Mutagenetix > Incidental Mutation

Incidental Mutation 'R1769:Pnpt1'

194717

Institutional Source

Beutler Lab

Gene Symbol

Pnpt1

Ensembl Gene

ENSMUSG00000020464

Gene Name

polyribonucleotide nucleotidyltransferase 1

Synonyms

1200003F12Rik, polynucleotide phosphorylase, PNPase

MMRRC Submission

039800-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1769 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

29080744-29111828 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 29104159 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Aspartic acid at position 540 (N540D)

Ref Sequence

ENSEMBL: ENSMUSP00000020756 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020756]

AlphaFold

Q8K1R3

PDB Structure

Solution structure of the alpha-helical domain from mouse hypothetical PNPase [SOLUTION NMR]

Predicted Effect

probably benign
Transcript: ENSMUST00000020756
AA Change: N540D

PolyPhen 2 Score 0.221 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000020756
Gene: ENSMUSG00000020464
AA Change: N540D

Domain	Start	End	E-Value	Type
low complexity region	4	26	N/A	INTRINSIC
Pfam:RNase_PH	52	183	1.9e-16	PFAM
Pfam:RNase_PH_C	186	251	3.8e-13	PFAM
Pfam:PNPase	282	363	3.7e-9	PFAM
Pfam:RNase_PH	366	501	3.4e-22	PFAM
Pfam:RNase_PH_C	504	581	7.1e-6	PFAM
KH	604	669	8e-7	SMART
S1	677	750	2.15e-4	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154924

Meta Mutation Damage Score

0.1198

Coding Region Coverage

1x: 97.5%
3x: 96.9%
10x: 95.3%
20x: 92.5%

Validation Efficiency

100% (91/91)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the evolutionary conserved polynucleotide phosphorylase family comprised of phosphate dependent 3'-to-5' exoribonucleases implicated in RNA processing and degradation. This enzyme is predominantly localized in the mitochondrial intermembrane space and is involved in import of RNA to mitochondria. Mutations in this gene have been associated with combined oxidative phosphorylation deficiency-13 and autosomal recessive nonsyndromic deafness-70. Related pseudogenes are found on chromosomes 3 and 7. [provided by RefSeq, Dec 2012]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality and impaired mitochondrial RNA import. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A430033K04Rik	A	G	5: 138,644,519 (GRCm39)	I135V	probably benign	Het
Abca1	T	A	4: 53,074,325 (GRCm39)	K1119N	probably damaging	Het
Abcb10	C	T	8: 124,688,791 (GRCm39)	G495D	probably damaging	Het
Abcc9	T	C	6: 142,573,194 (GRCm39)		probably benign	Het
Akap3	A	G	6: 126,842,809 (GRCm39)	E476G	possibly damaging	Het
Aldh3b1	A	G	19: 3,968,740 (GRCm39)	F271S	probably damaging	Het
Alkbh2	C	T	5: 114,262,287 (GRCm39)	E148K	probably damaging	Het
Ascc3	T	C	10: 50,576,586 (GRCm39)	V847A	probably damaging	Het
Best3	A	G	10: 116,859,883 (GRCm39)	N381S	probably benign	Het
Blm	A	T	7: 80,163,118 (GRCm39)	S78T	probably benign	Het
Bmpr2	T	A	1: 59,907,520 (GRCm39)	L871Q	probably damaging	Het
Car13	T	A	3: 14,715,795 (GRCm39)	H104Q	probably benign	Het
Ccdc39	T	C	3: 33,880,629 (GRCm39)	K446R	probably damaging	Het
Ccnb1ip1	T	C	14: 51,029,568 (GRCm39)	M165V	probably benign	Het
Cd4	A	T	6: 124,843,618 (GRCm39)	M431K	possibly damaging	Het
Cdh20	C	T	1: 109,980,606 (GRCm39)	T178I	probably damaging	Het
Ceacam3	C	T	7: 16,892,301 (GRCm39)	T348I	probably damaging	Het
Cfap54	C	T	10: 92,740,125 (GRCm39)		probably null	Het
Clcn6	A	T	4: 148,098,758 (GRCm39)		probably null	Het
Csf3	A	G	11: 98,593,246 (GRCm39)	Y121C	probably damaging	Het
Csmd3	C	T	15: 47,567,505 (GRCm39)		probably benign	Het
Cyp2c69	A	G	19: 39,864,815 (GRCm39)	I221T	probably benign	Het
Dgcr2	T	C	16: 17,675,115 (GRCm39)		probably benign	Het
Dhcr7	T	C	7: 143,401,250 (GRCm39)	F474S	probably damaging	Het
Dnah1	T	C	14: 31,032,839 (GRCm39)	I399V	probably null	Het
Efcab14	T	A	4: 115,610,188 (GRCm39)	L183Q	probably damaging	Het
Evx2	A	G	2: 74,489,501 (GRCm39)	V88A	probably benign	Het
Exph5	A	G	9: 53,285,109 (GRCm39)	N730S	probably benign	Het
Farsb	T	A	1: 78,443,620 (GRCm39)	K196I	probably benign	Het
Fbln7	C	T	2: 128,735,682 (GRCm39)		probably benign	Het
Fhdc1	A	G	3: 84,356,085 (GRCm39)	F453S	probably damaging	Het
Gast	T	A	11: 100,227,684 (GRCm39)	W89R	probably damaging	Het
Gata2	A	G	6: 88,182,237 (GRCm39)	S402G	probably benign	Het
Gin1	T	A	1: 97,720,162 (GRCm39)	S386T	probably benign	Het
Golgb1	A	G	16: 36,736,363 (GRCm39)	E1870G	probably damaging	Het
Hivep3	T	A	4: 119,954,768 (GRCm39)	V1028E	possibly damaging	Het
Ifi203	G	A	1: 173,756,326 (GRCm39)	R486*	probably null	Het
Ifi209	G	A	1: 173,468,728 (GRCm39)	S186N	probably benign	Het
Ifih1	C	T	2: 62,436,738 (GRCm39)	A562T	probably damaging	Het
Itch	T	C	2: 155,014,481 (GRCm39)	L106S	probably damaging	Het
Itga4	T	A	2: 79,146,050 (GRCm39)		probably null	Het
Kdm4c	A	G	4: 74,199,234 (GRCm39)	S141G	possibly damaging	Het
Kirrel1	C	T	3: 86,996,458 (GRCm39)	M380I	probably null	Het
Klra3	T	C	6: 130,307,226 (GRCm39)		probably null	Het
Lama2	A	T	10: 27,084,402 (GRCm39)	S923T	probably damaging	Het
Lama2	G	C	10: 27,084,403 (GRCm39)	F922L	probably benign	Het
Llgl1	G	A	11: 60,597,873 (GRCm39)	V331M	probably damaging	Het
Lrrc30	T	C	17: 67,938,676 (GRCm39)	*301W	probably null	Het
Map1lc3b	C	T	8: 122,320,226 (GRCm39)		probably benign	Het
Mbd2	A	G	18: 70,749,690 (GRCm39)	I302V	probably benign	Het
Med27	A	G	2: 29,390,307 (GRCm39)	Y78C	probably damaging	Het
Mei1	C	T	15: 81,996,771 (GRCm39)		probably null	Het
Mideas	G	A	12: 84,205,124 (GRCm39)		probably benign	Het
Miga1	T	C	3: 151,993,191 (GRCm39)	E346G	probably damaging	Het
Myef2	A	G	2: 124,957,363 (GRCm39)	S131P	probably damaging	Het
Myocd	T	C	11: 65,069,527 (GRCm39)	H899R	probably benign	Het
Ncam1	A	G	9: 49,456,556 (GRCm39)		probably benign	Het
Ngf	T	A	3: 102,427,513 (GRCm39)	N87K	possibly damaging	Het
Nol10	T	A	12: 17,466,709 (GRCm39)		probably benign	Het
Nrip2	A	G	6: 128,385,231 (GRCm39)	I221V	probably benign	Het
Nup205	G	A	6: 35,182,366 (GRCm39)	G777D	probably damaging	Het
Or5ac17	A	G	16: 59,036,344 (GRCm39)	F211L	probably benign	Het
Or5b96	A	G	19: 12,867,047 (GRCm39)	V298A	probably damaging	Het
Or6c1	T	A	10: 129,518,081 (GRCm39)	T176S	probably benign	Het
Or7g35	A	T	9: 19,496,682 (GRCm39)	Q283L	probably damaging	Het
Or8d6	G	T	9: 39,854,251 (GRCm39)	D232Y	probably benign	Het
Oxt	A	T	2: 130,418,220 (GRCm39)	R31W	probably damaging	Het
Pde4dip	A	G	3: 97,603,246 (GRCm39)	S2248P	probably benign	Het
Pias1	A	G	9: 62,859,460 (GRCm39)	V16A	probably damaging	Het
Pkp2	T	C	16: 16,080,561 (GRCm39)	S616P	probably damaging	Het
Plch2	T	C	4: 155,084,540 (GRCm39)	Y379C	probably damaging	Het
Ptpn23	G	A	9: 110,220,746 (GRCm39)	H255Y	possibly damaging	Het
Rad21	T	C	15: 51,835,703 (GRCm39)	N237D	probably benign	Het
Ryr3	A	C	2: 112,582,113 (GRCm39)		probably null	Het
Sgk1	C	A	10: 21,873,007 (GRCm39)		probably benign	Het
Slc1a5	G	T	7: 16,531,464 (GRCm39)	A490S	probably damaging	Het
Slc5a8	T	C	10: 88,755,326 (GRCm39)	Y478H	probably benign	Het
Slc5a8	T	A	10: 88,755,328 (GRCm39)	Y478*	probably null	Het
Slc9a3	A	T	13: 74,311,190 (GRCm39)	M562L	probably benign	Het
Spmip4	A	G	6: 50,568,801 (GRCm39)		probably benign	Het
Thsd7a	G	A	6: 12,555,714 (GRCm39)	R57*	probably null	Het
Tiam1	T	C	16: 89,657,167 (GRCm39)	R690G	probably damaging	Het
Tmem150b	A	G	7: 4,727,365 (GRCm39)	S47P	probably damaging	Het
Trim39	C	T	17: 36,574,832 (GRCm39)	R190Q	probably damaging	Het
Ttc32	A	T	12: 9,085,073 (GRCm39)	I98L	possibly damaging	Het
Vps13c	A	G	9: 67,873,003 (GRCm39)	T3304A	probably benign	Het
Wdr35	A	C	12: 9,062,728 (GRCm39)	D638A	probably damaging	Het
Wwc1	G	T	11: 35,752,671 (GRCm39)	P797T	probably benign	Het
Zan	T	A	5: 137,462,780 (GRCm39)	T800S	unknown	Het
Zbbx	A	G	3: 74,990,926 (GRCm39)		probably benign	Het
Zup1	T	C	10: 33,811,172 (GRCm39)	M291V	probably damaging	Het

Other mutations in Pnpt1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00229:Pnpt1	APN	11	29,104,217 (GRCm39)	critical splice donor site	probably null
IGL00920:Pnpt1	APN	11	29,107,087 (GRCm39)	splice site	probably benign
IGL01358:Pnpt1	APN	11	29,088,425 (GRCm39)	missense	possibly damaging	0.95
IGL01454:Pnpt1	APN	11	29,087,142 (GRCm39)	missense	probably benign	0.19
IGL01622:Pnpt1	APN	11	29,098,272 (GRCm39)	splice site	probably benign
IGL01623:Pnpt1	APN	11	29,098,272 (GRCm39)	splice site	probably benign
IGL01674:Pnpt1	APN	11	29,105,787 (GRCm39)	missense	probably benign	0.00
IGL01802:Pnpt1	APN	11	29,104,306 (GRCm39)	missense	probably damaging	1.00
IGL02222:Pnpt1	APN	11	29,080,842 (GRCm39)	missense	probably benign	0.00
IGL02222:Pnpt1	APN	11	29,109,327 (GRCm39)	missense	possibly damaging	0.71
IGL02616:Pnpt1	APN	11	29,085,505 (GRCm39)	splice site	probably benign
IGL02859:Pnpt1	APN	11	29,088,162 (GRCm39)	missense	probably damaging	1.00
IGL02965:Pnpt1	APN	11	29,106,939 (GRCm39)	missense	probably damaging	0.98
IGL03121:Pnpt1	APN	11	29,082,845 (GRCm39)	missense	probably benign	0.03
PIT4651001:Pnpt1	UTSW	11	29,106,945 (GRCm39)	critical splice donor site	probably null
R1023:Pnpt1	UTSW	11	29,091,328 (GRCm39)	splice site	probably benign
R1477:Pnpt1	UTSW	11	29,087,102 (GRCm39)	missense	probably benign	0.14
R1524:Pnpt1	UTSW	11	29,080,776 (GRCm39)	missense	unknown
R1839:Pnpt1	UTSW	11	29,104,342 (GRCm39)	missense	possibly damaging	0.82
R1975:Pnpt1	UTSW	11	29,091,256 (GRCm39)	missense	probably benign	0.16
R1977:Pnpt1	UTSW	11	29,091,256 (GRCm39)	missense	probably benign	0.16
R1996:Pnpt1	UTSW	11	29,091,679 (GRCm39)	missense	probably benign	0.01
R3771:Pnpt1	UTSW	11	29,088,174 (GRCm39)	missense	probably benign	0.05
R4346:Pnpt1	UTSW	11	29,095,478 (GRCm39)	missense	probably damaging	1.00
R4423:Pnpt1	UTSW	11	29,103,375 (GRCm39)	splice site	probably null
R5354:Pnpt1	UTSW	11	29,104,166 (GRCm39)	missense	probably damaging	1.00
R5503:Pnpt1	UTSW	11	29,088,156 (GRCm39)	missense	probably damaging	1.00
R5514:Pnpt1	UTSW	11	29,103,246 (GRCm39)	missense	possibly damaging	0.82
R5908:Pnpt1	UTSW	11	29,080,887 (GRCm39)	missense	probably benign	0.00
R6225:Pnpt1	UTSW	11	29,095,469 (GRCm39)	missense	probably benign	0.38
R6605:Pnpt1	UTSW	11	29,088,567 (GRCm39)	missense	possibly damaging	0.69
R7096:Pnpt1	UTSW	11	29,104,867 (GRCm39)	missense	probably benign	0.03
R7214:Pnpt1	UTSW	11	29,087,285 (GRCm39)	missense	probably damaging	1.00
R7365:Pnpt1	UTSW	11	29,111,334 (GRCm39)	missense	probably damaging	1.00
R7492:Pnpt1	UTSW	11	29,085,522 (GRCm39)	missense	probably benign	0.01
R7497:Pnpt1	UTSW	11	29,080,860 (GRCm39)	missense	probably benign	0.00
R7686:Pnpt1	UTSW	11	29,107,070 (GRCm39)	missense	probably damaging	0.97
R8166:Pnpt1	UTSW	11	29,106,875 (GRCm39)	missense	probably benign
R8309:Pnpt1	UTSW	11	29,103,277 (GRCm39)	missense	probably benign	0.01
R8389:Pnpt1	UTSW	11	29,080,758 (GRCm39)	start codon destroyed	unknown
R8542:Pnpt1	UTSW	11	29,082,773 (GRCm39)	splice site	probably null
R8737:Pnpt1	UTSW	11	29,104,815 (GRCm39)	critical splice acceptor site	probably null
R8876:Pnpt1	UTSW	11	29,096,769 (GRCm39)	intron	probably benign
R9308:Pnpt1	UTSW	11	29,097,535 (GRCm39)	critical splice donor site	probably null
R9545:Pnpt1	UTSW	11	29,106,840 (GRCm39)	missense	probably benign	0.13
Z1176:Pnpt1	UTSW	11	29,095,477 (GRCm39)	missense	possibly damaging	0.80
Z1176:Pnpt1	UTSW	11	29,095,475 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- CGATTGAACAGCAATCAAGCAGCAG -3'
(R):5'- GGAACAAGGCACACTGACTTACCTG -3'

Sequencing Primer
(F):5'- CAGAGGTGGCTCTTTGCATTTAAC -3'
(R):5'- ACACTGACTTACCTGACGCTTG -3'

Posted On

2014-05-23