Mutagenetix > Incidental Mutation

Incidental Mutation 'R5354:Pnpt1'

423988

Institutional Source

Beutler Lab

Gene Symbol

Pnpt1

Ensembl Gene

ENSMUSG00000020464

Gene Name

polyribonucleotide nucleotidyltransferase 1

Synonyms

1200003F12Rik, polynucleotide phosphorylase, PNPase

MMRRC Submission

042933-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5354 (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 29104166 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 542 (D542G)

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 damaging
Transcript: ENSMUST00000020756
AA Change: D542G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000020756
Gene: ENSMUSG00000020464
AA Change: D542G

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

0.9296

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.3%
20x: 95.4%

Validation Efficiency

100% (80/80)

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A630010A05Rik	A	G	16: 14,436,535 (GRCm39)	K196R	probably benign	Het
Ablim1	T	C	19: 57,119,355 (GRCm39)	E243G	probably benign	Het
Acat1	T	A	9: 53,500,483 (GRCm39)	E271V	possibly damaging	Het
Aco1	T	C	4: 40,180,290 (GRCm39)		probably null	Het
Adam22	C	A	5: 8,140,182 (GRCm39)	G202W	probably damaging	Het
Agbl3	T	A	6: 34,791,687 (GRCm39)	H596Q	probably benign	Het
Anxa7	A	G	14: 20,514,977 (GRCm39)	L177P	possibly damaging	Het
Atp11a	A	T	8: 12,856,753 (GRCm39)	N48I	probably damaging	Het
Bcas1	T	A	2: 170,191,316 (GRCm39)	N492I	possibly damaging	Het
Bclaf1	A	G	10: 20,209,278 (GRCm39)	Y498C	probably damaging	Het
Bltp3a	G	A	17: 28,106,489 (GRCm39)	S1005N	probably benign	Het
Bod1l	A	C	5: 41,988,880 (GRCm39)	V409G	probably damaging	Het
Ccdc170	G	A	10: 4,484,188 (GRCm39)	C338Y	probably benign	Het
Cdc45	C	T	16: 18,614,647 (GRCm39)	R205H	probably damaging	Het
Ckap2	A	C	8: 22,667,581 (GRCm39)	N93K	probably damaging	Het
Clca3a1	A	T	3: 144,442,766 (GRCm39)	S759R	possibly damaging	Het
Coro1c	A	T	5: 113,984,226 (GRCm39)	I347N	possibly damaging	Het
Cpox	A	G	16: 58,491,205 (GRCm39)	T139A	probably damaging	Het
Cyp4a12b	C	A	4: 115,290,661 (GRCm39)		probably null	Het
Dctn1	T	G	6: 83,160,108 (GRCm39)	V116G	possibly damaging	Het
Dhx38	A	G	8: 110,282,378 (GRCm39)	V683A	probably damaging	Het
Dnah12	G	A	14: 26,496,299 (GRCm39)		probably null	Het
Dnajb7	T	C	15: 81,292,208 (GRCm39)	E43G	probably damaging	Het
Dsc1	A	T	18: 20,220,632 (GRCm39)	V714E	probably damaging	Het
Dusp29	G	A	14: 21,727,091 (GRCm39)	R186W	probably benign	Het
Egfem1	T	C	3: 29,136,361 (GRCm39)		probably null	Het
Fchsd1	C	T	18: 38,092,926 (GRCm39)		probably benign	Het
Fmo1	T	C	1: 162,657,714 (GRCm39)	T476A	probably benign	Het
Gm10237	T	C	16: 35,741,099 (GRCm39)		noncoding transcript	Het
Gm14496	A	G	2: 181,642,602 (GRCm39)	S758G	probably damaging	Het
Gpat2	T	A	2: 127,270,643 (GRCm39)	L97Q	probably damaging	Het
Gpr162	T	C	6: 124,836,600 (GRCm39)	D357G	probably benign	Het
Hax1	A	T	3: 89,905,262 (GRCm39)	D34E	probably damaging	Het
Hmgcr	C	T	13: 96,791,404 (GRCm39)	V97M	probably benign	Het
Hsd3b2	T	C	3: 98,619,631 (GRCm39)	T105A	probably benign	Het
Ints1	A	G	5: 139,752,183 (GRCm39)		probably null	Het
Islr	T	C	9: 58,064,895 (GRCm39)	E204G	probably damaging	Het
Lrrc36	A	G	8: 106,151,996 (GRCm39)	N60D	probably damaging	Het
Maf1	T	C	15: 76,237,330 (GRCm39)		probably benign	Het
Mrgprb4	T	A	7: 47,848,077 (GRCm39)	R284W	probably benign	Het
Myh4	A	T	11: 67,146,551 (GRCm39)	N1508I	possibly damaging	Het
Nufip2	A	G	11: 77,577,103 (GRCm39)	H17R	unknown	Het
Oasl1	A	T	5: 115,075,055 (GRCm39)	I372L	probably damaging	Het
Or5ae1	T	A	7: 84,565,357 (GRCm39)	Y123*	probably null	Het
Or6p1	T	C	1: 174,258,252 (GRCm39)	L86P	probably damaging	Het
Pald1	A	T	10: 61,184,440 (GRCm39)	Y226N	probably damaging	Het
Pcdhb13	G	T	18: 37,577,844 (GRCm39)	G741C	probably damaging	Het
Pcdhga10	A	G	18: 37,881,259 (GRCm39)	D340G	probably damaging	Het
Pclo	C	A	5: 14,728,822 (GRCm39)		probably benign	Het
Pcsk4	G	T	10: 80,159,523 (GRCm39)	N416K	probably damaging	Het
Pde10a	C	A	17: 9,180,812 (GRCm39)	R398S	probably damaging	Het
Plin1	T	A	7: 79,375,469 (GRCm39)	T227S	possibly damaging	Het
Ppp4r3b	T	A	11: 29,161,646 (GRCm39)	D673E	probably benign	Het
Prr18	C	A	17: 8,559,892 (GRCm39)	P16Q	probably damaging	Het
Psmc3	T	A	2: 90,889,698 (GRCm39)	Y440N	probably damaging	Het
Rassf5	T	C	1: 131,108,385 (GRCm39)	I232V	probably benign	Het
Rims1	T	A	1: 22,577,592 (GRCm39)	D218V	probably damaging	Het
Skint10	T	C	4: 112,568,790 (GRCm39)	N309S	possibly damaging	Het
Slc6a1	T	C	6: 114,279,584 (GRCm39)	M121T	possibly damaging	Het
Slit3	A	G	11: 35,566,740 (GRCm39)	D1004G	probably damaging	Het
Snap91	C	T	9: 86,717,177 (GRCm39)	V215I	possibly damaging	Het
Son	T	C	16: 91,452,627 (GRCm39)	L458S	probably damaging	Het
St18	C	T	1: 6,914,395 (GRCm39)	A782V	probably damaging	Het
Synpo	A	G	18: 60,735,303 (GRCm39)		probably null	Het
Thbs3	A	G	3: 89,128,684 (GRCm39)	D458G	probably damaging	Het
Tpr	C	T	1: 150,321,675 (GRCm39)	R3C	probably damaging	Het
Trp63	A	G	16: 25,503,105 (GRCm39)		probably null	Het
Vmn1r27	C	A	6: 58,192,581 (GRCm39)	R141L	probably benign	Het
Wnk1	T	C	6: 119,945,484 (GRCm39)	I699V	probably benign	Het
Xkr6	A	G	14: 64,056,353 (GRCm39)	D88G	possibly damaging	Het
Zan	A	G	5: 137,379,050 (GRCm39)		probably benign	Het
Zbtb7b	T	C	3: 89,286,913 (GRCm39)		probably benign	Het
Zfp618	A	T	4: 62,998,265 (GRCm39)	D33V	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
R1769:Pnpt1	UTSW	11	29,104,159 (GRCm39)	missense	probably benign	0.22
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
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'- AGTGACAAGCTTTGTGCGATTG -3'
(R):5'- GACTTACCTGACGCTTGTTGG -3'

Sequencing Primer
(F):5'- TGACAAGCTTTGTGCGATTGAACAG -3'
(R):5'- ACGCTTGTTGGATGGCTTCC -3'

Posted On

2016-08-04