Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01886:Pnkp'

179146

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Pnkp

Ensembl Gene

ENSMUSG00000002963

Gene Name

polynucleotide kinase 3'- phosphatase

Synonyms

PNK, 1810009G08Rik

Accession Numbers

Essential gene?

Probably essential (E-score: 0.962) question?

Stock #

IGL01886

Quality Score

Status

Chromosome

Chromosomal Location

44506563-44512416 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 44511631 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 76 (A76T)

Ref Sequence

ENSEMBL: ENSMUSP00000144484 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000003044
AA Change: A437T

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

SMART Domains

Protein: ENSMUSP00000003044
Gene: ENSMUSG00000002963
AA Change: A437T

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 damaging
Transcript: ENSMUST00000098478
AA Change: A401T

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000096078
Gene: ENSMUSG00000002963
AA Change: A401T

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: A437T

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

SMART Domains

Protein: ENSMUSP00000103508
Gene: ENSMUSG00000002963
AA Change: A437T

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

probably damaging
Transcript: ENSMUST00000200892
AA Change: A58T

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

SMART Domains

Protein: ENSMUSP00000144163
Gene: ENSMUSG00000002963
AA Change: A58T

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000202646
AA Change: A76T

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

SMART Domains

Protein: ENSMUSP00000144484
Gene: ENSMUSG00000002963
AA Change: A76T

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: ENSMUST00000201882
AA Change: C400Y

PolyPhen 2 Score 0.221 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000144690
Gene: ENSMUSG00000002963
AA Change: C400Y

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: ENSMUST00000207393

Predicted Effect

probably benign
Transcript: ENSMUST00000207363

Predicted Effect

probably benign
Transcript: ENSMUST00000208385

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152747

Predicted Effect

probably benign
Transcript: ENSMUST00000207416

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000207303

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145850

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: 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: ENSMUST00000208666

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208991

Predicted Effect

probably benign
Transcript: ENSMUST00000209018

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208655

Predicted Effect

probably benign
Transcript: ENSMUST00000208682

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208687

Predicted Effect

probably benign
Transcript: ENSMUST00000208410

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000209003

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000209139

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208765

Coding Region Coverage

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: 43 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Akt1	C	T	12: 112,625,592 (GRCm39)	V136M	probably benign	Het
Ankrd34c	A	T	9: 89,612,318 (GRCm39)	L8M	possibly damaging	Het
Anks6	C	A	4: 47,044,850 (GRCm39)	W352L	probably damaging	Het
Arhgap12	A	T	18: 6,027,613 (GRCm39)	N768K	probably damaging	Het
Clec7a	A	T	6: 129,440,140 (GRCm39)		probably benign	Het
Cyp3a13	G	A	5: 137,897,082 (GRCm39)	P411S	probably damaging	Het
Elavl2	A	G	4: 91,152,330 (GRCm39)	V129A	probably damaging	Het
Ercc6	T	A	14: 32,291,537 (GRCm39)	S994T	possibly damaging	Het
Esco1	T	A	18: 10,595,262 (GRCm39)	K8I	probably damaging	Het
Esr1	T	A	10: 4,806,861 (GRCm39)	I259K	probably damaging	Het
Filip1l	A	G	16: 57,391,613 (GRCm39)	I734V	possibly damaging	Het
Gm10717	C	T	9: 3,025,616 (GRCm39)	S67L	probably benign	Het
Gm10718	A	T	9: 3,025,118 (GRCm39)	Y194F	probably benign	Het
Gm21738	G	A	14: 19,416,979 (GRCm38)	S144L	probably benign	Het
Grin3a	T	A	4: 49,702,814 (GRCm39)	I891F	probably damaging	Het
Kat7	T	C	11: 95,196,959 (GRCm39)	T27A	probably benign	Het
Kdm1a	A	G	4: 136,288,327 (GRCm39)		probably null	Het
Kifc5b	T	C	17: 27,151,091 (GRCm39)	V663A	probably damaging	Het
Lama1	T	G	17: 68,114,792 (GRCm39)	S2314A	probably benign	Het
Lrrc69	C	T	4: 14,703,984 (GRCm39)	V279I	probably benign	Het
Mast3	A	T	8: 71,234,783 (GRCm39)	L774Q	possibly damaging	Het
Med27	C	A	2: 29,303,494 (GRCm39)	P9Q	probably damaging	Het
Myo5a	C	A	9: 75,076,372 (GRCm39)		probably benign	Het
Myoz1	T	C	14: 20,705,377 (GRCm39)	K14E	probably damaging	Het
Neb	T	C	2: 52,073,857 (GRCm39)		probably benign	Het
Nlrp1a	T	C	11: 71,014,327 (GRCm39)	T308A	probably benign	Het
Or1l4b	A	G	2: 37,036,521 (GRCm39)	Y99C	probably damaging	Het
Or8d2b	G	T	9: 38,788,844 (GRCm39)	C124F	probably damaging	Het
Orc1	T	A	4: 108,461,154 (GRCm39)		probably null	Het
Polr3h	T	C	15: 81,801,591 (GRCm39)	E95G	probably damaging	Het
Prpf40b	T	A	15: 99,202,328 (GRCm39)	M62K	unknown	Het
Prpf8	C	A	11: 75,386,570 (GRCm39)	Q1075K	probably benign	Het
Ptprg	A	G	14: 12,179,280 (GRCm38)	K766E	probably benign	Het
Rabgap1l	A	T	1: 160,169,612 (GRCm39)	N778K	probably damaging	Het
Riok3	T	A	18: 12,272,442 (GRCm39)	N204K	probably damaging	Het
Shank3	A	G	15: 89,415,866 (GRCm39)	K650E	probably damaging	Het
Sim1	T	A	10: 50,860,411 (GRCm39)	S758T	probably damaging	Het
Slu7	T	G	11: 43,330,087 (GRCm39)	N171K	probably damaging	Het
Sp140l2	A	G	1: 85,231,907 (GRCm39)		probably benign	Het
Sult6b2	A	G	6: 142,735,852 (GRCm39)		probably null	Het
Taf6l	C	T	19: 8,755,450 (GRCm39)		probably null	Het
Ubtfl1	G	A	9: 18,321,017 (GRCm39)	V182M	possibly damaging	Het
Vmn2r129	C	T	4: 156,690,549 (GRCm39)		noncoding transcript	Het

Other mutations in Pnkp

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
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
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

Posted On

2014-05-07