Mutagenetix > Incidental Mutation

Incidental Mutation 'R4861:Pnkp'

380250

Institutional Source

Beutler Lab

Gene Symbol

Pnkp

Ensembl Gene

ENSMUSG00000002963

Gene Name

polynucleotide kinase 3'- phosphatase

Synonyms

PNK, 1810009G08Rik

MMRRC Submission

042472-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.964) question?

Stock #

R4861 (G1)

Quality Score

134

Status

Validated

Chromosome

Chromosomal Location

44506563-44512416 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 44511827 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Leucine at position 113 (S113L)

Ref Sequence

ENSEMBL: ENSMUSP00000144484 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000003044
AA Change: S474L

PolyPhen 2 Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000003044
Gene: ENSMUSG00000002963
AA Change: S474L

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

possibly damaging
Transcript: ENSMUST00000098478
AA Change: S438L

PolyPhen 2 Score 0.692 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000096078
Gene: ENSMUSG00000002963
AA Change: S438L

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: S474L

PolyPhen 2 Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000103508
Gene: ENSMUSG00000002963
AA Change: S474L

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

noncoding transcript
Transcript: ENSMUST00000144669

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145850

Predicted Effect

probably damaging
Transcript: ENSMUST00000200892
AA Change: S95L

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000144163
Gene: ENSMUSG00000002963
AA Change: S95L

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000202646
AA Change: S113L

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000144484
Gene: ENSMUSG00000002963
AA Change: S113L

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

probably benign
Transcript: ENSMUST00000207363

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000207393

Predicted Effect

probably benign
Transcript: ENSMUST00000207416

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152747

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000207303

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

probably benign
Transcript: ENSMUST00000154968

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: ENSMUST00000155050

SMART Domains

Protein: ENSMUSP00000144663
Gene: ENSMUSG00000002963

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000209139

Predicted Effect

probably benign
Transcript: ENSMUST00000208410

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208655

Predicted Effect

probably benign
Transcript: ENSMUST00000209018

Predicted Effect

probably benign
Transcript: ENSMUST00000208682

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000209003

Predicted Effect

probably benign
Transcript: ENSMUST00000208666

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208765

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208687

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208991

Meta Mutation Damage Score

0.2697

Coding Region Coverage

1x: 98.8%
3x: 97.8%
10x: 94.2%
20x: 84.7%

Validation Efficiency

100% (53/53)

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: 33 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb11	C	T	2: 69,076,249 (GRCm39)	R1153H	probably damaging	Het
Ahcy	T	C	2: 154,902,436 (GRCm39)	E411G	probably benign	Het
Alpi	T	A	1: 87,028,191 (GRCm39)	I211F	probably damaging	Het
Arfgef3	G	A	10: 18,483,479 (GRCm39)	A1415V	probably benign	Het
Car3	T	C	3: 14,931,956 (GRCm39)	V109A	probably damaging	Het
Cdk13	A	T	13: 17,941,171 (GRCm39)	V17D	probably damaging	Het
Cept1	A	C	3: 106,413,048 (GRCm39)	S226A	probably damaging	Het
Dbt	A	T	3: 116,341,727 (GRCm39)	I443L	probably benign	Het
Dync1h1	C	A	12: 110,624,560 (GRCm39)	T3700N	probably damaging	Het
Farp2	T	C	1: 93,533,141 (GRCm39)	L633S	probably damaging	Het
Frmd6	T	G	12: 70,940,500 (GRCm39)	S382A	probably damaging	Het
Gm26727	T	C	2: 67,263,289 (GRCm39)	I79M	probably damaging	Het
Gm5800	T	A	14: 51,953,504 (GRCm39)	N37I	probably damaging	Het
Hapln1	G	A	13: 89,749,571 (GRCm39)	G39S	possibly damaging	Het
Ice2	T	A	9: 69,322,730 (GRCm39)	S408R	probably benign	Het
Lctl	T	C	9: 64,027,045 (GRCm39)	I131T	possibly damaging	Het
Mvk	C	T	5: 114,598,258 (GRCm39)		probably benign	Het
Mzt1	T	C	14: 99,284,910 (GRCm39)		probably null	Het
Ncoa7	T	A	10: 30,580,608 (GRCm39)	M117L	probably benign	Het
Npy4r	C	T	14: 33,868,840 (GRCm39)	W149*	probably null	Het
Nr5a2	A	G	1: 136,876,458 (GRCm39)		probably null	Het
Odad1	A	G	7: 45,592,297 (GRCm39)	E359G	probably damaging	Het
Plg	G	A	17: 12,614,622 (GRCm39)	E301K	probably benign	Het
Rapgef2	T	C	3: 78,981,743 (GRCm39)	K1084R	probably benign	Het
Slc41a2	T	C	10: 83,152,322 (GRCm39)	Q51R	probably damaging	Het
Slc47a2	A	T	11: 61,227,059 (GRCm39)	C170S	probably benign	Het
Slco1b2	A	T	6: 141,616,948 (GRCm39)	N427I	possibly damaging	Het
Smc2	G	A	4: 52,461,090 (GRCm39)	R571H	probably benign	Het
Sp4	G	T	12: 118,264,546 (GRCm39)		probably null	Het
Tas2r117	T	C	6: 132,780,092 (GRCm39)	F77L	probably benign	Het
Tbcd	C	T	11: 121,492,787 (GRCm39)	R875C	probably damaging	Het
Thumpd2	A	G	17: 81,334,230 (GRCm39)	S453P	probably benign	Het
Vars2	G	T	17: 35,972,825 (GRCm39)	Q13K	probably benign	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
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'- AGCTGTTTTGCCTCCACAG -3'
(R):5'- ATGCTCCTGTAACCGGAATG -3'

Sequencing Primer
(F):5'- GTACATCCAATGTGCCAAAGATG -3'
(R):5'- TGCTCCTGTAACCGGAATGGAATC -3'

Posted On

2016-04-15