Mutagenetix > Incidental Mutation

Incidental Mutation 'R2504:Phf3'

252040

Institutional Source

Beutler Lab

Gene Symbol

Phf3

Ensembl Gene

ENSMUSG00000048874

Gene Name

PHD finger protein 3

Synonyms

AU020177, 2310061N19Rik

MMRRC Submission

040412-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2504 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

30841417-30912989 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 30849870 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 1181 (L1181Q)

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: L1181Q

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

SMART Domains

Protein: ENSMUSP00000085650
Gene: ENSMUSG00000048874
AA Change: L1181Q

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: L1181Q

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

SMART Domains

Protein: ENSMUSP00000139610
Gene: ENSMUSG00000048874
AA Change: L1181Q

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

noncoding transcript
Transcript: ENSMUST00000191245

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

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.4%
20x: 95.4%

Validation Efficiency

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: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aatk	T	C	11: 119,909,681 (GRCm39)	D28G	probably benign	Het
Abcg1	T	A	17: 31,311,369 (GRCm39)	S125T	probably damaging	Het
Actbl2	T	C	13: 111,392,717 (GRCm39)	S351P	possibly damaging	Het
Ankrd34b	A	G	13: 92,575,569 (GRCm39)		probably null	Het
BC051665	C	T	13: 60,930,468 (GRCm39)	V295I	probably benign	Het
C1qtnf2	A	G	11: 43,381,983 (GRCm39)	N265S	probably damaging	Het
Ccdc14	C	T	16: 34,542,220 (GRCm39)	R573*	probably null	Het
Cd55b	A	T	1: 130,337,612 (GRCm39)	Y247N	probably damaging	Het
Celsr2	A	T	3: 108,320,907 (GRCm39)	V635E	probably benign	Het
Clec16a	T	C	16: 10,377,551 (GRCm39)		probably benign	Het
Clec4b1	A	G	6: 123,042,904 (GRCm39)	Y41C	probably damaging	Het
Cntn5	A	T	9: 10,172,126 (GRCm39)	D19E	probably benign	Het
Cop1	A	G	1: 159,060,375 (GRCm39)	N53S	probably damaging	Het
Cplane1	G	A	15: 8,248,700 (GRCm39)	E1750K	probably damaging	Het
Csad	A	T	15: 102,097,102 (GRCm39)	M1K	probably null	Het
Cyb5rl	A	G	4: 106,938,142 (GRCm39)	I200V	probably benign	Het
Cyp26a1	A	G	19: 37,686,790 (GRCm39)	T81A	probably damaging	Het
Cyp2d12	A	T	15: 82,443,237 (GRCm39)	H433L	probably benign	Het
D7Ertd443e	T	A	7: 133,951,208 (GRCm39)		probably null	Het
Dennd1b	A	G	1: 139,097,908 (GRCm39)		probably benign	Het
Dmap1	G	T	4: 117,532,495 (GRCm39)	T357K	probably damaging	Het
Dzip1	G	T	14: 119,118,456 (GRCm39)	T759K	probably benign	Het
Elmo2	A	G	2: 165,140,607 (GRCm39)	V300A	probably damaging	Het
Eml5	T	C	12: 98,810,364 (GRCm39)	D864G	possibly damaging	Het
Ep400	A	G	5: 110,816,511 (GRCm39)	V2670A	probably damaging	Het
Epha3	T	A	16: 63,423,988 (GRCm39)	I534F	probably damaging	Het
Epha4	A	C	1: 77,359,628 (GRCm39)	Y742D	probably damaging	Het
Ergic2	A	G	6: 148,106,272 (GRCm39)		probably null	Het
Ero1a	A	T	14: 45,536,545 (GRCm39)		probably null	Het
Fam229a	A	G	4: 129,385,279 (GRCm39)	D70G	probably damaging	Het
Fbn2	C	T	18: 58,226,431 (GRCm39)	R781Q	probably damaging	Het
Fbxo16	A	T	14: 65,508,163 (GRCm39)		probably benign	Het
Fbxo39	T	A	11: 72,208,111 (GRCm39)	S154R	probably benign	Het
Fer	T	A	17: 64,298,575 (GRCm39)		probably null	Het
Filip1l	A	T	16: 57,391,410 (GRCm39)	D428V	probably damaging	Het
Filip1l	A	G	16: 57,391,025 (GRCm39)	I538V	possibly damaging	Het
Fsip2	T	C	2: 82,809,954 (GRCm39)	I2091T	possibly damaging	Het
Glyat	A	C	19: 12,628,762 (GRCm39)	T186P	possibly damaging	Het
Gm10604	A	G	4: 11,980,083 (GRCm39)	S74P	unknown	Het
Gm4787	T	G	12: 81,425,911 (GRCm39)	K82N	possibly damaging	Het
Hectd4	T	C	5: 121,358,683 (GRCm39)	I50T	unknown	Het
Hectd4	T	C	5: 121,402,030 (GRCm39)	S373P	possibly damaging	Het
Hmcn1	A	T	1: 150,562,618 (GRCm39)	C2313*	probably null	Het
Hrob	T	C	11: 102,146,122 (GRCm39)	Y133H	possibly damaging	Het
Igfn1	A	T	1: 135,897,054 (GRCm39)	S1171T	probably benign	Het
Ints8	T	C	4: 11,241,642 (GRCm39)	D267G	probably benign	Het
Itln1	A	G	1: 171,356,727 (GRCm39)	C251R	probably damaging	Het
Jcad	C	T	18: 4,674,026 (GRCm39)	T596M	probably damaging	Het
Kcnj16	C	T	11: 110,916,409 (GRCm39)	T357M	probably benign	Het
Kif13a	G	A	13: 46,967,676 (GRCm39)	T346M	probably damaging	Het
Klhl24	G	A	16: 19,938,917 (GRCm39)	A491T	probably benign	Het
Kntc1	C	T	5: 123,916,410 (GRCm39)	Q748*	probably null	Het
Krt25	T	A	11: 99,208,122 (GRCm39)	K369*	probably null	Het
Krt75	C	T	15: 101,476,466 (GRCm39)	R433Q	probably benign	Het
Krt76	A	G	15: 101,793,293 (GRCm39)	F582L	unknown	Het
Lysmd1	G	A	3: 95,045,708 (GRCm39)	V182I	probably benign	Het
Mab21l2	T	A	3: 86,454,862 (GRCm39)	E46V	probably damaging	Het
Magi2	A	T	5: 20,563,934 (GRCm39)	K355N	probably damaging	Het
Marchf10	T	C	11: 105,276,398 (GRCm39)	D630G	probably damaging	Het
Mast4	A	T	13: 102,875,147 (GRCm39)	I1215N	probably damaging	Het
Nckap1	G	A	2: 80,360,562 (GRCm39)	T523I	probably benign	Het
Nexmif	T	A	X: 103,127,999 (GRCm39)	D1306V	probably damaging	Het
Nfkb1	A	C	3: 135,295,090 (GRCm39)	I918R	possibly damaging	Het
Nt5el	A	G	13: 105,246,250 (GRCm39)	I270M	probably benign	Het
Nup50	A	T	15: 84,817,859 (GRCm39)	T93S	probably benign	Het
Nwd2	T	C	5: 63,961,717 (GRCm39)	Y434H	probably benign	Het
Or13a28	T	C	7: 140,218,397 (GRCm39)	V261A	probably benign	Het
Osbpl1a	C	A	18: 13,038,088 (GRCm39)	V288L	probably benign	Het
Pan3	A	G	5: 147,463,846 (GRCm39)	E562G	possibly damaging	Het
Pappa	T	A	4: 65,099,126 (GRCm39)	Y548*	probably null	Het
Phip	T	C	9: 82,797,392 (GRCm39)	H537R	possibly damaging	Het
Pkhd1l1	T	C	15: 44,348,824 (GRCm39)	I240T	probably damaging	Het
Pole	G	A	5: 110,438,368 (GRCm39)		probably null	Het
Polq	T	A	16: 36,832,304 (GRCm39)	S15T	unknown	Het
Prrt2	T	C	7: 126,619,396 (GRCm39)	E23G	possibly damaging	Het
Prss37	A	T	6: 40,494,760 (GRCm39)		probably null	Het
Prune2	T	C	19: 16,977,400 (GRCm39)	L45P	probably damaging	Het
Psd	A	T	19: 46,313,352 (GRCm39)	M6K	possibly damaging	Het
Psmd1	A	G	1: 86,017,719 (GRCm39)	E510G	possibly damaging	Het
Ptch1	T	G	13: 63,672,773 (GRCm39)	E944A	probably benign	Het
Pxdn	T	A	12: 30,053,405 (GRCm39)	I1194N	probably damaging	Het
Rbp3	C	T	14: 33,677,975 (GRCm39)	T641M	probably damaging	Het
Rgmb	C	A	17: 16,027,909 (GRCm39)	R270L	probably benign	Het
Rpgrip1l	A	G	8: 92,007,344 (GRCm39)		probably null	Het
Rps2	G	A	17: 24,939,353 (GRCm39)		probably benign	Het
Rsbn1l	G	T	5: 21,107,364 (GRCm39)	A550E	probably damaging	Het
S1pr4	C	T	10: 81,335,138 (GRCm39)	R112H	probably benign	Het
Scfd2	T	C	5: 74,691,838 (GRCm39)	N148S	probably damaging	Het
Scin	C	T	12: 40,131,705 (GRCm39)	M276I	probably benign	Het
Sec24d	T	C	3: 123,147,255 (GRCm39)	I708T	possibly damaging	Het
Skint11	T	A	4: 114,086,009 (GRCm39)	F41I	possibly damaging	Het
Slc15a4	A	T	5: 127,694,303 (GRCm39)	F44Y	possibly damaging	Het
Slc6a18	A	G	13: 73,823,925 (GRCm39)	Y72H	probably benign	Het
Slc7a11	A	T	3: 50,332,195 (GRCm39)		probably null	Het
Slc7a14	G	T	3: 31,291,650 (GRCm39)	N209K	possibly damaging	Het
Sstr2	T	C	11: 113,515,257 (GRCm39)	C59R	probably damaging	Het
Stab1	A	G	14: 30,884,997 (GRCm39)		probably null	Het
Stag1	G	T	9: 100,748,263 (GRCm39)	S475I	probably damaging	Het
Stxbp5l	A	G	16: 36,936,029 (GRCm39)	Y1183H	probably damaging	Het
Svep1	A	T	4: 58,135,628 (GRCm39)		probably null	Het
Tm9sf2	A	G	14: 122,396,096 (GRCm39)	T653A	probably benign	Het
Tmeff1	T	C	4: 48,662,059 (GRCm39)	S366P	possibly damaging	Het
Tnnt2	G	T	1: 135,779,803 (GRCm39)	W300L	probably damaging	Het
Traj32	A	G	14: 54,423,560 (GRCm39)		probably benign	Het
Trp53bp2	A	T	1: 182,269,204 (GRCm39)	M223L	probably benign	Het
Tsga10	G	A	1: 37,854,758 (GRCm39)	T246M	probably damaging	Het
Txn2	A	T	15: 77,810,870 (GRCm39)		probably benign	Het
Ubr3	T	A	2: 69,768,542 (GRCm39)	F450I	probably damaging	Het
Usp47	T	C	7: 111,703,677 (GRCm39)		probably null	Het
Vars2	C	T	17: 35,975,685 (GRCm39)	R244Q	probably damaging	Het
Xrra1	T	A	7: 99,546,803 (GRCm39)	F251L	probably damaging	Het
Zfp804a	G	A	2: 82,087,863 (GRCm39)	R564Q	probably benign	Het
Zfp983	T	C	17: 21,877,883 (GRCm39)	C29R	probably damaging	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
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
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'- ACAGCATGTTTCCCTGCCTG -3'
(R):5'- GAAAGTAGACTCACTCATTCATGG -3'

Sequencing Primer
(F):5'- ATGTTTCCCTGCCTGCTGTTTTC -3'
(R):5'- TTGTGCTACAATACTCATGTGGAG -3'

Posted On

2014-12-04