Mutagenetix > Incidental Mutations

Incidental Mutation 'R1953:Pnkp'

217471

Institutional Source

Beutler Lab

Gene Symbol

Pnkp

Ensembl Gene

ENSMUSG00000002963

Gene Name

polynucleotide kinase 3'- phosphatase

Synonyms

PNK, 1810009G08Rik

MMRRC Submission

039967-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R1953 (G1)

Quality Score

217

Status

Not validated

Chromosome

Chromosomal Location

44857139-44862992 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 44862602 bp

Zygosity

Heterozygous

Amino Acid Change

Arginine to Serine at position 517 (R517S)

Ref Sequence

ENSEMBL: ENSMUSP00000103508 (fasta)

Gene Model

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

Predicted Effect

probably benign
Transcript: ENSMUST00000003044
AA Change: R517S

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000003044
Gene: ENSMUSG00000002963
AA Change: R517S

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 benign
Transcript: ENSMUST00000098478
AA Change: R481S

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000096078
Gene: ENSMUSG00000002963
AA Change: R481S

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 benign
Transcript: ENSMUST00000107876
AA Change: R517S

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000103508
Gene: ENSMUSG00000002963
AA Change: R517S

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: ENSMUST00000139003

SMART Domains

Protein: ENSMUSP00000143904
Gene: ENSMUSG00000002963

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144669

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145850

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152747

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

silent
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: 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

silent
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: ENSMUST00000207416

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208765

Predicted Effect

probably benign
Transcript: ENSMUST00000208666

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208687

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208991

Predicted Effect

probably benign
Transcript: ENSMUST00000208682

Predicted Effect

probably benign
Transcript: ENSMUST00000208385

Predicted Effect

probably benign
Transcript: ENSMUST00000207363

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000209003

Predicted Effect

probably benign
Transcript: ENSMUST00000209018

Predicted Effect

probably benign
Transcript: ENSMUST00000208410

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000207303

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000207393

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000209139

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208655

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.4%

Validation Efficiency

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930435E12Rik	G	T	16: 38,827,913	T278K	possibly damaging	Het
5730455P16Rik	A	T	11: 80,377,946	D12E	probably damaging	Het
Abca15	C	T	7: 120,361,432	R706C	probably damaging	Het
Actr1a	G	A	19: 46,380,948	S209F	probably benign	Het
Adcy1	A	G	11: 7,078,991	N247S	probably benign	Het
Anapc4	T	C	5: 52,839,688	L101S	probably damaging	Het
Asap3	C	T	4: 136,227,456	R60*	probably null	Het
Ascc3	T	C	10: 50,845,630	S2060P	probably benign	Het
Atp9b	G	A	18: 80,754,307	T851I	possibly damaging	Het
Borcs5	A	G	6: 134,710,267	H196R	unknown	Het
Bpifb9b	A	C	2: 154,311,314	D100A	probably damaging	Het
Cant1	G	C	11: 118,408,783	P247A	probably damaging	Het
Capza3	A	T	6: 140,042,568	I298L	possibly damaging	Het
Cdh10	T	C	15: 18,966,911		probably null	Het
Celsr3	T	C	9: 108,843,182	V2551A	probably benign	Het
Ces4a	G	A	8: 105,138,097	G69S	probably damaging	Het
Cmtr2	T	C	8: 110,221,919	L287P	probably damaging	Het
Crebbp	G	A	16: 4,179,449	T257I	probably benign	Het
Crispld2	G	A	8: 120,015,296	V128M	probably damaging	Het
Crnkl1	G	A	2: 145,928,200	A241V	probably damaging	Het
Dmd	T	A	X: 83,830,517	I1342N	probably damaging	Het
Dnah10	A	G	5: 124,782,268	T2043A	probably benign	Het
Dscaml1	C	T	9: 45,670,224	T447I	probably benign	Het
Eif2ak3	A	G	6: 70,892,554	T742A	probably benign	Het
Farp1	A	G	14: 121,255,482	T499A	probably benign	Het
Fcgr1	G	A	3: 96,287,070	T167I	probably damaging	Het
Fgd5	C	A	6: 92,024,630	H935Q	probably benign	Het
Fhl4	A	T	10: 85,098,307	D203E	probably benign	Het
Gapt	T	G	13: 110,353,806	T108P	probably damaging	Het
Gm12800	T	C	4: 101,910,115	I187T	probably benign	Het
Gm13762	G	A	2: 88,973,880	Q4*	probably null	Het
Gpt2	A	G	8: 85,521,384	T419A	probably benign	Het
Gucy2c	A	G	6: 136,704,293	V907A	probably damaging	Het
Hmbs	T	C	9: 44,337,444	D211G	probably damaging	Het
Irx5	A	G	8: 92,359,810	N174D	probably damaging	Het
Itfg1	A	G	8: 85,831,231	V170A	probably benign	Het
Itga2b	T	A	11: 102,458,183	T732S	probably benign	Het
Klhl3	A	G	13: 58,011,208	Y546H	probably damaging	Het
Lama5	G	A	2: 180,190,747	H1670Y	possibly damaging	Het
Mlst8	AT	ATT	17: 24,478,013		probably null	Het
Nbeal1	T	C	1: 60,234,840	V409A	probably damaging	Het
Nlgn1	T	A	3: 25,436,300	D421V	probably damaging	Het
Nlrp10	T	C	7: 108,925,118	D385G	probably benign	Het
Nr2e3	T	A	9: 59,949,796	D30V	probably benign	Het
Nyap1	A	G	5: 137,735,032	S580P	probably benign	Het
Olfr1259	A	G	2: 89,943,923	L64P	probably damaging	Het
Olfr1509	T	A	14: 52,450,887	V158E	probably benign	Het
Pex1	A	G	5: 3,630,038	H952R	probably damaging	Het
Plin4	T	A	17: 56,103,849	I1061F	possibly damaging	Het
Polr2e	T	A	10: 80,038,554	E39D	probably benign	Het
Prokr1	T	C	6: 87,588,593	Y90C	probably benign	Het
Ptprm	A	T	17: 66,940,580	S587T	probably benign	Het
Rere	G	A	4: 150,616,837	E1225K	probably damaging	Het
Rsl24d1	G	T	9: 73,114,614		probably benign	Het
Selp	A	G	1: 164,126,512	N127S	probably benign	Het
Slc22a18	C	T	7: 143,476,247	T17I	probably damaging	Het
Smad2	A	G	18: 76,262,705	T72A	possibly damaging	Het
Snx29	G	A	16: 11,399,783	W149*	probably null	Het
Stk31	G	T	6: 49,446,478		probably null	Het
Sult1e1	T	G	5: 87,587,671		probably null	Het
Syngap1	G	A	17: 26,944,687	R41H	possibly damaging	Het
Tbc1d17	T	A	7: 44,841,398		probably null	Het
Tie1	A	T	4: 118,472,790		probably null	Het
Ttn	A	T	2: 76,811,243	L5176Q	possibly damaging	Het
Usp47	T	A	7: 112,092,876	D848E	probably benign	Het
Vmn1r72	A	G	7: 11,669,804	L239P	probably damaging	Het
Vmn2r124	T	C	17: 18,062,860	I272T	probably benign	Het
Vwa1	C	T	4: 155,773,114	V76M	probably damaging	Het
Xrn1	G	T	9: 96,024,221		probably null	Het
Zfp667	G	T	7: 6,305,088	V252F	probably benign	Het
Zranb3	A	T	1: 127,999,399	V343D	probably damaging	Het

Other mutations in Pnkp

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01886:Pnkp	APN	7	44862207	missense	probably damaging	1.00
IGL02750:Pnkp	APN	7	44860187	unclassified	probably benign
IGL02822:Pnkp	APN	7	44862424	missense	probably damaging	1.00
R1168:Pnkp	UTSW	7	44862537	missense	probably benign	0.00
R1437:Pnkp	UTSW	7	44860402	missense	possibly damaging	0.87
R2879:Pnkp	UTSW	7	44858678	missense	probably damaging	0.99
R4329:Pnkp	UTSW	7	44858594	missense	probably benign	0.02
R4732:Pnkp	UTSW	7	44860454	unclassified	probably benign
R4842:Pnkp	UTSW	7	44861646	splice site	probably null
R4846:Pnkp	UTSW	7	44862403	missense	probably damaging	0.99
R4861:Pnkp	UTSW	7	44862403	missense	probably damaging	0.99
R4861:Pnkp	UTSW	7	44862403	missense	probably damaging	0.99
R4872:Pnkp	UTSW	7	44862403	missense	probably damaging	0.99
R4873:Pnkp	UTSW	7	44862403	missense	probably damaging	0.99
R4875:Pnkp	UTSW	7	44862403	missense	probably damaging	0.99
R5068:Pnkp	UTSW	7	44862403	missense	probably damaging	0.99
R5120:Pnkp	UTSW	7	44862403	missense	probably damaging	0.99
R5121:Pnkp	UTSW	7	44862403	missense	probably damaging	0.99
R5266:Pnkp	UTSW	7	44862403	missense	probably damaging	0.99
R5267:Pnkp	UTSW	7	44862403	missense	probably damaging	0.99
R6532:Pnkp	UTSW	7	44857405	start codon destroyed	probably null	0.99
R6974:Pnkp	UTSW	7	44861038	missense	probably damaging	1.00
R7289:Pnkp	UTSW	7	44858690	missense	probably damaging	1.00
R7326:Pnkp	UTSW	7	44859734	missense	probably damaging	1.00
R7394:Pnkp	UTSW	7	44858678	missense	probably damaging	0.99
R7573:Pnkp	UTSW	7	44857428	missense	probably damaging	1.00
R7995:Pnkp	UTSW	7	44858536	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- CATGGTCATGTTTAGCTACAGGTTC -3'
(R):5'- GTTCTGAAACCTGGTGCTGG -3'

Sequencing Primer
(F):5'- AGCTACAGGTTCGGGGG -3'
(R):5'- ACAAAATGGCTGTGGCTGCTC -3'

Posted On

2014-08-01