Mutagenetix > Incidental Mutation

Incidental Mutation 'R8165:Phf1'

633746

Institutional Source

Beutler Lab

Gene Symbol

Phf1

Ensembl Gene

ENSMUSG00000024193

Gene Name

PHD finger protein 1

Synonyms

PHF2, Tctex3, Tctex-3, D17Ertd455e, mPcl1

MMRRC Submission

067591-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8165 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

27152101-27156882 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 27156044 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 444 (F444L)

Ref Sequence

ENSEMBL: ENSMUSP00000073402 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025027] [ENSMUST00000073724] [ENSMUST00000078961] [ENSMUST00000114935] [ENSMUST00000177932] [ENSMUST00000194598] [ENSMUST00000201702]

AlphaFold

Q9Z1B8

Predicted Effect

probably benign
Transcript: ENSMUST00000025027

SMART Domains

Protein: ENSMUSP00000025027
Gene: ENSMUSG00000024194

Domain	Start	End	E-Value	Type
transmembrane domain	7	29	N/A	INTRINSIC
low complexity region	45	60	N/A	INTRINSIC
Pfam:CutA1	67	165	6.9e-44	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000073724
AA Change: F444L

PolyPhen 2 Score 0.955 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000073402
Gene: ENSMUSG00000024193
AA Change: F444L

Domain	Start	End	E-Value	Type
TUDOR	29	86	5.61e-11	SMART
PHD	89	140	2.81e-8	SMART
PHD	188	238	2.42e0	SMART
low complexity region	410	416	N/A	INTRINSIC
low complexity region	481	495	N/A	INTRINSIC
Pfam:Mtf2_C	523	557	7.7e-11	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000078961

SMART Domains

Protein: ENSMUSP00000077984
Gene: ENSMUSG00000024301

Domain	Start	End	E-Value	Type
low complexity region	25	36	N/A	INTRINSIC
low complexity region	108	117	N/A	INTRINSIC
low complexity region	222	240	N/A	INTRINSIC
KISc	307	670	1.34e-143	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000114935

SMART Domains

Protein: ENSMUSP00000110585
Gene: ENSMUSG00000024194

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
Pfam:CutA1	43	144	1.7e-44	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000177932

SMART Domains

Protein: ENSMUSP00000137587
Gene: ENSMUSG00000067629

Domain	Start	End	E-Value	Type
PH	27	253	3.23e-8	SMART
C2	263	362	7.4e-10	SMART
RasGAP	392	729	3.33e-118	SMART
low complexity region	787	803	N/A	INTRINSIC
low complexity region	938	973	N/A	INTRINSIC
low complexity region	1040	1068	N/A	INTRINSIC
low complexity region	1110	1125	N/A	INTRINSIC
coiled coil region	1186	1259	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000193200

SMART Domains

Protein: ENSMUSP00000141245
Gene: ENSMUSG00000067629

Domain	Start	End	E-Value	Type
PH	12	238	1.5e-10	SMART
C2	248	347	4.8e-12	SMART
RasGAP	377	714	2.1e-120	SMART
low complexity region	772	788	N/A	INTRINSIC
low complexity region	923	958	N/A	INTRINSIC
low complexity region	1025	1053	N/A	INTRINSIC
low complexity region	1095	1110	N/A	INTRINSIC
coiled coil region	1171	1244	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000194598

SMART Domains

Protein: ENSMUSP00000141686
Gene: ENSMUSG00000067629

Domain	Start	End	E-Value	Type
PH	27	253	3.23e-8	SMART
C2	263	362	7.4e-10	SMART
RasGAP	392	729	3.33e-118	SMART
low complexity region	787	803	N/A	INTRINSIC
low complexity region	938	973	N/A	INTRINSIC
low complexity region	1040	1068	N/A	INTRINSIC
low complexity region	1110	1125	N/A	INTRINSIC
coiled coil region	1186	1259	N/A	INTRINSIC
low complexity region	1308	1326	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000201349

SMART Domains

Protein: ENSMUSP00000144666
Gene: ENSMUSG00000067629

Domain	Start	End	E-Value	Type
RasGAP	9	346	2.2e-120	SMART
low complexity region	404	420	N/A	INTRINSIC
low complexity region	555	590	N/A	INTRINSIC
low complexity region	657	685	N/A	INTRINSIC
low complexity region	727	742	N/A	INTRINSIC
Blast:RasGAP	761	876	3e-21	BLAST
low complexity region	884	894	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000201702

SMART Domains

Protein: ENSMUSP00000144248
Gene: ENSMUSG00000067629

Domain	Start	End	E-Value	Type
PH	27	253	1.5e-10	SMART
C2	263	362	4.9e-12	SMART
RasGAP	392	729	2.2e-120	SMART
low complexity region	773	789	N/A	INTRINSIC
low complexity region	924	959	N/A	INTRINSIC
low complexity region	1026	1054	N/A	INTRINSIC
low complexity region	1096	1111	N/A	INTRINSIC
coiled coil region	1171	1243	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

100% (65/65)

MGI Phenotype

FUNCTION: The protein encoded by this gene belongs to the polycomb-like protein family, which is a component of polycomb repressive complex-2. This complex represses gene expression by catalyzing the trimethylation of histone H3 lysine 27 and is required for the regulation of developmental genes including homeotic genes. The gene is expressed primarily in testis tissue. Small interfering RNA-mediated knockdown in cultured cell lines results in changes in homeotic gene expression coincident with alterations in promoter methylation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]

Allele List at MGI

Other mutations in this stock

Total: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610040J01Rik	C	A	5: 64,055,289 (GRCm39)		probably null	Het
Amph	A	G	13: 19,279,007 (GRCm39)	K161E	probably benign	Het
Aox1	A	T	1: 58,348,088 (GRCm39)	H602L	probably benign	Het
Areg	A	G	5: 91,291,492 (GRCm39)	N145S	probably damaging	Het
Arhgap29	C	T	3: 121,782,222 (GRCm39)	T142I	probably damaging	Het
Bcar3	C	T	3: 122,304,805 (GRCm39)		probably benign	Het
Brpf3	C	T	17: 29,025,248 (GRCm39)	A107V	probably benign	Het
Btnl2	T	A	17: 34,587,682 (GRCm39)	S509T	possibly damaging	Het
Cacna2d2	A	G	9: 107,402,653 (GRCm39)		probably null	Het
Casz1	C	T	4: 149,028,888 (GRCm39)	P1111L	probably damaging	Het
Ccdc91	C	T	6: 147,533,086 (GRCm39)	T411I	unknown	Het
Chd9	A	C	8: 91,767,769 (GRCm39)	E2422A	probably damaging	Het
Clrn3	T	C	7: 135,130,133 (GRCm39)	I34V	probably benign	Het
Cnksr3	C	T	10: 7,104,467 (GRCm39)	D79N	probably damaging	Het
Cops8	A	G	1: 90,539,729 (GRCm39)		probably null	Het
Cpa2	A	G	6: 30,564,345 (GRCm39)	K392R	probably benign	Het
Dnajc28	G	A	16: 91,413,795 (GRCm39)	R150*	probably null	Het
Dnase1l3	T	C	14: 7,994,299 (GRCm38)		probably benign	Het
Gdpd5	A	T	7: 99,105,689 (GRCm39)	T502S	probably benign	Het
Gp2	A	T	7: 119,049,375 (GRCm39)	D387E	probably damaging	Het
Gpr179	A	G	11: 97,242,364 (GRCm39)	L160P	probably benign	Het
Hmcn1	G	A	1: 150,522,409 (GRCm39)	T3497M	probably benign	Het
Idh3b	T	A	2: 130,122,420 (GRCm39)	T322S	possibly damaging	Het
Kit	A	T	5: 75,781,540 (GRCm39)	N323I	possibly damaging	Het
Kng2	T	C	16: 22,806,246 (GRCm39)	S445G	unknown	Het
Lin54	A	G	5: 100,602,358 (GRCm39)	V393A	probably benign	Het
Lyst	T	A	13: 13,872,945 (GRCm39)	W2715R	probably damaging	Het
Mad1l1	T	C	5: 140,300,813 (GRCm39)	T28A	probably benign	Het
Med7	T	A	11: 46,332,073 (GRCm39)	C223S	probably benign	Het
Megf8	T	A	7: 25,053,298 (GRCm39)	L1823Q	probably damaging	Het
Mga	C	A	2: 119,777,719 (GRCm39)	Q1755K	probably benign	Het
Mgat4b	A	T	11: 50,101,801 (GRCm39)	N22I	probably benign	Het
Ndufb6	C	T	4: 40,270,665 (GRCm39)		probably null	Het
Neil3	A	G	8: 54,042,129 (GRCm39)	L490P	probably benign	Het
Nek9	C	T	12: 85,350,417 (GRCm39)	V886I	probably benign	Het
Nol4l	A	T	2: 153,262,473 (GRCm39)	Y366*	probably null	Het
Nt5dc2	A	G	14: 30,860,886 (GRCm39)	T354A	probably damaging	Het
Or1j11	T	A	2: 36,311,715 (GRCm39)	Y102N	probably damaging	Het
Pde2a	G	A	7: 101,149,655 (GRCm39)		probably null	Het
Plin4	G	A	17: 56,414,019 (GRCm39)	T202I	possibly damaging	Het
Plk4	G	C	3: 40,768,009 (GRCm39)	V851L	probably damaging	Het
Pp2d1	A	G	17: 53,822,257 (GRCm39)	S270P	probably damaging	Het
Ripor1	C	A	8: 106,347,520 (GRCm39)	L1028M	unknown	Het
Scn9a	A	G	2: 66,370,874 (GRCm39)	F569L	probably damaging	Het
Sel1l2	T	A	2: 140,104,626 (GRCm39)	L306F	probably damaging	Het
Spic	A	T	10: 88,513,428 (GRCm39)	S86T	probably damaging	Het
Spmip10	T	A	18: 56,722,547 (GRCm39)		probably benign	Het
Stkld1	A	G	2: 26,836,668 (GRCm39)	N278S	probably benign	Het
Taar7d	T	A	10: 23,903,495 (GRCm39)	F126I	probably benign	Het
Tbc1d31	A	G	15: 57,824,345 (GRCm39)	E869G	possibly damaging	Het
Tbcd	C	T	11: 121,384,711 (GRCm39)	T315M	probably benign	Het
Terf2	T	C	8: 107,809,656 (GRCm39)	K221E	possibly damaging	Het
Thsd7a	T	A	6: 12,468,962 (GRCm39)	T539S		Het
Tll2	A	G	19: 41,077,313 (GRCm39)	F818L	possibly damaging	Het
Tmem87a	T	C	2: 120,200,959 (GRCm39)	T427A	possibly damaging	Het
Ush2a	C	A	1: 188,183,952 (GRCm39)	Q1419K	possibly damaging	Het
Vill	T	A	9: 118,895,821 (GRCm39)	F511Y	probably damaging	Het
Virma	T	A	4: 11,542,128 (GRCm39)	D1521E	probably benign	Het
Vps13c	A	G	9: 67,766,072 (GRCm39)	D63G	probably benign	Het
Vrk2	A	G	11: 26,485,575 (GRCm39)	F138L	probably benign	Het
Zfp710	T	C	7: 79,735,775 (GRCm39)	I514T	probably damaging	Het
Zgrf1	T	A	3: 127,357,032 (GRCm39)	F753I	possibly damaging	Het

Other mutations in Phf1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00905:Phf1	APN	17	27,155,568 (GRCm39)	missense	possibly damaging	0.90
IGL01629:Phf1	APN	17	27,153,247 (GRCm39)	missense	probably benign	0.07
IGL01931:Phf1	APN	17	27,154,509 (GRCm39)	unclassified	probably benign
IGL02008:Phf1	APN	17	27,154,260 (GRCm39)	missense	possibly damaging	0.95
IGL02048:Phf1	APN	17	27,153,515 (GRCm39)	unclassified	probably benign
IGL02206:Phf1	APN	17	27,155,843 (GRCm39)	unclassified	probably benign
IGL02252:Phf1	APN	17	27,154,109 (GRCm39)	missense	possibly damaging	0.65
IGL02548:Phf1	APN	17	27,154,600 (GRCm39)	missense	probably damaging	1.00
IGL03145:Phf1	APN	17	27,153,344 (GRCm39)	critical splice donor site	probably null
R0539:Phf1	UTSW	17	27,153,432 (GRCm39)	splice site	probably null
R0815:Phf1	UTSW	17	27,156,114 (GRCm39)	unclassified	probably benign
R0863:Phf1	UTSW	17	27,156,114 (GRCm39)	unclassified	probably benign
R1028:Phf1	UTSW	17	27,153,307 (GRCm39)	missense	possibly damaging	0.90
R1083:Phf1	UTSW	17	27,156,244 (GRCm39)	unclassified	probably benign
R1537:Phf1	UTSW	17	27,154,372 (GRCm39)	critical splice donor site	probably null
R1587:Phf1	UTSW	17	27,156,466 (GRCm39)	missense	probably damaging	0.99
R1656:Phf1	UTSW	17	27,156,333 (GRCm39)	missense	possibly damaging	0.93
R1956:Phf1	UTSW	17	27,154,719 (GRCm39)	splice site	probably null
R2566:Phf1	UTSW	17	27,156,062 (GRCm39)	missense	probably damaging	1.00
R3196:Phf1	UTSW	17	27,153,429 (GRCm39)	missense	probably damaging	1.00
R4223:Phf1	UTSW	17	27,156,474 (GRCm39)	nonsense	probably null
R4835:Phf1	UTSW	17	27,153,652 (GRCm39)	missense	probably benign
R6439:Phf1	UTSW	17	27,155,586 (GRCm39)	missense	probably benign
R7070:Phf1	UTSW	17	27,153,307 (GRCm39)	missense	possibly damaging	0.90
R7289:Phf1	UTSW	17	27,154,289 (GRCm39)	missense	probably damaging	1.00
R7846:Phf1	UTSW	17	27,154,291 (GRCm39)	nonsense	probably null
R9645:Phf1	UTSW	17	27,154,130 (GRCm39)	critical splice donor site	probably null
X0028:Phf1	UTSW	17	27,155,162 (GRCm39)	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- CAGACTCTGTCACCTGCAACTC -3'
(R):5'- TGTGAAGTCCCAGAGGTGAC -3'

Sequencing Primer
(F):5'- GACTCTGTCACCTGCAACTCTTTTC -3'
(R):5'- TCCCAGAGGTGACCTGGAAG -3'

Posted On

2020-07-13