Mutagenetix > Incidental Mutation

Incidental Mutation 'R7497:Pnpt1'

581154

Institutional Source

Beutler Lab

Gene Symbol

Pnpt1

Ensembl Gene

ENSMUSG00000020464

Gene Name

polyribonucleotide nucleotidyltransferase 1

Synonyms

1200003F12Rik, polynucleotide phosphorylase, PNPase

MMRRC Submission

045570-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7497 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

29080744-29111828 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 29080860 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Leucine at position 35 (M35L)

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: M35L

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000020756
Gene: ENSMUSG00000020464
AA Change: M35L

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

100% (70/70)

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcd2	T	A	15: 91,075,379 (GRCm39)	I145F	probably benign	Het
Acvr2b	T	A	9: 119,262,352 (GRCm39)	V455E	probably benign	Het
Adgrv1	A	T	13: 81,588,344 (GRCm39)	V4414E	possibly damaging	Het
Agap2	T	C	10: 126,926,834 (GRCm39)	V977A	probably damaging	Het
Aph1b	A	C	9: 66,701,401 (GRCm39)	S79A	probably damaging	Het
Atm	G	A	9: 53,423,191 (GRCm39)	S645L	probably benign	Het
Cdh11	T	C	8: 103,400,456 (GRCm39)	R171G	probably benign	Het
Ces2f	T	A	8: 105,681,330 (GRCm39)	D556E	probably benign	Het
Cfap210	A	C	2: 69,588,792 (GRCm39)	N439K	probably benign	Het
Cyp26b1	C	A	6: 84,553,964 (GRCm39)	V218L	possibly damaging	Het
Diaph1	T	C	18: 38,028,353 (GRCm39)		probably null	Het
Dock1	A	G	7: 134,367,003 (GRCm39)	I482V	probably benign	Het
Dok4	A	T	8: 95,594,053 (GRCm39)	D47E	possibly damaging	Het
Dqx1	T	A	6: 83,036,028 (GRCm39)	L120Q	probably damaging	Het
Duxf3	A	T	10: 58,066,558 (GRCm39)	V157E	probably damaging	Het
Efcab3	T	C	11: 104,653,516 (GRCm39)		probably null	Het
Eif2a	C	A	3: 58,456,102 (GRCm39)	P367Q	probably damaging	Het
Elp2	C	T	18: 24,744,985 (GRCm39)	R102C	probably damaging	Het
Erich2	T	C	2: 70,364,666 (GRCm39)	S347P	probably damaging	Het
Fgfr3	GGACCTCTCCGTG	GG	5: 33,892,766 (GRCm39)		probably null	Het
Flacc1	T	A	1: 58,717,467 (GRCm39)	D148V	probably damaging	Het
Gadl1	A	T	9: 115,903,155 (GRCm39)	I495L	probably benign	Het
Gcnt4	A	G	13: 97,083,468 (GRCm39)	T255A	possibly damaging	Het
Gm10972	A	G	3: 94,550,887 (GRCm39)	K21E	unknown	Het
Gm57859	T	A	11: 113,583,223 (GRCm39)	W517R	probably damaging	Het
Gm7361	C	A	5: 26,466,188 (GRCm39)	H183Q	probably benign	Het
Gp2	C	T	7: 119,053,829 (GRCm39)	C44Y	probably damaging	Het
Hcar2	C	T	5: 124,003,249 (GRCm39)	V85I	probably benign	Het
Hira	T	C	16: 18,770,829 (GRCm39)	V822A	probably damaging	Het
Ighv1-5	T	A	12: 114,477,156 (GRCm39)	T49S	probably damaging	Het
Ints1	C	T	5: 139,754,731 (GRCm39)	V603M	probably damaging	Het
Kdm2a	A	C	19: 4,374,404 (GRCm39)	L909R	probably damaging	Het
Klkb1	T	A	8: 45,747,827 (GRCm39)		probably benign	Het
Krit1	A	G	5: 3,862,349 (GRCm39)	H168R	possibly damaging	Het
Map3k21	A	T	8: 126,654,340 (GRCm39)	E386D	probably damaging	Het
Muc16	C	T	9: 18,556,385 (GRCm39)	E3303K	unknown	Het
Muc5b	T	G	7: 141,415,250 (GRCm39)	V2732G	possibly damaging	Het
Myo5a	T	C	9: 75,104,983 (GRCm39)	L189P		Het
Nlrc5	T	C	8: 95,248,598 (GRCm39)	L1740S	probably damaging	Het
Nolc1	A	G	19: 46,071,257 (GRCm39)	K402R	probably benign	Het
Or4b1b	T	A	2: 90,112,098 (GRCm39)	T274S	possibly damaging	Het
Or4k15	T	A	14: 50,364,952 (GRCm39)	L306Q	probably benign	Het
Or52s19	T	C	7: 103,008,219 (GRCm39)	M61V	probably damaging	Het
Or8u8	T	C	2: 86,012,417 (GRCm39)	I13V	probably benign	Het
Pnma8b	A	G	7: 16,678,874 (GRCm39)		probably benign	Het
Postn	A	G	3: 54,270,091 (GRCm39)	K57E	probably damaging	Het
Ppp1r9a	A	C	6: 4,905,775 (GRCm39)	D110A	probably damaging	Het
Pptc7	G	A	5: 122,422,942 (GRCm39)	V71M	possibly damaging	Het
Prdm11	T	A	2: 92,843,052 (GRCm39)	I136F	possibly damaging	Het
Rfc1	A	G	5: 65,436,841 (GRCm39)	L613P	probably damaging	Het
Ryr3	T	C	2: 112,560,818 (GRCm39)	D2981G	probably benign	Het
Sbf2	C	A	7: 110,213,923 (GRCm39)	E16*	probably null	Het
Scara3	T	C	14: 66,168,651 (GRCm39)	E322G	probably damaging	Het
Sema5b	T	A	16: 35,481,700 (GRCm39)	C893S	probably damaging	Het
Setdb1	T	C	3: 95,249,139 (GRCm39)	D323G	probably damaging	Het
Slc19a3	T	C	1: 82,991,649 (GRCm39)	Y453C	probably damaging	Het
Snx5	T	C	2: 144,099,894 (GRCm39)	K137E	probably damaging	Het
Taar8c	G	A	10: 23,977,116 (GRCm39)	T232I	probably benign	Het
Taok2	G	A	7: 126,474,050 (GRCm39)	T352I	probably damaging	Het
Ttc3	C	A	16: 94,219,541 (GRCm39)	R489S	possibly damaging	Het
Usp12	A	T	5: 146,689,264 (GRCm39)		probably null	Het
Usp16	T	A	16: 87,263,174 (GRCm39)	C125*	probably null	Het
Vmn2r106	C	T	17: 20,488,201 (GRCm39)	E733K	probably damaging	Het
Vps13b	T	A	15: 35,876,843 (GRCm39)	I2832K	probably benign	Het
Vps13c	A	G	9: 67,747,761 (GRCm39)	Y18C	probably damaging	Het
Zfp160	T	A	17: 21,246,455 (GRCm39)	I335K	probably benign	Het
Zfp788	A	T	7: 41,298,275 (GRCm39)	I304F	possibly 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
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
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'- ATTGCTTTCCCGGCAGTTTG -3'
(R):5'- CTCGACCTTAGGTTTGGAGTAGAG -3'

Sequencing Primer
(F):5'- TTTGCAGGCTCCACGGAAAC -3'
(R):5'- GAACTTAAGAGACTTAGGCTGCTTG -3'

Posted On

2019-10-17