Mutagenetix > Incidental Mutation

Incidental Mutation 'R7289:Pnkp'

566231

Institutional Source

Beutler Lab

Gene Symbol

Pnkp

Ensembl Gene

ENSMUSG00000002963

Gene Name

polynucleotide kinase 3'- phosphatase

Synonyms

PNK, 1810009G08Rik

MMRRC Submission

045396-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.962) question?

Stock #

R7289 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

44506563-44512416 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 44508114 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tryptophan to Arginine at position 146 (W146R)

Ref Sequence

ENSEMBL: ENSMUSP00000003044 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000003044] [ENSMUST00000046575] [ENSMUST00000054343] [ENSMUST00000098478] [ENSMUST00000107876] [ENSMUST00000107880] [ENSMUST00000107882] [ENSMUST00000107885] [ENSMUST00000123015] [ENSMUST00000124168] [ENSMUST00000127783] [ENSMUST00000139003] [ENSMUST00000141311] [ENSMUST00000154968] [ENSMUST00000155050] [ENSMUST00000200892] [ENSMUST00000201882] [ENSMUST00000202646] [ENSMUST00000207363] [ENSMUST00000209018]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000003044
AA Change: W146R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000003044
Gene: ENSMUSG00000002963
AA Change: W146R

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: ENSMUST00000054343

SMART Domains

Protein: ENSMUSP00000049764
Gene: ENSMUSG00000011096

Domain	Start	End	E-Value	Type
low complexity region	33	60	N/A	INTRINSIC
low complexity region	66	101	N/A	INTRINSIC
low complexity region	102	116	N/A	INTRINSIC
low complexity region	161	180	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000098478
AA Change: W146R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000096078
Gene: ENSMUSG00000002963
AA Change: W146R

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 damaging
Transcript: ENSMUST00000107876
AA Change: W146R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000103508
Gene: ENSMUSG00000002963
AA Change: W146R

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: ENSMUST00000107880

SMART Domains

Protein: ENSMUSP00000103512
Gene: ENSMUSG00000011096

Domain	Start	End	E-Value	Type
low complexity region	33	60	N/A	INTRINSIC
low complexity region	66	101	N/A	INTRINSIC
low complexity region	102	116	N/A	INTRINSIC
low complexity region	161	180	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000107882

SMART Domains

Protein: ENSMUSP00000103514
Gene: ENSMUSG00000011096

Domain	Start	End	E-Value	Type
low complexity region	59	86	N/A	INTRINSIC
low complexity region	92	127	N/A	INTRINSIC
low complexity region	128	142	N/A	INTRINSIC
low complexity region	187	206	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000107885

SMART Domains

Protein: ENSMUSP00000103517
Gene: ENSMUSG00000011096

Domain	Start	End	E-Value	Type
low complexity region	104	131	N/A	INTRINSIC
low complexity region	137	172	N/A	INTRINSIC
low complexity region	173	187	N/A	INTRINSIC
Pfam:PRAS	199	323	1.2e-51	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000123015
AA Change: W146R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000143862
Gene: ENSMUSG00000002963
AA Change: W146R

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

probably benign
Transcript: ENSMUST00000127783

SMART Domains

Protein: ENSMUSP00000116149
Gene: ENSMUSG00000011096

Domain	Start	End	E-Value	Type
low complexity region	33	60	N/A	INTRINSIC
low complexity region	66	101	N/A	INTRINSIC
low complexity region	102	116	N/A	INTRINSIC
Pfam:PRAS	134	247	1.3e-39	PFAM

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: ENSMUST00000141311

SMART Domains

Protein: ENSMUSP00000120690
Gene: ENSMUSG00000011096

Domain	Start	End	E-Value	Type
low complexity region	40	67	N/A	INTRINSIC
low complexity region	73	108	N/A	INTRINSIC
low complexity region	109	123	N/A	INTRINSIC
low complexity region	168	187	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000142880

Predicted Effect

probably benign
Transcript: ENSMUST00000154968

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 benign
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 damaging
Transcript: ENSMUST00000201882
AA Change: W146R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000144690
Gene: ENSMUSG00000002963
AA Change: W146R

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

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: ENSMUST00000207363

Predicted Effect

probably benign
Transcript: ENSMUST00000207416

Predicted Effect

probably benign
Transcript: ENSMUST00000208385

Predicted Effect

probably benign
Transcript: ENSMUST00000208410

Predicted Effect

probably benign
Transcript: ENSMUST00000209018

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

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: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aars2	G	A	17: 45,818,550 (GRCm39)	D112N	probably damaging	Het
Abca7	T	A	10: 79,845,778 (GRCm39)	I1580K	probably damaging	Het
Aebp1	A	G	11: 5,815,059 (GRCm39)	D234G	probably damaging	Het
Agap1	T	A	1: 89,383,153 (GRCm39)	M1K	probably null	Het
Agrn	A	T	4: 156,263,389 (GRCm39)	L345H	probably damaging	Het
Amfr	A	G	8: 94,725,754 (GRCm39)	M209T	possibly damaging	Het
Angel2	G	A	1: 190,673,371 (GRCm39)	R338H	possibly damaging	Het
Ankrd27	C	T	7: 35,330,674 (GRCm39)	A866V	probably damaging	Het
Apc	G	A	18: 34,448,324 (GRCm39)	R1740Q	probably damaging	Het
Arhgap32	A	T	9: 32,168,233 (GRCm39)	S739C	possibly damaging	Het
Arhgap32	G	C	9: 32,168,234 (GRCm39)	S739T	probably benign	Het
Arhgef2	C	T	3: 88,543,192 (GRCm39)	S418L	probably benign	Het
Arhgef25	T	C	10: 127,019,641 (GRCm39)	T472A	possibly damaging	Het
Atrnl1	C	T	19: 57,638,846 (GRCm39)	S328F	probably benign	Het
Bahcc1	C	T	11: 120,171,000 (GRCm39)	A1514V	probably benign	Het
Calcoco2	C	T	11: 95,990,823 (GRCm39)	E305K	unknown	Het
Ccn1	C	T	3: 145,354,428 (GRCm39)	W161*	probably null	Het
Cdc42bpa	A	T	1: 179,889,362 (GRCm39)	K203*	probably null	Het
Cmc1	A	T	9: 117,904,250 (GRCm39)	I47N	possibly damaging	Het
Cntln	A	G	4: 84,964,540 (GRCm39)	E656G	possibly damaging	Het
Dcun1d3	T	C	7: 119,458,864 (GRCm39)	K57R	possibly damaging	Het
Ddx23	T	C	15: 98,546,492 (GRCm39)	E559G	probably damaging	Het
Dennd6a	G	A	14: 26,333,193 (GRCm39)	R367Q	probably damaging	Het
Desi2	A	T	1: 178,083,702 (GRCm39)		probably benign	Het
Dido1	T	C	2: 180,301,424 (GRCm39)	D2160G	unknown	Het
Efcab3	T	C	11: 104,929,184 (GRCm39)	M4838T	probably benign	Het
Epb41	A	G	4: 131,718,520 (GRCm39)		probably null	Het
Esrrb	T	A	12: 86,517,331 (GRCm39)		probably null	Het
Fabp1	C	A	6: 71,180,111 (GRCm39)	T94N	probably benign	Het
Fam120a	A	T	13: 49,045,482 (GRCm39)	C785S	probably damaging	Het
Fam243	T	C	16: 92,117,710 (GRCm39)	I193V	probably damaging	Het
Foxc1	A	G	13: 31,991,243 (GRCm39)	Y18C	probably damaging	Het
Fshr	T	C	17: 89,293,272 (GRCm39)	T469A	probably benign	Het
Gm14399	T	A	2: 174,972,204 (GRCm39)	H517L	unknown	Het
Gm39115	G	T	7: 141,689,297 (GRCm39)	Q159K	unknown	Het
Gm7347	T	A	5: 26,262,306 (GRCm39)	I72F	possibly damaging	Het
Hmcn1	A	G	1: 150,559,466 (GRCm39)	V2395A	possibly damaging	Het
Ighv5-17	T	G	12: 113,822,858 (GRCm39)	T88P	probably damaging	Het
Insm2	T	A	12: 55,647,329 (GRCm39)	Y358N	probably damaging	Het
Kazn	A	T	4: 141,844,486 (GRCm39)	L409Q		Het
Kcnj5	A	C	9: 32,234,045 (GRCm39)	L90R	probably damaging	Het
Kcnv2	A	T	19: 27,311,084 (GRCm39)	T484S	probably damaging	Het
Kdm3b	T	C	18: 34,927,557 (GRCm39)	Y140H	probably benign	Het
Kifbp	A	C	10: 62,401,895 (GRCm39)	C261W	probably damaging	Het
Krt25	C	T	11: 99,212,098 (GRCm39)	A180T	probably benign	Het
Mmp1a	A	G	9: 7,467,294 (GRCm39)	E290G	probably damaging	Het
Muc21	G	A	17: 35,929,761 (GRCm39)	A1475V	unknown	Het
Nr3c1	T	C	18: 39,547,654 (GRCm39)	T755A	probably benign	Het
Nr3c1	A	T	18: 39,555,786 (GRCm39)	I517N	probably benign	Het
Nxpe2	A	G	9: 48,234,339 (GRCm39)		probably null	Het
Oaz1	C	A	10: 80,662,673 (GRCm39)	T27K	possibly damaging	Het
Or4p7	A	T	2: 88,222,050 (GRCm39)	H153L	probably damaging	Het
Or51f5	T	C	7: 102,424,634 (GRCm39)	I301T	probably damaging	Het
Or5t5	G	T	2: 86,617,034 (GRCm39)	C320F	probably benign	Het
Or6z3	T	A	7: 6,463,777 (GRCm39)	W90R	probably benign	Het
Or8k21	A	G	2: 86,145,369 (GRCm39)	M87T	probably benign	Het
Or8s5	A	G	15: 98,237,943 (GRCm39)	V309A	probably damaging	Het
Pafah2	A	T	4: 134,147,308 (GRCm39)	K319M	probably damaging	Het
Pask	A	T	1: 93,259,309 (GRCm39)	V236E	probably damaging	Het
Pcdh1	T	C	18: 38,322,966 (GRCm39)	T956A	probably damaging	Het
Pcdhb18	C	A	18: 37,623,700 (GRCm39)	N343K	probably damaging	Het
Pcsk2	A	T	2: 143,532,343 (GRCm39)	I164F	probably damaging	Het
Phf1	T	C	17: 27,154,289 (GRCm39)	Y169H	probably damaging	Het
Pkdrej	T	A	15: 85,705,301 (GRCm39)	I212F	probably benign	Het
Prkcb	A	T	7: 122,143,910 (GRCm39)	I325F	probably benign	Het
Ptpn21	C	T	12: 98,670,450 (GRCm39)	D239N	probably benign	Het
Ptprb	A	G	10: 116,164,070 (GRCm39)	T626A	probably damaging	Het
Pttg1	T	C	11: 43,311,916 (GRCm39)	N180D	probably benign	Het
Raly	G	A	2: 154,703,774 (GRCm39)	R115Q	probably damaging	Het
Rims2	A	T	15: 39,301,114 (GRCm39)	M474L	probably benign	Het
Sash1	A	T	10: 8,605,960 (GRCm39)	I810N	probably damaging	Het
Scnn1g	T	A	7: 121,337,304 (GRCm39)	L55*	probably null	Het
Sema6b	A	T	17: 56,432,573 (GRCm39)	D543E	possibly damaging	Het
Serpina11	C	T	12: 103,952,761 (GRCm39)	G5E	unknown	Het
Sesn3	A	T	9: 14,187,848 (GRCm39)	M1L	probably benign	Het
Sez6	T	A	11: 77,865,149 (GRCm39)	I632N	possibly damaging	Het
Sgo2b	A	T	8: 64,394,192 (GRCm39)	I49N	probably damaging	Het
Slc30a2	A	T	4: 134,071,524 (GRCm39)	I86F	possibly damaging	Het
Slc38a6	T	A	12: 73,333,786 (GRCm39)	W30R	probably benign	Het
Spata31g1	A	T	4: 42,972,379 (GRCm39)	T571S	probably benign	Het
Spata31g1	A	T	4: 42,973,252 (GRCm39)	I862F	possibly damaging	Het
Stk31	T	G	6: 49,415,393 (GRCm39)	V576G	probably benign	Het
Szt2	G	A	4: 118,233,075 (GRCm39)	T2297I	unknown	Het
Tmem208	T	C	8: 106,061,418 (GRCm39)	F148S	possibly damaging	Het
Tprg1l	A	G	4: 154,245,031 (GRCm39)	L19P	possibly damaging	Het
Tubg2	C	A	11: 101,050,897 (GRCm39)	N207K	probably damaging	Het
Ube2n	G	T	10: 95,377,612 (GRCm39)	K130N	probably benign	Het
Usp36	T	C	11: 118,164,355 (GRCm39)	Y384C	probably damaging	Het
Vcan	A	T	13: 89,840,852 (GRCm39)	L1564*	probably null	Het
Xkr6	A	T	14: 64,035,748 (GRCm39)	D283V	unknown	Het
Zfp654	T	C	16: 64,605,523 (GRCm39)	H352R	probably benign	Het
Zfp819	T	A	7: 43,266,506 (GRCm39)	C330S	probably damaging	Het
Zfp970	G	T	2: 177,167,086 (GRCm39)	C220F	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
R4842:Pnkp	UTSW	7	44,511,070 (GRCm39)	splice site	probably null
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
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'- TTAACCCGTCAACTGTTGGGG -3'
(R):5'- CTGCACAGAACAGTTGAGGC -3'

Sequencing Primer
(F):5'- CAGGACTGTCTGGCTCTCTAAG -3'
(R):5'- GCTCAGGAACTTTGATAAGACTAGC -3'

Posted On

2019-06-26