Mutagenetix > Incidental Mutation

Incidental Mutation 'R1549:Phf3'

169759

Institutional Source

Beutler Lab

Gene Symbol

Phf3

Ensembl Gene

ENSMUSG00000048874

Gene Name

PHD finger protein 3

Synonyms

AU020177, 2310061N19Rik

MMRRC Submission

039588-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1549 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

30841417-30912989 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 30843923 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 1679 (V1679I)

Ref Sequence

ENSEMBL: ENSMUSP00000139610 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000088310] [ENSMUST00000186733] [ENSMUST00000191329]

AlphaFold

B2RQG2

Predicted Effect

probably benign
Transcript: ENSMUST00000088310
AA Change: V1679I

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000085650
Gene: ENSMUSG00000048874
AA Change: V1679I

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

probably benign
Transcript: ENSMUST00000186733
AA Change: V1679I

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000139610
Gene: ENSMUSG00000048874
AA Change: V1679I

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: ENSMUST00000190190

Predicted Effect

probably benign
Transcript: ENSMUST00000191329

SMART Domains

Protein: ENSMUSP00000139662
Gene: ENSMUSG00000048874

Domain	Start	End	E-Value	Type
Pfam:SPOC	1	88	1.9e-17	PFAM

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.8%
20x: 90.8%

Validation Efficiency

97% (58/60)

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: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006A11Rik	A	T	3: 124,210,441 (GRCm39)	I157K	probably benign	Het
Ank3	A	T	10: 69,837,812 (GRCm39)	N727Y	probably benign	Het
Atg16l1	A	G	1: 87,701,910 (GRCm39)	T251A	probably benign	Het
Bcl11b	T	A	12: 107,883,422 (GRCm39)	I226F	probably damaging	Het
Birc6	A	G	17: 74,969,737 (GRCm39)	H4260R	probably damaging	Het
Camta1	A	G	4: 151,670,920 (GRCm39)	I85T	probably damaging	Het
Cblb	A	G	16: 51,853,373 (GRCm39)		probably benign	Het
Ccnd1	T	G	7: 144,491,073 (GRCm39)	I178L	probably benign	Het
Clcn4	A	G	7: 7,294,681 (GRCm39)	V329A	probably damaging	Het
Col17a1	C	T	19: 47,637,349 (GRCm39)		probably benign	Het
Col7a1	A	G	9: 108,785,034 (GRCm39)	T254A	unknown	Het
Ctif	C	A	18: 75,698,096 (GRCm39)	R188L	probably damaging	Het
Cyp2c69	A	T	19: 39,831,430 (GRCm39)	L461Q	probably benign	Het
Ddc	A	G	11: 11,796,656 (GRCm39)		probably null	Het
Dpp10	T	A	1: 123,269,109 (GRCm39)		probably null	Het
Eef2	CCC	CCCC	10: 81,014,602 (GRCm39)		probably null	Het
Eif2b4	T	C	5: 31,350,265 (GRCm39)	E19G	possibly damaging	Het
Fmnl2	A	G	2: 52,995,549 (GRCm39)	E424G	probably damaging	Het
Galnt14	A	G	17: 73,832,308 (GRCm39)	L269P	possibly damaging	Het
Gm2381	T	A	7: 42,471,825 (GRCm39)	H18L	probably benign	Het
Gpbp1	G	T	13: 111,573,113 (GRCm39)	D326E	probably benign	Het
Gpr162	C	T	6: 124,837,051 (GRCm39)	R331H	probably damaging	Het
Iigp1	G	A	18: 60,522,948 (GRCm39)	G22D	probably benign	Het
Kcns3	T	C	12: 11,142,084 (GRCm39)	H205R	probably damaging	Het
Klk1b26	C	T	7: 43,665,826 (GRCm39)		probably benign	Het
Lime1	A	G	2: 181,025,169 (GRCm39)	Y242C	probably benign	Het
Manba	A	G	3: 135,250,567 (GRCm39)	D398G	probably damaging	Het
Mapk3	A	T	7: 126,362,684 (GRCm39)	K219*	probably null	Het
Mdfic	G	T	6: 15,799,844 (GRCm39)	G324C	probably damaging	Het
Mdga1	G	A	17: 30,056,972 (GRCm39)	H837Y	probably damaging	Het
Nck1	T	A	9: 100,379,925 (GRCm39)	M109L	probably benign	Het
Or1d2	A	G	11: 74,256,076 (GRCm39)	I194V	probably benign	Het
Or2w1b	T	C	13: 21,300,288 (GRCm39)	V142A	probably benign	Het
Pabpc1l	G	T	2: 163,879,091 (GRCm39)	V313F	possibly damaging	Het
Pou4f1	T	C	14: 104,705,076 (GRCm39)	I32V	probably benign	Het
Pspc1	T	G	14: 56,986,398 (GRCm39)	H351P	probably damaging	Het
Ptk7	T	C	17: 46,883,578 (GRCm39)	E829G	probably damaging	Het
Rab23	A	G	1: 33,777,378 (GRCm39)	Y164C	possibly damaging	Het
Slc36a3	A	G	11: 55,033,596 (GRCm39)	W141R	probably damaging	Het
Slc7a14	T	C	3: 31,278,267 (GRCm39)	E446G	possibly damaging	Het
Stim2	G	A	5: 54,262,667 (GRCm39)	R303Q	probably damaging	Het
Tbcd	A	G	11: 121,451,579 (GRCm39)	I550V	probably benign	Het
Tmed3	A	C	9: 89,581,998 (GRCm39)	L155R	probably damaging	Het
Trav16d-dv11	A	G	14: 53,284,799 (GRCm39)		probably benign	Het
Ubap2	C	T	4: 41,199,872 (GRCm39)	A752T	probably benign	Het
Usp16	G	T	16: 87,261,722 (GRCm39)	V113F	probably damaging	Het
Vmn2r12	T	G	5: 109,240,696 (GRCm39)	Y139S	probably benign	Het
Vmn2r5	G	T	3: 64,411,421 (GRCm39)	D382E	probably damaging	Het
Zfp1010	T	C	2: 176,957,378 (GRCm39)	E40G	probably damaging	Het
Zfp217	A	C	2: 169,956,390 (GRCm39)	N869K	probably benign	Het
Zswim2	G	T	2: 83,754,092 (GRCm39)	D189E	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
R0052:Phf3	UTSW	1	30,847,848 (GRCm39)	missense	probably damaging	1.00
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
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'- AGCCGATCCTCTTCTAAACGGGTG -3'
(R):5'- AGGACTTCAAGTGACTCTCCCTGC -3'

Sequencing Primer
(F):5'- AACGGGTGGACCGTTTC -3'
(R):5'- ATGGGGATgggagcggg -3'

Posted On

2014-04-13