnah11	T	C	12: 118,106,027 (GRCm39)	E625G	possibly damaging	Het
Dnah5	T	G	15: 28,372,557 (GRCm39)	V2936G	probably damaging	Het
Dock9	A	G	14: 121,783,433 (GRCm39)	M2055T	probably damaging	Het
Epb41l2	A	T	10: 25,344,026 (GRCm39)	R274S	probably damaging	Het
Erich3	A	T	3: 154,433,139 (GRCm39)	H371L	probably damaging	Het
Evi5l	C	A	8: 4,253,080 (GRCm39)	P454T	probably benign	Het
Gm10549	C	A	18: 33,597,358 (GRCm39)		probably benign	Het
Gm11595	G	A	11: 99,663,381 (GRCm39)	R100C	unknown	Het
Golgb1	T	A	16: 36,738,559 (GRCm39)	C2299*	probably null	Het
Heca	G	C	10: 17,790,991 (GRCm39)		probably null	Het
Hecw1	C	T	13: 14,697,414 (GRCm39)	A9T	probably benign	Het
Hs3st6	T	A	17: 24,977,542 (GRCm39)	W341R	probably damaging	Het
Kidins220	C	T	12: 25,107,533 (GRCm39)	S1571L	probably benign	Het
Klk1b9	A	G	7: 43,443,732 (GRCm39)	E82G	probably damaging	Het
Ltbp3	C	A	19: 5,795,685 (GRCm39)	H180Q	probably benign	Het
Mecom	A	G	3: 30,034,741 (GRCm39)	Y502H	probably damaging	Het
Mfsd2a	A	G	4: 122,843,165 (GRCm39)	V372A	probably benign	Het
Mrgprd	A	G	7: 144,875,879 (GRCm39)	D250G	probably benign	Het
Muc2	A	G	7: 141,287,397 (GRCm39)	D191G	probably benign	Het
Myl10	G	C	5: 136,726,825 (GRCm39)	V70L	probably benign	Het
Naip6	C	A	13: 100,436,909 (GRCm39)	S538I	probably benign	Het
Or4f59	A	G	2: 111,873,113 (GRCm39)	V88A	probably benign	Het
Or52w1	A	G	7: 105,018,109 (GRCm39)	Y192C	probably damaging	Het
Pnpla6	T	C	8: 3,594,015 (GRCm39)	V1342A	probably benign	Het
Ppp1r9a	A	G	6: 5,115,151 (GRCm39)	E789G	probably damaging	Het
Prkdc	A	G	16: 15,532,783 (GRCm39)	T1471A	probably benign	Het
Scarb1	T	A	5: 125,381,395 (GRCm39)	S50C	probably damaging	Het
Slc4a8	C	T	15: 100,687,045 (GRCm39)	T283M	probably damaging	Het
Smc2	C	A	4: 52,462,814 (GRCm39)	D601E	probably benign	Het
Snx6	C	A	12: 54,798,798 (GRCm39)	V221F	probably damaging	Het
Spag17	A	C	3: 99,995,743 (GRCm39)	K1794T	probably benign	Het
Tpo	A	G	12: 30,153,107 (GRCm39)	W416R	probably damaging	Het
Ttc13	C	A	8: 125,409,930 (GRCm39)	K427N	probably damaging	Het
Ush2a	C	T	1: 188,581,243 (GRCm39)	Q3708*	probably null	Het
Zbtb17	G	A	4: 141,190,694 (GRCm39)	G171S	probably benign	Het
Zfp451	A	G	1: 33,852,816 (GRCm39)	F33L	probably damaging	Het
Zfp454	A	G	11: 50,763,876 (GRCm39)	F408L	probably damaging	Het
Zfp639	T	C	3: 32,571,237 (GRCm39)	Y40H	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
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
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'- AAGGCTTCAGTTAATGGTTGC -3'
(R):5'- AGCCTGTGAGAACTTACTCCC -3'

Sequencing Primer
(F):5'- CTCGGGCATGAAAAAGTATTTGC -3'
(R):5'- TGTGAGAACTTACTCCCCAGCAAG -3'

Posted On

2018-04-02