Incidental Mutation 'R4872:Pnkp'
| ID |
376658 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pnkp
|
| Ensembl Gene |
ENSMUSG00000002963 |
| Gene Name |
polynucleotide kinase 3'- phosphatase |
| Synonyms |
PNK, 1810009G08Rik |
| MMRRC Submission |
042482-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.964)
|
| Stock # |
R4872 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
7 |
| 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: 99.2%
- 3x: 98.5%
- 10x: 96.9%
- 20x: 94.1%
|
| Validation Efficiency |
98% (81/83) |
| 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: 73 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcd2 |
C |
A |
15: 91,075,514 (GRCm39) |
V100L |
probably benign |
Het |
| Acad11 |
G |
A |
9: 103,963,465 (GRCm39) |
|
probably benign |
Het |
| Actb |
C |
T |
5: 142,891,307 (GRCm39) |
|
probably benign |
Het |
| Ano9 |
G |
A |
7: 140,687,117 (GRCm39) |
A374V |
probably damaging |
Het |
| Baz2b |
T |
C |
2: 59,773,103 (GRCm39) |
|
probably null |
Het |
| Bltp3a |
G |
T |
17: 28,109,110 (GRCm39) |
D1110Y |
probably benign |
Het |
| Bpifb9b |
T |
A |
2: 154,155,551 (GRCm39) |
L350Q |
probably damaging |
Het |
| Cd27 |
T |
A |
6: 125,211,281 (GRCm39) |
|
probably null |
Het |
| Cd72 |
A |
G |
4: 43,449,563 (GRCm39) |
|
probably benign |
Het |
| Cdadc1 |
A |
T |
14: 59,801,973 (GRCm39) |
S516T |
probably benign |
Het |
| Chst5 |
T |
A |
8: 112,617,192 (GRCm39) |
I143F |
possibly damaging |
Het |
| Col20a1 |
T |
C |
2: 180,639,156 (GRCm39) |
V452A |
possibly damaging |
Het |
| Cox11 |
C |
A |
11: 90,535,229 (GRCm39) |
Q227K |
probably benign |
Het |
| Cpa6 |
A |
G |
1: 10,665,843 (GRCm39) |
|
probably null |
Het |
| Dnase1l1 |
C |
T |
X: 73,320,644 (GRCm39) |
|
probably null |
Het |
| Dpm2 |
T |
C |
2: 32,461,203 (GRCm39) |
|
probably benign |
Het |
| Dync1h1 |
C |
A |
12: 110,624,560 (GRCm39) |
T3700N |
probably damaging |
Het |
| Frem1 |
A |
C |
4: 82,881,387 (GRCm39) |
N1273K |
probably damaging |
Het |
| Fry |
T |
C |
5: 150,317,704 (GRCm39) |
|
probably null |
Het |
| Gm10306 |
G |
T |
4: 94,445,069 (GRCm39) |
|
probably benign |
Het |
| Gm5565 |
T |
C |
5: 146,094,913 (GRCm39) |
T278A |
probably benign |
Het |
| Gm8180 |
A |
G |
14: 44,019,802 (GRCm39) |
I40T |
probably benign |
Het |
| Iah1 |
T |
C |
12: 21,367,426 (GRCm39) |
V44A |
probably benign |
Het |
| Iqgap3 |
C |
T |
3: 88,020,435 (GRCm39) |
P360S |
probably damaging |
Het |
| Klhl28 |
T |
A |
12: 65,003,896 (GRCm39) |
I206F |
possibly damaging |
Het |
| Krt13 |
A |
G |
11: 100,012,332 (GRCm39) |
|
probably benign |
Het |
| Lipo2 |
T |
A |
19: 33,726,914 (GRCm39) |
D41V |
probably benign |
Het |
| Lrig2 |
C |
G |
3: 104,398,842 (GRCm39) |
V229L |
possibly damaging |
Het |
| Lrrc32 |
C |
T |
7: 98,147,727 (GRCm39) |
T169I |
probably damaging |
Het |
| Lrriq1 |
T |
C |
10: 103,014,649 (GRCm39) |
N1053S |
possibly damaging |
Het |
| Mfng |
C |
T |
15: 78,648,588 (GRCm39) |
R163H |
probably benign |
Het |
| Mgat4c |
G |
C |
10: 102,224,599 (GRCm39) |
R271P |
probably damaging |
Het |
| Mylk |
A |
G |
16: 34,735,360 (GRCm39) |
N780S |
possibly damaging |
Het |
| N4bp1 |
T |
C |
8: 87,587,676 (GRCm39) |
T421A |
probably benign |
Het |
| Nat8f1 |
T |
C |
6: 85,887,295 (GRCm39) |
T222A |
probably benign |
Het |
| Nsun2 |
T |
C |
13: 69,691,992 (GRCm39) |
|
probably benign |
Het |
| Oas2 |
T |
A |
5: 120,876,599 (GRCm39) |
D448V |
probably damaging |
Het |
| Or10al7 |
C |
A |
17: 38,366,467 (GRCm39) |
V6F |
probably benign |
Het |
| Or2l13b |
A |
T |
16: 19,349,383 (GRCm39) |
C96S |
probably damaging |
Het |
| Or5ak22 |
T |
C |
2: 85,230,772 (GRCm39) |
Y35C |
probably damaging |
Het |
| Pgm2l1 |
T |
A |
7: 99,877,204 (GRCm39) |
L25Q |
probably damaging |
Het |
| Pigp |
A |
T |
16: 94,166,309 (GRCm39) |
V133D |
probably benign |
Het |
| Pomt2 |
C |
T |
12: 87,156,881 (GRCm39) |
D752N |
possibly damaging |
Het |
| Ppat |
T |
C |
5: 77,074,640 (GRCm39) |
K65E |
probably damaging |
Het |
| Ptprn2 |
T |
C |
12: 117,125,314 (GRCm39) |
L616P |
probably damaging |
Het |
| Rad54l2 |
A |
G |
9: 106,595,091 (GRCm39) |
S289P |
probably damaging |
Het |
| Rbm39 |
G |
A |
2: 156,019,266 (GRCm39) |
R31C |
possibly damaging |
Het |
| Rhbdf2 |
C |
A |
11: 116,492,771 (GRCm39) |
V417L |
probably benign |
Het |
| Rnf157 |
T |
A |
11: 116,246,298 (GRCm39) |
E255D |
possibly damaging |
Het |
| Rpl6l |
A |
T |
10: 110,962,304 (GRCm39) |
|
noncoding transcript |
Het |
| Sec24c |
A |
G |
14: 20,743,813 (GRCm39) |
D1006G |
probably damaging |
Het |
| Sh3bp1 |
G |
T |
15: 78,792,237 (GRCm39) |
A401S |
probably benign |
Het |
| Slc17a8 |
A |
T |
10: 89,412,367 (GRCm39) |
D539E |
probably benign |
Het |
| Slc38a9 |
T |
A |
13: 112,826,098 (GRCm39) |
S136R |
probably damaging |
Het |
| Smoc2 |
A |
C |
17: 14,589,295 (GRCm39) |
T255P |
probably benign |
Het |
| Smyd2 |
T |
C |
1: 189,628,847 (GRCm39) |
D152G |
probably damaging |
Het |
| Stab1 |
A |
G |
14: 30,862,350 (GRCm39) |
V2328A |
probably damaging |
Het |
| Taar2 |
A |
G |
10: 23,816,591 (GRCm39) |
I44V |
probably benign |
Het |
| Tbc1d4 |
T |
C |
14: 101,682,144 (GRCm39) |
K1251E |
probably benign |
Het |
| Thada |
G |
A |
17: 84,754,027 (GRCm39) |
L315F |
probably damaging |
Het |
| Trbv14 |
T |
C |
6: 41,112,259 (GRCm39) |
S19P |
probably benign |
Het |
| Ttc39c |
T |
C |
18: 12,820,173 (GRCm39) |
|
probably benign |
Het |
| Ttc39d |
A |
G |
17: 80,524,527 (GRCm39) |
I395M |
probably benign |
Het |
| Ttn |
T |
C |
2: 76,548,728 (GRCm39) |
E31891G |
probably damaging |
Het |
| Ubr3 |
T |
C |
2: 69,800,527 (GRCm39) |
V950A |
probably damaging |
Het |
| Usp9y |
T |
A |
Y: 1,307,920 (GRCm39) |
K2305N |
probably damaging |
Het |
| Vmn1r158 |
G |
A |
7: 22,490,179 (GRCm39) |
T10I |
possibly damaging |
Het |
| Vmn2r129 |
G |
T |
4: 156,686,692 (GRCm39) |
|
noncoding transcript |
Het |
| Vmn2r78 |
T |
A |
7: 86,603,916 (GRCm39) |
I698K |
possibly damaging |
Het |
| Vmn2r86 |
G |
T |
10: 130,289,460 (GRCm39) |
T145K |
probably damaging |
Het |
| Zfp51 |
T |
C |
17: 21,684,933 (GRCm39) |
V516A |
probably benign |
Het |
| Zfp654 |
A |
T |
16: 64,606,145 (GRCm39) |
S686T |
probably benign |
Het |
| Zfp846 |
T |
A |
9: 20,502,111 (GRCm39) |
C55S |
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 |
|
R4861: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 |
2016-03-17 |
Incidental Mutation