Mutagenetix > Incidental Mutation

Incidental Mutation 'R1839:Pnpt1'

205616

Institutional Source

Beutler Lab

Gene Symbol

Pnpt1

Ensembl Gene

ENSMUSG00000020464

Gene Name

polyribonucleotide nucleotidyltransferase 1

Synonyms

1200003F12Rik, polynucleotide phosphorylase, PNPase

MMRRC Submission

045015-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1839 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

29080744-29111828 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 29104342 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Threonine at position 572 (M572T)

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

possibly damaging
Transcript: ENSMUST00000020756
AA Change: M572T

PolyPhen 2 Score 0.819 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000020756
Gene: ENSMUSG00000020464
AA Change: M572T

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

0.0952

Coding Region Coverage

1x: 97.4%
3x: 96.7%
10x: 94.7%
20x: 90.6%

Validation Efficiency

98% (90/92)

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: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006A11Rik	T	C	3: 124,203,369 (GRCm39)	T403A	probably damaging	Het
Acat3	T	A	17: 13,147,493 (GRCm39)	R175*	probably null	Het
Adam1b	C	A	5: 121,639,104 (GRCm39)	C647F	probably damaging	Het
Adam28	T	C	14: 68,876,659 (GRCm39)	N197S	possibly damaging	Het
Adcy2	C	T	13: 68,837,380 (GRCm39)		probably null	Het
Adcy5	A	T	16: 35,069,310 (GRCm39)	N426I	probably damaging	Het
Adgre1	T	C	17: 57,748,299 (GRCm39)	S500P	probably benign	Het
Aloxe3	A	G	11: 69,020,911 (GRCm39)	Y212C	probably damaging	Het
Ap3d1	A	G	10: 80,562,942 (GRCm39)	S180P	probably damaging	Het
Arhgap20	C	T	9: 51,760,626 (GRCm39)	R790W	probably damaging	Het
Atp8b4	C	A	2: 126,203,702 (GRCm39)	A757S	possibly damaging	Het
Begain	G	A	12: 109,001,249 (GRCm39)		probably benign	Het
Ccdc141	T	C	2: 76,842,009 (GRCm39)	E1474G	probably benign	Het
Ccdc88b	A	G	19: 6,831,477 (GRCm39)		probably benign	Het
Ccnk	A	G	12: 108,161,333 (GRCm39)	T195A	probably damaging	Het
Cd55b	C	A	1: 130,341,842 (GRCm39)	C265F	probably damaging	Het
Celsr3	A	G	9: 108,707,105 (GRCm39)	H1196R	probably benign	Het
Cenpt	T	C	8: 106,575,646 (GRCm39)	S190G	possibly damaging	Het
Chd8	T	C	14: 52,442,340 (GRCm39)	S2077G	probably benign	Het
Col6a5	G	A	9: 105,742,032 (GRCm39)	H2296Y	probably benign	Het
Cxxc4	C	A	3: 133,946,414 (GRCm39)	H332N	probably damaging	Het
Cyp24a1	T	C	2: 170,338,661 (GRCm39)	I12V	probably benign	Het
Cyp3a57	T	A	5: 145,318,111 (GRCm39)	L364Q	probably damaging	Het
Ddi2	T	C	4: 141,440,837 (GRCm39)	I47V	probably benign	Het
Ddx5	A	T	11: 106,675,723 (GRCm39)	D322E	probably benign	Het
Dhx40	A	G	11: 86,680,123 (GRCm39)	C405R	possibly damaging	Het
Emc1	T	C	4: 139,087,796 (GRCm39)	F100S	probably damaging	Het
Exoc2	T	C	13: 31,090,480 (GRCm39)		probably benign	Het
Gm10110	A	T	14: 90,135,272 (GRCm39)		noncoding transcript	Het
Gm17332	T	C	11: 31,132,386 (GRCm39)	H26R	possibly damaging	Het
Gna12	T	C	5: 140,748,367 (GRCm39)	N183S	probably benign	Het
Gpx6	A	G	13: 21,496,497 (GRCm39)	N24D	probably benign	Het
Gsdma3	C	T	11: 98,520,684 (GRCm39)	A105V	probably benign	Het
Hsd3b5	T	C	3: 98,527,044 (GRCm39)	Y134C	probably benign	Het
Ifi213	T	C	1: 173,417,166 (GRCm39)	I415M	probably damaging	Het
Ints9	C	A	14: 65,253,979 (GRCm39)	P278T	probably damaging	Het
Krt79	C	T	15: 101,846,373 (GRCm39)	E192K	possibly damaging	Het
Lrrk2	A	G	15: 91,567,337 (GRCm39)	N132S	probably benign	Het
Ltn1	T	A	16: 87,213,152 (GRCm39)	K470*	probably null	Het
Magi2	A	T	5: 20,670,825 (GRCm39)	T163S	probably damaging	Het
Mcm9	A	G	10: 53,417,649 (GRCm39)	M18T	probably damaging	Het
Med12l	A	G	3: 58,975,740 (GRCm39)	T212A	probably benign	Het
Mfhas1	T	C	8: 36,058,012 (GRCm39)	L829P	possibly damaging	Het
Mgme1	T	A	2: 144,121,407 (GRCm39)	C288S	probably benign	Het
Muc4	G	C	16: 32,753,919 (GRCm38)	R1265P	probably benign	Het
Myh7	T	C	14: 55,210,637 (GRCm39)	N1725S	possibly damaging	Het
Naa80	G	A	9: 107,460,216 (GRCm39)	R37H	possibly damaging	Het
Nme4	A	T	17: 26,311,071 (GRCm39)	W165R	probably damaging	Het
Nup205	T	A	6: 35,196,649 (GRCm39)	D1128E	probably benign	Het
Or2t48	A	T	11: 58,420,199 (GRCm39)	Y204*	probably null	Het
Or5ae2	T	C	7: 84,505,756 (GRCm39)	Y60H	probably damaging	Het
Pcdh1	T	C	18: 38,332,538 (GRCm39)	D155G	possibly damaging	Het
Pex12	A	T	11: 83,188,648 (GRCm39)	S116T	probably damaging	Het
Plekhh1	C	T	12: 79,125,731 (GRCm39)		probably benign	Het
Plekhh3	A	G	11: 101,054,426 (GRCm39)		probably benign	Het
Ppp1r12b	T	C	1: 134,765,719 (GRCm39)	R667G	probably benign	Het
Rbpms2	ACTGCTGCTGCTGCTGC	ACTGCTGCTGCTGCTGCTGC	9: 65,558,948 (GRCm39)		probably benign	Het
Rgs14	T	C	13: 55,530,651 (GRCm39)		probably benign	Het
Rhbdf2	A	T	11: 116,491,017 (GRCm39)	V645E	possibly damaging	Het
Robo3	A	G	9: 37,333,623 (GRCm39)	V696A	probably benign	Het
Sall1	A	G	8: 89,755,344 (GRCm39)	F1212L	possibly damaging	Het
Sdc4	T	C	2: 164,270,932 (GRCm39)	E109G	probably benign	Het
Serpind1	G	T	16: 17,160,856 (GRCm39)	R462L	probably damaging	Het
Smad9	CTTT	CTT	3: 54,696,600 (GRCm39)		probably benign	Het
Sstr4	C	A	2: 148,237,453 (GRCm39)	N21K	probably benign	Het
Tap1	C	T	17: 34,407,083 (GRCm39)	A77V	possibly damaging	Het
Thap4	T	C	1: 93,678,009 (GRCm39)	E259G	probably benign	Het
Thra	A	G	11: 98,646,969 (GRCm39)	N30S	probably benign	Het
Tmem207	A	T	16: 26,343,571 (GRCm39)	V27E	possibly damaging	Het
Top3a	A	G	11: 60,644,714 (GRCm39)	V305A	probably damaging	Het
Trim59	A	T	3: 68,944,971 (GRCm39)	I123K	probably damaging	Het
Ttn	T	C	2: 76,691,839 (GRCm39)		probably benign	Het
Ubac1	T	A	2: 25,897,750 (GRCm39)	E290V	possibly damaging	Het
Unc13b	T	C	4: 43,258,308 (GRCm39)		probably benign	Het
Uri1	A	T	7: 37,666,814 (GRCm39)	D206E	probably benign	Het
Utp4	A	G	8: 107,640,086 (GRCm39)	H465R	probably benign	Het
Uvssa	T	C	5: 33,547,096 (GRCm39)	S221P	probably benign	Het
Vmn1r39	T	C	6: 66,782,217 (GRCm39)		probably null	Het
Vps39	A	T	2: 120,155,878 (GRCm39)	L514H	probably damaging	Het
Vps72	G	A	3: 95,026,529 (GRCm39)	R158Q	possibly damaging	Het
Wdr59	T	C	8: 112,211,972 (GRCm39)	D366G	probably benign	Het
Zfp366	C	A	13: 99,365,000 (GRCm39)	Q54K	probably damaging	Het
Zfp523	T	A	17: 28,413,967 (GRCm39)	I34N	probably damaging	Het
Zfp974	G	A	7: 27,609,781 (GRCm39)	P648L	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
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'- GACATGGATTTCAAAATAGCCGG -3'
(R):5'- AGACTGACTCAGAAAGTTGCTTAC -3'

Sequencing Primer
(F):5'- CCGGTACAAATAAAGGAATAACTGC -3'
(R):5'- GCTGTGGAGCAAACCCAATTC -3'

Posted On

2014-06-23