Mutagenetix > Incidental Mutation

Incidental Mutation 'R6653:Phf3'

526487

Institutional Source

Beutler Lab

Gene Symbol

Phf3

Ensembl Gene

ENSMUSG00000048874

Gene Name

PHD finger protein 3

Synonyms

AU020177, 2310061N19Rik

MMRRC Submission

044774-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6653 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

30841417-30912989 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 30844104 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 1618 (S1618R)

Ref Sequence

ENSEMBL: ENSMUSP00000139610 (fasta)

Gene Model

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

AlphaFold

B2RQG2

Predicted Effect

possibly damaging
Transcript: ENSMUST00000088310
AA Change: S1618R

PolyPhen 2 Score 0.754 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000085650
Gene: ENSMUSG00000048874
AA Change: S1618R

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

possibly damaging
Transcript: ENSMUST00000186733
AA Change: S1618R

PolyPhen 2 Score 0.754 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000139610
Gene: ENSMUSG00000048874
AA Change: S1618R

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

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.6%
20x: 96.3%

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: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca15	T	G	7: 119,945,229 (GRCm39)	L435R	probably benign	Het
Abcc2	T	A	19: 43,800,941 (GRCm39)	H627Q	probably benign	Het
Ankhd1	A	T	18: 36,733,836 (GRCm39)		probably null	Het
Ankrd50	T	A	3: 38,511,510 (GRCm39)	I286F	probably damaging	Het
Asb15	A	G	6: 24,562,632 (GRCm39)	N198S	probably benign	Het
B4galnt2	T	A	11: 95,782,747 (GRCm39)	M22L	probably benign	Het
Bcdin3d	T	C	15: 99,368,696 (GRCm39)	T168A	probably damaging	Het
Bmp1	A	T	14: 70,728,058 (GRCm39)	W624R	probably damaging	Het
Cdh4	C	T	2: 179,422,221 (GRCm39)	A115V	probably benign	Het
Cfap53	A	G	18: 74,433,280 (GRCm39)	T122A	probably damaging	Het
Chsy1	A	G	7: 65,759,941 (GRCm39)	K95E	probably benign	Het
Csde1	C	A	3: 102,960,184 (GRCm39)	P604T	probably damaging	Het
Cts7	A	T	13: 61,502,817 (GRCm39)	L237Q	probably damaging	Het
Cutal	C	T	2: 34,775,933 (GRCm39)	T88I	probably benign	Het
Dlg4	G	T	11: 69,914,779 (GRCm39)		probably benign	Het
Dnah7c	C	A	1: 46,688,500 (GRCm39)	T1890K	probably benign	Het
Dnah7c	A	G	1: 46,688,511 (GRCm39)	S1894G	probably benign	Het
Eif2b4	C	T	5: 31,349,551 (GRCm39)	E53K	possibly damaging	Het
Erp44	T	C	4: 48,205,130 (GRCm39)	I288V	probably null	Het
Fcamr	A	G	1: 130,740,939 (GRCm39)	T453A	possibly damaging	Het
Glb1l3	T	C	9: 26,770,884 (GRCm39)	T61A	probably benign	Het
Gpr26	T	C	7: 131,585,830 (GRCm39)	S267P	probably benign	Het
Heatr6	A	T	11: 83,650,191 (GRCm39)	T216S	probably benign	Het
Hephl1	C	T	9: 14,993,260 (GRCm39)	V525I	probably damaging	Het
Jak2	T	A	19: 29,266,110 (GRCm39)	I517N	probably benign	Het
Kbtbd4	T	A	2: 90,740,113 (GRCm39)	Y499*	probably null	Het
Kif1a	A	T	1: 93,005,420 (GRCm39)	I118N	probably damaging	Het
Klhdc7b	A	G	15: 89,271,292 (GRCm39)	S725G	probably benign	Het
Mfsd13a	T	C	19: 46,356,305 (GRCm39)	F137L	probably damaging	Het
Myo7a	T	A	7: 97,703,710 (GRCm39)	Y1977F	probably damaging	Het
Naip2	T	G	13: 100,298,352 (GRCm39)	K561N	probably benign	Het
Naip2	C	T	13: 100,288,644 (GRCm39)	V1194I	probably benign	Het
Nkx2-4	G	T	2: 146,925,860 (GRCm39)	A334E	possibly damaging	Het
Nlrp9c	T	A	7: 26,070,747 (GRCm39)	N945Y	probably damaging	Het
Or2z2	A	T	11: 58,346,394 (GRCm39)	I127N	probably damaging	Het
Or4e5	C	T	14: 52,728,250 (GRCm39)	R57Q	probably benign	Het
Or8g20	A	G	9: 39,396,048 (GRCm39)	V164A	probably benign	Het
Pcdha7	A	G	18: 37,107,539 (GRCm39)	Q188R	probably benign	Het
Phip	C	A	9: 82,782,794 (GRCm39)	E884*	probably null	Het
Plxnc1	C	A	10: 94,779,738 (GRCm39)	V235L	probably damaging	Het
Qser1	A	G	2: 104,610,605 (GRCm39)	V1226A	possibly damaging	Het
Ros1	G	T	10: 52,018,299 (GRCm39)	S786R	probably damaging	Het
Rps6ka5	A	G	12: 100,517,795 (GRCm39)	S769P	probably damaging	Het
Sfxn3	G	A	19: 45,038,354 (GRCm39)		probably null	Het
Specc1	T	G	11: 62,037,244 (GRCm39)	S813A	probably damaging	Het
Spry1	T	C	3: 37,696,871 (GRCm39)	I38T	probably damaging	Het
Tagap	T	C	17: 8,152,546 (GRCm39)	V577A	probably benign	Het
Tmem44	T	C	16: 30,356,369 (GRCm39)	D110G	probably damaging	Het
Ubn2	A	G	6: 38,411,397 (GRCm39)	E97G	possibly damaging	Het
Ubr4	C	A	4: 139,200,935 (GRCm39)	H4706Q	possibly damaging	Het
Usp25	T	A	16: 76,856,176 (GRCm39)	N256K	probably benign	Het
Vmn2r112	T	A	17: 22,820,160 (GRCm39)	L11Q	probably null	Het
Wnt2b	C	A	3: 104,860,502 (GRCm39)	R135L	probably damaging	Het
Zfp60	T	C	7: 27,448,151 (GRCm39)	F273S	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
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
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'- CCTCTGCTAAGGGCTCTTTG -3'
(R):5'- CACCAGATGTTTCTACAGAAGC -3'

Sequencing Primer
(F):5'- CTCTGCTAAGGGCTCTTTGTTGTG -3'
(R):5'- CTCAAAACAAGAGGAAAGTGTGG -3'

Posted On

2018-07-23