Incidental Mutation 'R0052:Phf3'
ID |
33017 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Phf3
|
Ensembl Gene |
ENSMUSG00000048874 |
Gene Name |
PHD finger protein 3 |
Synonyms |
AU020177, 2310061N19Rik |
MMRRC Submission |
038346-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R0052 (G1)
|
Quality Score |
211 |
Status
|
Validated
|
Chromosome |
1 |
Chromosomal Location |
30841417-30912989 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 30847848 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Alanine
at position 1232
(T1232A)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000139610
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000088310]
[ENSMUST00000186733]
[ENSMUST00000191329]
|
AlphaFold |
B2RQG2 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000088310
AA Change: T1232A
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000085650 Gene: ENSMUSG00000048874 AA Change: T1232A
Domain | Start | End | E-Value | Type |
low complexity region
|
212 |
223 |
N/A |
INTRINSIC |
low complexity region
|
337 |
344 |
N/A |
INTRINSIC |
low complexity region
|
600 |
611 |
N/A |
INTRINSIC |
low complexity region
|
651 |
660 |
N/A |
INTRINSIC |
PHD
|
697 |
748 |
3.82e-10 |
SMART |
low complexity region
|
847 |
859 |
N/A |
INTRINSIC |
low complexity region
|
876 |
887 |
N/A |
INTRINSIC |
TFS2M
|
908 |
1008 |
1.28e-47 |
SMART |
Pfam:SPOC
|
1188 |
1294 |
4.2e-26 |
PFAM |
low complexity region
|
1367 |
1373 |
N/A |
INTRINSIC |
low complexity region
|
1516 |
1529 |
N/A |
INTRINSIC |
low complexity region
|
1597 |
1620 |
N/A |
INTRINSIC |
low complexity region
|
1796 |
1811 |
N/A |
INTRINSIC |
low complexity region
|
1813 |
1846 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000186105
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000186733
AA Change: T1232A
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000139610 Gene: ENSMUSG00000048874 AA Change: T1232A
Domain | Start | End | E-Value | Type |
low complexity region
|
212 |
223 |
N/A |
INTRINSIC |
low complexity region
|
337 |
344 |
N/A |
INTRINSIC |
low complexity region
|
600 |
611 |
N/A |
INTRINSIC |
low complexity region
|
651 |
660 |
N/A |
INTRINSIC |
PHD
|
697 |
748 |
3.82e-10 |
SMART |
low complexity region
|
847 |
859 |
N/A |
INTRINSIC |
low complexity region
|
876 |
887 |
N/A |
INTRINSIC |
TFS2M
|
908 |
1008 |
1.28e-47 |
SMART |
Pfam:SPOC
|
1188 |
1294 |
4.2e-26 |
PFAM |
low complexity region
|
1367 |
1373 |
N/A |
INTRINSIC |
low complexity region
|
1516 |
1529 |
N/A |
INTRINSIC |
low complexity region
|
1597 |
1620 |
N/A |
INTRINSIC |
low complexity region
|
1796 |
1811 |
N/A |
INTRINSIC |
low complexity region
|
1813 |
1846 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000187316
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000190190
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000191329
AA Change: T26A
PolyPhen 2
Score 0.611 (Sensitivity: 0.87; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000139662 Gene: ENSMUSG00000048874 AA Change: T26A
Domain | Start | End | E-Value | Type |
Pfam:SPOC
|
1 |
88 |
1.9e-17 |
PFAM |
|
Meta Mutation Damage Score |
0.1609 |
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.2%
- 20x: 92.2%
|
Validation Efficiency |
97% (65/67) |
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of a PHD finger-containing gene family. This gene may function as a transcription factor and may be involved in glioblastomas development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 64 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Apba1 |
T |
C |
19: 23,893,315 (GRCm39) |
S438P |
possibly damaging |
Het |
Atosa |
A |
G |
9: 74,926,265 (GRCm39) |
|
probably benign |
Het |
Atp2a1 |
A |
G |
7: 126,057,069 (GRCm39) |
|
probably benign |
Het |
Axin2 |
T |
C |
11: 108,840,096 (GRCm39) |
Y735H |
probably damaging |
Het |
Bicd2 |
T |
A |
13: 49,528,790 (GRCm39) |
L184Q |
probably damaging |
Het |
Bub1 |
G |
A |
2: 127,650,959 (GRCm39) |
T618I |
probably benign |
Het |
Catsperg2 |
A |
G |
7: 29,424,445 (GRCm39) |
|
probably benign |
Het |
Ccdc73 |
T |
A |
2: 104,759,915 (GRCm39) |
|
probably benign |
Het |
Crybg3 |
A |
T |
16: 59,386,019 (GRCm39) |
|
probably benign |
Het |
Dsp |
A |
G |
13: 38,381,340 (GRCm39) |
D2096G |
possibly damaging |
Het |
Eef2 |
C |
CN |
10: 81,014,602 (GRCm39) |
|
probably null |
Het |
Elp3 |
A |
G |
14: 65,768,975 (GRCm39) |
*548Q |
probably null |
Het |
Eno4 |
A |
G |
19: 58,956,985 (GRCm39) |
D357G |
probably damaging |
Het |
Fcrl2 |
A |
T |
3: 87,164,085 (GRCm39) |
I348N |
possibly damaging |
Het |
Fgl2 |
A |
T |
5: 21,580,347 (GRCm39) |
S230C |
probably damaging |
Het |
Ginm1 |
T |
A |
10: 7,655,070 (GRCm39) |
E57D |
possibly damaging |
Het |
Gtf3c1 |
A |
T |
7: 125,267,143 (GRCm39) |
|
probably null |
Het |
Herc1 |
G |
T |
9: 66,307,438 (GRCm39) |
G1044V |
probably damaging |
Het |
Hmcn1 |
G |
A |
1: 150,553,157 (GRCm39) |
T2511M |
probably damaging |
Het |
Iba57 |
C |
T |
11: 59,049,727 (GRCm39) |
A207T |
probably benign |
Het |
Itga9 |
T |
A |
9: 118,465,617 (GRCm39) |
I157N |
probably damaging |
Het |
Kalrn |
A |
G |
16: 34,177,541 (GRCm39) |
L208P |
probably damaging |
Het |
Kcnj10 |
A |
G |
1: 172,196,491 (GRCm39) |
T2A |
probably benign |
Het |
Kdm1b |
T |
A |
13: 47,217,593 (GRCm39) |
C351S |
probably damaging |
Het |
Kif21a |
T |
C |
15: 90,855,060 (GRCm39) |
E700G |
probably damaging |
Het |
Mmd |
C |
T |
11: 90,150,824 (GRCm39) |
|
probably benign |
Het |
Mocs3 |
C |
T |
2: 168,073,602 (GRCm39) |
P350S |
probably benign |
Het |
Morn3 |
T |
C |
5: 123,184,726 (GRCm39) |
Y38C |
probably damaging |
Het |
Nacc1 |
A |
T |
8: 85,402,854 (GRCm39) |
V313D |
probably benign |
Het |
Nbeal1 |
T |
A |
1: 60,267,771 (GRCm39) |
|
probably benign |
Het |
Neb |
T |
C |
2: 52,163,992 (GRCm39) |
K1989E |
possibly damaging |
Het |
Nlrp3 |
C |
T |
11: 59,455,954 (GRCm39) |
R917* |
probably null |
Het |
Nlrp4b |
T |
A |
7: 10,459,889 (GRCm39) |
Y463* |
probably null |
Het |
Perm1 |
A |
T |
4: 156,302,572 (GRCm39) |
D372V |
probably damaging |
Het |
Phldb3 |
G |
A |
7: 24,312,004 (GRCm39) |
R106Q |
probably benign |
Het |
Pld4 |
T |
A |
12: 112,734,291 (GRCm39) |
F386I |
probably benign |
Het |
Prex2 |
T |
A |
1: 11,230,380 (GRCm39) |
L802Q |
probably damaging |
Het |
Psd3 |
A |
G |
8: 68,335,631 (GRCm39) |
|
probably null |
Het |
Ralgds |
T |
A |
2: 28,434,400 (GRCm39) |
|
probably null |
Het |
Rmdn2 |
A |
G |
17: 79,957,760 (GRCm39) |
E16G |
probably damaging |
Het |
Rnf111 |
A |
T |
9: 70,383,671 (GRCm39) |
S87R |
probably benign |
Het |
Slc4a4 |
A |
C |
5: 89,304,195 (GRCm39) |
H502P |
possibly damaging |
Het |
Slc9c1 |
A |
G |
16: 45,427,219 (GRCm39) |
|
probably benign |
Het |
Slco3a1 |
A |
T |
7: 74,154,074 (GRCm39) |
I166N |
probably benign |
Het |
Snx5 |
A |
T |
2: 144,101,112 (GRCm39) |
|
probably null |
Het |
Srgap1 |
T |
C |
10: 121,636,732 (GRCm39) |
D741G |
possibly damaging |
Het |
St8sia2 |
G |
T |
7: 73,593,038 (GRCm39) |
Y339* |
probably null |
Het |
St8sia2 |
A |
T |
7: 73,621,700 (GRCm39) |
W86R |
probably damaging |
Het |
Stk33 |
A |
G |
7: 108,878,876 (GRCm39) |
L491P |
possibly damaging |
Het |
Sult2a7 |
T |
C |
7: 14,199,133 (GRCm39) |
Y298C |
probably damaging |
Het |
Tdo2 |
T |
A |
3: 81,874,332 (GRCm39) |
N210I |
probably benign |
Het |
Thada |
A |
T |
17: 84,762,586 (GRCm39) |
N104K |
probably damaging |
Het |
Timm8b |
A |
T |
9: 50,516,330 (GRCm39) |
D61V |
possibly damaging |
Het |
Tshz1 |
G |
A |
18: 84,033,070 (GRCm39) |
T446I |
possibly damaging |
Het |
Ubap2l |
T |
C |
3: 89,946,235 (GRCm39) |
N123S |
possibly damaging |
Het |
Vmn1r48 |
T |
C |
6: 90,013,246 (GRCm39) |
E193G |
possibly damaging |
Het |
Vmn1r69 |
C |
T |
7: 10,314,327 (GRCm39) |
V135I |
probably benign |
Het |
Vmn2r103 |
G |
T |
17: 20,031,903 (GRCm39) |
G559V |
probably benign |
Het |
Vmn2r26 |
T |
A |
6: 124,038,992 (GRCm39) |
*856R |
probably null |
Het |
Vmn2r88 |
A |
G |
14: 51,656,157 (GRCm39) |
I798V |
possibly damaging |
Het |
Vsir |
C |
T |
10: 60,193,861 (GRCm39) |
A108V |
probably benign |
Het |
Zfp14 |
G |
T |
7: 29,737,753 (GRCm39) |
Q411K |
probably damaging |
Het |
Zfp236 |
A |
T |
18: 82,657,457 (GRCm39) |
M762K |
probably damaging |
Het |
Zfp462 |
G |
A |
4: 55,011,762 (GRCm39) |
G1243S |
probably benign |
Het |
|
Other mutations in Phf3 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00234:Phf3
|
APN |
1 |
30,850,928 (GRCm39) |
missense |
probably damaging |
0.99 |
IGL00704:Phf3
|
APN |
1 |
30,843,919 (GRCm39) |
missense |
probably benign |
|
IGL01147:Phf3
|
APN |
1 |
30,843,250 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01360:Phf3
|
APN |
1 |
30,847,809 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01376:Phf3
|
APN |
1 |
30,869,566 (GRCm39) |
missense |
possibly damaging |
0.62 |
IGL01396:Phf3
|
APN |
1 |
30,843,386 (GRCm39) |
nonsense |
probably null |
|
IGL01830:Phf3
|
APN |
1 |
30,853,148 (GRCm39) |
nonsense |
probably null |
|
IGL02108:Phf3
|
APN |
1 |
30,869,032 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL02156:Phf3
|
APN |
1 |
30,847,859 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL02576:Phf3
|
APN |
1 |
30,869,117 (GRCm39) |
missense |
probably benign |
0.01 |
IGL03031:Phf3
|
APN |
1 |
30,843,734 (GRCm39) |
missense |
probably benign |
0.00 |
IGL03334:Phf3
|
APN |
1 |
30,844,810 (GRCm39) |
missense |
probably damaging |
0.99 |
IGL03411:Phf3
|
APN |
1 |
30,843,482 (GRCm39) |
missense |
probably damaging |
1.00 |
FR4976:Phf3
|
UTSW |
1 |
30,844,104 (GRCm39) |
utr 3 prime |
probably benign |
|
PIT4458001:Phf3
|
UTSW |
1 |
30,855,622 (GRCm39) |
missense |
probably damaging |
1.00 |
R0037:Phf3
|
UTSW |
1 |
30,843,999 (GRCm39) |
missense |
probably benign |
0.03 |
R0114:Phf3
|
UTSW |
1 |
30,844,524 (GRCm39) |
missense |
possibly damaging |
0.87 |
R0123:Phf3
|
UTSW |
1 |
30,844,146 (GRCm39) |
missense |
probably benign |
0.01 |
R0225:Phf3
|
UTSW |
1 |
30,844,146 (GRCm39) |
missense |
probably benign |
0.01 |
R0715:Phf3
|
UTSW |
1 |
30,850,919 (GRCm39) |
missense |
probably damaging |
1.00 |
R0835:Phf3
|
UTSW |
1 |
30,869,632 (GRCm39) |
missense |
probably benign |
0.02 |
R0848:Phf3
|
UTSW |
1 |
30,902,253 (GRCm39) |
missense |
probably damaging |
1.00 |
R1473:Phf3
|
UTSW |
1 |
30,845,021 (GRCm39) |
missense |
probably damaging |
1.00 |
R1522:Phf3
|
UTSW |
1 |
30,844,729 (GRCm39) |
missense |
probably benign |
0.05 |
R1549:Phf3
|
UTSW |
1 |
30,843,923 (GRCm39) |
missense |
probably benign |
0.00 |
R1555:Phf3
|
UTSW |
1 |
30,844,958 (GRCm39) |
missense |
possibly damaging |
0.86 |
R1780:Phf3
|
UTSW |
1 |
30,851,023 (GRCm39) |
missense |
probably damaging |
1.00 |
R1789:Phf3
|
UTSW |
1 |
30,845,287 (GRCm39) |
missense |
probably damaging |
1.00 |
R1875:Phf3
|
UTSW |
1 |
30,869,704 (GRCm39) |
missense |
possibly damaging |
0.81 |
R1912:Phf3
|
UTSW |
1 |
30,843,426 (GRCm39) |
missense |
probably damaging |
1.00 |
R1957:Phf3
|
UTSW |
1 |
30,870,601 (GRCm39) |
missense |
probably damaging |
1.00 |
R2019:Phf3
|
UTSW |
1 |
30,850,928 (GRCm39) |
missense |
probably damaging |
0.99 |
R2259:Phf3
|
UTSW |
1 |
30,843,424 (GRCm39) |
missense |
probably benign |
0.20 |
R2305:Phf3
|
UTSW |
1 |
30,844,556 (GRCm39) |
nonsense |
probably null |
|
R2345:Phf3
|
UTSW |
1 |
30,844,432 (GRCm39) |
nonsense |
probably null |
|
R2424:Phf3
|
UTSW |
1 |
30,845,430 (GRCm39) |
missense |
probably damaging |
1.00 |
R2497:Phf3
|
UTSW |
1 |
30,869,095 (GRCm39) |
missense |
probably damaging |
1.00 |
R2504:Phf3
|
UTSW |
1 |
30,849,870 (GRCm39) |
missense |
probably damaging |
1.00 |
R3522:Phf3
|
UTSW |
1 |
30,844,684 (GRCm39) |
missense |
probably damaging |
1.00 |
R3816:Phf3
|
UTSW |
1 |
30,844,834 (GRCm39) |
missense |
probably damaging |
1.00 |
R4152:Phf3
|
UTSW |
1 |
30,870,539 (GRCm39) |
missense |
probably benign |
0.13 |
R4403:Phf3
|
UTSW |
1 |
30,843,490 (GRCm39) |
missense |
probably damaging |
1.00 |
R4658:Phf3
|
UTSW |
1 |
30,902,169 (GRCm39) |
missense |
probably damaging |
1.00 |
R4663:Phf3
|
UTSW |
1 |
30,860,296 (GRCm39) |
missense |
probably damaging |
1.00 |
R4669:Phf3
|
UTSW |
1 |
30,869,027 (GRCm39) |
missense |
probably damaging |
1.00 |
R4706:Phf3
|
UTSW |
1 |
30,844,687 (GRCm39) |
missense |
probably damaging |
1.00 |
R4757:Phf3
|
UTSW |
1 |
30,859,908 (GRCm39) |
missense |
probably damaging |
1.00 |
R4766:Phf3
|
UTSW |
1 |
30,853,020 (GRCm39) |
unclassified |
probably benign |
|
R4786:Phf3
|
UTSW |
1 |
30,855,638 (GRCm39) |
nonsense |
probably null |
|
R5107:Phf3
|
UTSW |
1 |
30,870,566 (GRCm39) |
missense |
probably benign |
0.03 |
R5155:Phf3
|
UTSW |
1 |
30,863,457 (GRCm39) |
missense |
possibly damaging |
0.87 |
R5310:Phf3
|
UTSW |
1 |
30,842,887 (GRCm39) |
missense |
probably damaging |
1.00 |
R5823:Phf3
|
UTSW |
1 |
30,843,764 (GRCm39) |
missense |
probably damaging |
1.00 |
R5944:Phf3
|
UTSW |
1 |
30,859,785 (GRCm39) |
missense |
probably damaging |
1.00 |
R5979:Phf3
|
UTSW |
1 |
30,844,827 (GRCm39) |
missense |
probably damaging |
1.00 |
R6007:Phf3
|
UTSW |
1 |
30,843,426 (GRCm39) |
missense |
probably damaging |
1.00 |
R6024:Phf3
|
UTSW |
1 |
30,902,307 (GRCm39) |
missense |
probably damaging |
1.00 |
R6072:Phf3
|
UTSW |
1 |
30,869,769 (GRCm39) |
missense |
probably benign |
0.08 |
R6533:Phf3
|
UTSW |
1 |
30,845,399 (GRCm39) |
missense |
probably damaging |
1.00 |
R6649:Phf3
|
UTSW |
1 |
30,844,104 (GRCm39) |
missense |
possibly damaging |
0.75 |
R6653:Phf3
|
UTSW |
1 |
30,844,104 (GRCm39) |
missense |
possibly damaging |
0.75 |
R6852:Phf3
|
UTSW |
1 |
30,843,711 (GRCm39) |
missense |
probably damaging |
0.97 |
R6855:Phf3
|
UTSW |
1 |
30,859,204 (GRCm39) |
missense |
probably damaging |
1.00 |
R6862:Phf3
|
UTSW |
1 |
30,853,063 (GRCm39) |
missense |
probably damaging |
1.00 |
R6930:Phf3
|
UTSW |
1 |
30,850,958 (GRCm39) |
missense |
probably damaging |
1.00 |
R7135:Phf3
|
UTSW |
1 |
30,870,190 (GRCm39) |
missense |
possibly damaging |
0.61 |
R7323:Phf3
|
UTSW |
1 |
30,852,211 (GRCm39) |
missense |
probably benign |
0.01 |
R7352:Phf3
|
UTSW |
1 |
30,843,407 (GRCm39) |
missense |
possibly damaging |
0.87 |
R7455:Phf3
|
UTSW |
1 |
30,876,239 (GRCm39) |
missense |
probably damaging |
0.96 |
R7549:Phf3
|
UTSW |
1 |
30,870,556 (GRCm39) |
missense |
probably benign |
0.01 |
R7609:Phf3
|
UTSW |
1 |
30,844,582 (GRCm39) |
missense |
probably benign |
0.05 |
R7720:Phf3
|
UTSW |
1 |
30,868,938 (GRCm39) |
missense |
probably damaging |
1.00 |
R7745:Phf3
|
UTSW |
1 |
30,843,305 (GRCm39) |
missense |
probably damaging |
1.00 |
R8134:Phf3
|
UTSW |
1 |
30,863,552 (GRCm39) |
missense |
unknown |
|
R8264:Phf3
|
UTSW |
1 |
30,870,138 (GRCm39) |
missense |
possibly damaging |
0.48 |
R8545:Phf3
|
UTSW |
1 |
30,863,391 (GRCm39) |
missense |
possibly damaging |
0.48 |
R8821:Phf3
|
UTSW |
1 |
30,860,347 (GRCm39) |
nonsense |
probably null |
|
R8831:Phf3
|
UTSW |
1 |
30,860,347 (GRCm39) |
nonsense |
probably null |
|
R8873:Phf3
|
UTSW |
1 |
30,843,773 (GRCm39) |
missense |
possibly damaging |
0.74 |
R9101:Phf3
|
UTSW |
1 |
30,843,026 (GRCm39) |
missense |
possibly damaging |
0.56 |
R9402:Phf3
|
UTSW |
1 |
30,850,928 (GRCm39) |
missense |
probably damaging |
0.99 |
R9426:Phf3
|
UTSW |
1 |
30,870,625 (GRCm39) |
nonsense |
probably null |
|
R9594:Phf3
|
UTSW |
1 |
30,869,003 (GRCm39) |
missense |
probably benign |
0.07 |
R9707:Phf3
|
UTSW |
1 |
30,868,923 (GRCm39) |
critical splice donor site |
probably null |
|
R9803:Phf3
|
UTSW |
1 |
30,869,872 (GRCm39) |
missense |
probably benign |
0.16 |
Z1177:Phf3
|
UTSW |
1 |
30,851,049 (GRCm39) |
critical splice acceptor site |
probably null |
|
Z1177:Phf3
|
UTSW |
1 |
30,844,132 (GRCm39) |
missense |
unknown |
|
Z1177:Phf3
|
UTSW |
1 |
30,843,376 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Predicted Primers |
PCR Primer
(F):5'- ACTGAGTTGTCTATCACCACCCAGG -3'
(R):5'- ACCACCATTGAGTAGCTGAGAGCC -3'
Sequencing Primer
(F):5'- AGGCCCATTTCCTCCTAGAGAG -3'
(R):5'- tgctctattaccatgttctaagcc -3'
|
Posted On |
2013-05-09 |