Mutagenetix > Incidental Mutation

Incidental Mutation 'R4842:Pnkp'

374461

Institutional Source

Beutler Lab

Gene Symbol

Pnkp

Ensembl Gene

ENSMUSG00000002963

Gene Name

polynucleotide kinase 3'- phosphatase

Synonyms

PNK, 1810009G08Rik

MMRRC Submission

042455-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.964) question?

Stock #

R4842 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

44506563-44512416 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

C to A at 44511070 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000144163 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000003044] [ENSMUST00000046575] [ENSMUST00000098478] [ENSMUST00000098478] [ENSMUST00000107876] [ENSMUST00000123015] [ENSMUST00000124168] [ENSMUST00000155050] [ENSMUST00000200892] [ENSMUST00000200892] [ENSMUST00000202646] [ENSMUST00000207363] [ENSMUST00000139003] [ENSMUST00000154968] [ENSMUST00000201882] [ENSMUST00000209018]

AlphaFold

no structure available at present

Predicted Effect

probably null
Transcript: ENSMUST00000003044

SMART Domains

Protein: ENSMUSP00000003044
Gene: ENSMUSG00000002963

Domain	Start	End	E-Value	Type
PDB:1YJM\|C	1	110	4e-62	PDB
SCOP:d1lgpa_	8	114	5e-12	SMART
Blast:FHA	31	74	1e-10	BLAST
low complexity region	116	134	N/A	INTRINSIC
Pfam:PNK3P	165	327	9.3e-58	PFAM
low complexity region	350	364	N/A	INTRINSIC
Pfam:AAA_33	366	488	1.6e-17	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000046575

SMART Domains

Protein: ENSMUSP00000035281
Gene: ENSMUSG00000038502

Domain	Start	End	E-Value	Type
low complexity region	10	50	N/A	INTRINSIC
low complexity region	64	82	N/A	INTRINSIC
Pfam:Med25	89	238	1.7e-58	PFAM
Pfam:Med25	254	399	4.2e-57	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000098478

SMART Domains

Protein: ENSMUSP00000096078
Gene: ENSMUSG00000002963

Domain	Start	End	E-Value	Type
PDB:1YJM\|C	1	110	2e-62	PDB
SCOP:d1lgpa_	8	114	5e-12	SMART
Blast:FHA	31	74	1e-10	BLAST
low complexity region	116	134	N/A	INTRINSIC
Pfam:PNK3P	165	220	2.9e-16	PFAM
Pfam:PNK3P	211	291	5.3e-27	PFAM
low complexity region	314	328	N/A	INTRINSIC
Pfam:AAA_33	330	452	5.6e-26	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000098478

SMART Domains

Protein: ENSMUSP00000096078
Gene: ENSMUSG00000002963

Domain	Start	End	E-Value	Type
PDB:1YJM\|C	1	110	2e-62	PDB
SCOP:d1lgpa_	8	114	5e-12	SMART
Blast:FHA	31	74	1e-10	BLAST
low complexity region	116	134	N/A	INTRINSIC
Pfam:PNK3P	165	220	2.9e-16	PFAM
Pfam:PNK3P	211	291	5.3e-27	PFAM
low complexity region	314	328	N/A	INTRINSIC
Pfam:AAA_33	330	452	5.6e-26	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000107876

SMART Domains

Protein: ENSMUSP00000103508
Gene: ENSMUSG00000002963

Domain	Start	End	E-Value	Type
PDB:1YJM\|C	1	110	4e-62	PDB
SCOP:d1lgpa_	8	114	5e-12	SMART
Blast:FHA	31	74	1e-10	BLAST
low complexity region	116	134	N/A	INTRINSIC
Pfam:PNK3P	165	327	1.9e-57	PFAM
low complexity region	350	364	N/A	INTRINSIC
Pfam:AAA_33	366	488	5.9e-26	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000123015

SMART Domains

Protein: ENSMUSP00000143862
Gene: ENSMUSG00000002963

Domain	Start	End	E-Value	Type
PDB:1YJ5\|C	1	143	8e-72	PDB
SCOP:d1lgpa_	8	114	7e-13	SMART
Blast:FHA	31	74	2e-10	BLAST
PDB:3U7G\|A	144	165	7e-6	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000124168

SMART Domains

Protein: ENSMUSP00000144330
Gene: ENSMUSG00000002963

Domain	Start	End	E-Value	Type
PDB:1YJM\|C	1	51	3e-30	PDB

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126860

Predicted Effect

probably benign
Transcript: ENSMUST00000155050

SMART Domains

Protein: ENSMUSP00000144663
Gene: ENSMUSG00000002963

Domain	Start	End	E-Value	Type
PDB:1YJM\|C	1	50	9e-30	PDB

Predicted Effect

probably null
Transcript: ENSMUST00000200892

SMART Domains

Protein: ENSMUSP00000144163
Gene: ENSMUSG00000002963

Domain	Start	End	E-Value	Type
Pfam:AAA_33	18	100	3.9e-9	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000200892

SMART Domains

Protein: ENSMUSP00000144163
Gene: ENSMUSG00000002963

Domain	Start	End	E-Value	Type
Pfam:AAA_33	18	100	3.9e-9	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000202646

SMART Domains

Protein: ENSMUSP00000144484
Gene: ENSMUSG00000002963

Domain	Start	End	E-Value	Type
Pfam:AAA_33	5	44	6.1e-7	PFAM
Pfam:AAA_33	37	117	4.2e-9	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000208385

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145850

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144669

Predicted Effect

probably benign
Transcript: ENSMUST00000207363

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152747

Predicted Effect

probably benign
Transcript: ENSMUST00000207416

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000207303

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000207393

Predicted Effect

probably benign
Transcript: ENSMUST00000139003

SMART Domains

Protein: ENSMUSP00000143904
Gene: ENSMUSG00000002963

Domain	Start	End	E-Value	Type
PDB:1YJM\|C	1	51	3e-30	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000154968

Predicted Effect

probably benign
Transcript: ENSMUST00000201882

SMART Domains

Protein: ENSMUSP00000144690
Gene: ENSMUSG00000002963

Domain	Start	End	E-Value	Type
PDB:1YJM\|C	1	110	6e-63	PDB
SCOP:d1lgpa_	8	114	3e-12	SMART
Blast:FHA	31	74	2e-10	BLAST
low complexity region	116	134	N/A	INTRINSIC
Pfam:PNK3P	165	327	9.9e-55	PFAM
low complexity region	350	364	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000209003

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208765

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000209139

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208687

Predicted Effect

probably benign
Transcript: ENSMUST00000208682

Predicted Effect

probably benign
Transcript: ENSMUST00000208666

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208991

Predicted Effect

probably benign
Transcript: ENSMUST00000209018

Predicted Effect

probably benign
Transcript: ENSMUST00000208410

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.7%
20x: 93.6%

Validation Efficiency

95% (107/113)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This locus represents a gene involved in DNA repair. In response to ionizing radiation or oxidative damage, the protein encoded by this locus catalyzes 5' phosphorylation and 3' dephosphorylation of nucleic acids. Mutations at this locus have been associated with microcephaly, seizures, and developmental delay.[provided by RefSeq, Sep 2010]
PHENOTYPE: Homozygotes for a frame-shift allele are embryonic lethal. Homozygotes for a hypomorphic allele exhibit smaller brain (cortex and cerebellum) and defects in both single- and double-strand DNA break repair associated with increased brain apoptosis and decreased proliferation in cortical progenitors. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 99 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1600012H06Rik	A	T	17: 15,164,001 (GRCm39)	I43L	possibly damaging	Het
4930449A18Rik	T	A	3: 59,749,153 (GRCm39)		noncoding transcript	Het
Abcc8	T	C	7: 45,800,252 (GRCm39)	K510R	probably damaging	Het
Adamtsl3	C	T	7: 82,178,069 (GRCm39)	R511C	probably damaging	Het
Arhgap11a	T	C	2: 113,670,107 (GRCm39)	S339G	probably damaging	Het
C2cd3	A	G	7: 100,065,397 (GRCm39)	T728A	probably benign	Het
Cand1	C	A	10: 119,049,451 (GRCm39)		probably null	Het
Catspere1	A	T	1: 177,699,624 (GRCm39)		noncoding transcript	Het
Ccdc121rt2	A	T	5: 112,598,106 (GRCm39)	K218*	probably null	Het
Cd209c	G	T	8: 3,995,905 (GRCm39)	R2S	probably benign	Het
Cdc16	A	G	8: 13,831,644 (GRCm39)		probably benign	Het
Ces1g	C	T	8: 94,060,323 (GRCm39)	E99K	probably benign	Het
Chrna7	A	C	7: 62,862,196 (GRCm39)	L10R	probably benign	Het
Clnk	C	T	5: 38,870,412 (GRCm39)		probably null	Het
Cntrob	C	G	11: 69,206,220 (GRCm39)	L315F	possibly damaging	Het
Ctdp1	A	G	18: 80,451,941 (GRCm39)	S145P	unknown	Het
Dennd2a	T	C	6: 39,474,044 (GRCm39)	D430G	probably damaging	Het
Dnajc16	A	G	4: 141,501,936 (GRCm39)	F298S	probably damaging	Het
Dock5	T	C	14: 68,055,012 (GRCm39)	D618G	probably damaging	Het
Drc3	G	A	11: 60,261,361 (GRCm39)	A171T	probably benign	Het
Ecel1	A	T	1: 87,081,023 (GRCm39)	N322K	probably damaging	Het
Eftud2	A	G	11: 102,745,640 (GRCm39)	F362L	probably damaging	Het
Egfr	C	T	11: 16,861,607 (GRCm39)	H1129Y	probably benign	Het
Eif2b1	A	G	5: 124,714,971 (GRCm39)	S102P	probably damaging	Het
Erich3	T	A	3: 154,410,480 (GRCm39)	F112I	possibly damaging	Het
Fam107b	T	C	2: 3,779,580 (GRCm39)	L261S	probably damaging	Het
Fat3	A	C	9: 15,908,883 (GRCm39)	V2373G	probably damaging	Het
Fcgbpl1	T	A	7: 27,850,147 (GRCm39)	C1198S	probably damaging	Het
Gadd45a	A	T	6: 67,013,873 (GRCm39)	L58Q	probably damaging	Het
Gask1b	G	A	3: 79,843,912 (GRCm39)	R377H	probably damaging	Het
Gipr	C	T	7: 18,896,601 (GRCm39)	R165H	probably damaging	Het
Gje1	C	T	10: 14,593,082 (GRCm39)	G45R	probably null	Het
Gldc	T	A	19: 30,111,132 (GRCm39)	N548I	possibly damaging	Het
Gm13035	A	G	4: 146,009,993 (GRCm39)		noncoding transcript	Het
Gm27013	T	A	6: 130,497,700 (GRCm39)		noncoding transcript	Het
Gm5436	A	T	12: 84,305,584 (GRCm39)		noncoding transcript	Het
Grik3	C	A	4: 125,584,969 (GRCm39)	N612K	probably damaging	Het
H2bc13	C	T	13: 21,900,234 (GRCm39)		probably benign	Het
Hfm1	C	A	5: 107,040,617 (GRCm39)	W716L	probably damaging	Het
Il5ra	T	C	6: 106,715,336 (GRCm39)	Y166C	probably damaging	Het
Iqcb1	A	G	16: 36,655,952 (GRCm39)	E113G	probably benign	Het
Kcnk10	A	T	12: 98,401,175 (GRCm39)	M486K	probably benign	Het
Kcnv2	A	G	19: 27,301,190 (GRCm39)	D347G	probably damaging	Het
Kif21b	C	A	1: 136,072,958 (GRCm39)	H119N	probably damaging	Het
Lamb1	C	T	12: 31,337,432 (GRCm39)	H388Y	probably damaging	Het
Leng9	T	C	7: 4,152,385 (GRCm39)	D97G	probably damaging	Het
Lmbr1	G	A	5: 29,492,424 (GRCm39)	T55I	probably damaging	Het
Lrp1	G	T	10: 127,419,805 (GRCm39)	R935S	probably damaging	Het
Lrp2	A	T	2: 69,299,755 (GRCm39)	V3099E	probably benign	Het
Lrrcc1	C	A	3: 14,627,571 (GRCm39)	D503E	probably benign	Het
Map1a	T	A	2: 121,132,567 (GRCm39)	S890T	probably damaging	Het
Msh2	C	A	17: 88,030,841 (GRCm39)	A906E	probably benign	Het
Mybph	A	T	1: 134,126,233 (GRCm39)	E349V	probably damaging	Het
Myh7b	C	A	2: 155,475,909 (GRCm39)	L1935M	probably benign	Het
Myh9	T	C	15: 77,653,453 (GRCm39)	E1348G	probably damaging	Het
Myzap	A	G	9: 71,456,037 (GRCm39)	S328P	probably damaging	Het
Nbeal1	T	C	1: 60,292,534 (GRCm39)	L1062P	probably damaging	Het
Nepro	G	A	16: 44,555,160 (GRCm39)	S412N	probably null	Het
Nr1h3	A	G	2: 91,020,563 (GRCm39)	F257L	probably benign	Het
Nudt5	T	C	2: 5,869,239 (GRCm39)	V155A	probably benign	Het
Ofcc1	G	A	13: 40,168,864 (GRCm39)	T841I	probably damaging	Het
Or13a25	A	T	7: 140,247,502 (GRCm39)	I94F	probably damaging	Het
Or52d3	A	T	7: 104,229,422 (GRCm39)	I190L	probably benign	Het
Or6ae1	A	G	7: 139,742,602 (GRCm39)	L87P	possibly damaging	Het
Pde1a	T	A	2: 79,959,181 (GRCm39)		probably benign	Het
Pde4dip	T	A	3: 97,700,844 (GRCm39)	H220L	probably damaging	Het
Pde9a	T	A	17: 31,662,135 (GRCm39)		probably null	Het
Pnpla7	A	G	2: 24,870,064 (GRCm39)	T15A	probably benign	Het
Polq	G	T	16: 36,869,145 (GRCm39)		probably null	Het
Ppfia2	C	T	10: 106,690,818 (GRCm39)	T553I	probably benign	Het
Ptk6	T	G	2: 180,838,784 (GRCm39)	N323T	possibly damaging	Het
Rhox3c	G	A	X: 36,652,077 (GRCm39)	A60T	probably damaging	Het
Rnf4	T	A	5: 34,506,053 (GRCm39)	V61E	probably damaging	Het
Rnf5	A	G	17: 34,820,977 (GRCm39)		probably benign	Het
Sardh	A	G	2: 27,081,967 (GRCm39)	V853A	probably benign	Het
Scfd1	T	C	12: 51,436,109 (GRCm39)	V86A	probably damaging	Het
Scube3	G	A	17: 28,383,097 (GRCm39)	C425Y	probably damaging	Het
Sema5a	C	T	15: 32,609,563 (GRCm39)	H490Y	probably benign	Het
Sfta2	T	C	17: 35,960,773 (GRCm39)		probably benign	Het
Sh3d19	T	C	3: 86,031,049 (GRCm39)	Y738H	probably damaging	Het
Shc2	T	C	10: 79,458,295 (GRCm39)	R463G	probably damaging	Het
Socs7	T	A	11: 97,267,829 (GRCm39)	I320N	possibly damaging	Het
Speer2	A	T	16: 69,654,988 (GRCm39)	M159K	probably benign	Het
Sppl2c	A	C	11: 104,078,478 (GRCm39)	H426P	probably benign	Het
Stag3	T	G	5: 138,307,627 (GRCm39)		probably null	Het
Stxbp5	C	A	10: 9,638,635 (GRCm39)	V1055L	probably benign	Het
Synpo	A	T	18: 60,736,684 (GRCm39)	S421T	probably damaging	Het
Taf6l	A	G	19: 8,759,770 (GRCm39)	V135A	possibly damaging	Het
Tas2r116	G	A	6: 132,832,660 (GRCm39)	S87N	probably benign	Het
Tomm6	T	C	17: 47,998,994 (GRCm39)		probably benign	Het
Trabd	T	C	15: 88,966,915 (GRCm39)	M113T	probably benign	Het
Trim58	G	A	11: 58,542,150 (GRCm39)	G370E	probably damaging	Het
Ttc41	C	T	10: 86,566,989 (GRCm39)	R552C	probably benign	Het
Vit	T	C	17: 78,909,308 (GRCm39)	S252P	probably benign	Het
Vma21-ps	T	A	4: 52,496,943 (GRCm39)	D101V	probably damaging	Het
Vmn1r173	A	T	7: 23,402,361 (GRCm39)	I199F	probably damaging	Het
Vmn2r114	T	A	17: 23,529,336 (GRCm39)	R255S	probably benign	Het
Vmn2r17	A	G	5: 109,582,246 (GRCm39)	N545S	probably damaging	Het
Zfp865	A	G	7: 5,034,640 (GRCm39)	Y875C	probably damaging	Het

Other mutations in Pnkp

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01886:Pnkp	APN	7	44,511,631 (GRCm39)	missense	probably damaging	1.00
IGL02750:Pnkp	APN	7	44,509,611 (GRCm39)	unclassified	probably benign
IGL02822:Pnkp	APN	7	44,511,848 (GRCm39)	missense	probably damaging	1.00
R1168:Pnkp	UTSW	7	44,511,961 (GRCm39)	missense	probably benign	0.00
R1437:Pnkp	UTSW	7	44,509,826 (GRCm39)	missense	possibly damaging	0.87
R1953:Pnkp	UTSW	7	44,512,026 (GRCm39)	missense	probably benign	0.02
R2879:Pnkp	UTSW	7	44,508,102 (GRCm39)	missense	probably damaging	0.99
R4329:Pnkp	UTSW	7	44,508,018 (GRCm39)	missense	probably benign	0.02
R4732:Pnkp	UTSW	7	44,509,878 (GRCm39)	unclassified	probably benign
R4846:Pnkp	UTSW	7	44,511,827 (GRCm39)	missense	probably damaging	0.99
R4861:Pnkp	UTSW	7	44,511,827 (GRCm39)	missense	probably damaging	0.99
R4861:Pnkp	UTSW	7	44,511,827 (GRCm39)	missense	probably damaging	0.99
R4872:Pnkp	UTSW	7	44,511,827 (GRCm39)	missense	probably damaging	0.99
R4873:Pnkp	UTSW	7	44,511,827 (GRCm39)	missense	probably damaging	0.99
R4875:Pnkp	UTSW	7	44,511,827 (GRCm39)	missense	probably damaging	0.99
R5068:Pnkp	UTSW	7	44,511,827 (GRCm39)	missense	probably damaging	0.99
R5120:Pnkp	UTSW	7	44,511,827 (GRCm39)	missense	probably damaging	0.99
R5121:Pnkp	UTSW	7	44,511,827 (GRCm39)	missense	probably damaging	0.99
R5266:Pnkp	UTSW	7	44,511,827 (GRCm39)	missense	probably damaging	0.99
R5267:Pnkp	UTSW	7	44,511,827 (GRCm39)	missense	probably damaging	0.99
R6532:Pnkp	UTSW	7	44,506,829 (GRCm39)	start codon destroyed	probably null	0.99
R6974:Pnkp	UTSW	7	44,510,462 (GRCm39)	missense	probably damaging	1.00
R7289:Pnkp	UTSW	7	44,508,114 (GRCm39)	missense	probably damaging	1.00
R7326:Pnkp	UTSW	7	44,509,158 (GRCm39)	missense	probably damaging	1.00
R7394:Pnkp	UTSW	7	44,508,102 (GRCm39)	missense	probably damaging	0.99
R7573:Pnkp	UTSW	7	44,506,852 (GRCm39)	missense	probably damaging	1.00
R7995:Pnkp	UTSW	7	44,507,960 (GRCm39)	nonsense	probably null
R8951:Pnkp	UTSW	7	44,507,617 (GRCm39)	missense	possibly damaging	0.64

Predicted Primers

PCR Primer
(F):5'- ACTAGCTGATGACTCTACTGCC -3'
(R):5'- TACTCCCCTAGTACACGCAG -3'

Sequencing Primer
(F):5'- GATGACTCTACTGCCCCCACAG -3'
(R):5'- TAGTACGTGCAGTGCTCCC -3'

Posted On

2016-03-16