Mutagenetix > Incidental Mutation

Incidental Mutation 'R1656:Phf1'

189143

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

039692-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1656 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

27152101-27156882 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 27156333 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 492 (S492P)

Ref Sequence

ENSEMBL: ENSMUSP00000073402 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025027] [ENSMUST00000073724] [ENSMUST00000078961] [ENSMUST00000114935] [ENSMUST00000177932] [ENSMUST00000229490] [ENSMUST00000201702] [ENSMUST00000194598]

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: S492P

PolyPhen 2 Score 0.930 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000073402
Gene: ENSMUSG00000024193
AA Change: S492P

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

noncoding transcript
Transcript: ENSMUST00000184739

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: ENSMUST00000229490

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

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: 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

Meta Mutation Damage Score

0.0734

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.6%
20x: 93.3%

Validation Efficiency

96% (79/82)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700024G13Rik	A	T	14: 32,099,901 (GRCm39)	I42N	possibly damaging	Het
Adarb2	T	A	13: 8,253,287 (GRCm39)	S11T	unknown	Het
Adgrg1	C	T	8: 95,738,438 (GRCm39)	Q644*	probably null	Het
Akr1c18	T	G	13: 4,195,252 (GRCm39)	I69L	probably benign	Het
Anxa9	C	T	3: 95,207,884 (GRCm39)	V219I	probably benign	Het
Aqp9	T	C	9: 71,045,385 (GRCm39)	T101A	probably benign	Het
Arhgef1	C	T	7: 24,613,057 (GRCm39)	R251W	probably damaging	Het
Arl13b	T	A	16: 62,627,007 (GRCm39)	E231D	possibly damaging	Het
Atosa	C	T	9: 74,916,241 (GRCm39)	A280V	probably benign	Het
Bcl2l11	C	T	2: 128,000,176 (GRCm39)	A173V	probably benign	Het
Ccni	A	T	5: 93,335,933 (GRCm39)		probably null	Het
Cdh18	A	G	15: 23,474,485 (GRCm39)	E785G	probably benign	Het
Cdk4	A	G	10: 126,900,849 (GRCm39)	Y167C	probably benign	Het
Clip1	A	C	5: 123,768,466 (GRCm39)	V757G	possibly damaging	Het
Ctsc	T	C	7: 87,930,616 (GRCm39)	V65A	possibly damaging	Het
Cuedc2	G	A	19: 46,320,427 (GRCm39)	S48L	probably damaging	Het
Cyp39a1	T	A	17: 43,978,510 (GRCm39)	M4K	possibly damaging	Het
Dgcr8	T	C	16: 18,074,577 (GRCm39)	S733G	probably benign	Het
Dnhd1	T	C	7: 105,363,488 (GRCm39)	S4017P	probably damaging	Het
Ehbp1	A	G	11: 22,096,694 (GRCm39)	I255T	probably benign	Het
Fam83e	T	C	7: 45,371,687 (GRCm39)	V28A	probably benign	Het
Fanci	A	G	7: 79,054,936 (GRCm39)		probably benign	Het
Fat1	C	T	8: 45,478,567 (GRCm39)	Q2538*	probably null	Het
Fshr	A	G	17: 89,508,009 (GRCm39)	F11S	unknown	Het
Gab1	G	T	8: 81,515,388 (GRCm39)	P310Q	probably damaging	Het
Galnt18	A	G	7: 111,215,699 (GRCm39)		probably benign	Het
Gm28042	C	A	2: 119,869,370 (GRCm39)	P355Q	probably damaging	Het
H2-DMa	A	G	17: 34,357,116 (GRCm39)	T205A	possibly damaging	Het
Hnf4g	A	T	3: 3,718,011 (GRCm39)	D420V	probably benign	Het
Ift70b	T	C	2: 75,767,760 (GRCm39)	K331R	probably benign	Het
Il1b	A	G	2: 129,207,989 (GRCm39)	V164A	probably damaging	Het
Irf4	C	A	13: 30,941,485 (GRCm39)	H279Q	probably benign	Het
Loxhd1	A	G	18: 77,409,364 (GRCm39)	T203A	possibly damaging	Het
Lsamp	C	T	16: 41,775,682 (GRCm39)	P178S	probably damaging	Het
Mcm6	T	C	1: 128,277,155 (GRCm39)	S223G	possibly damaging	Het
Misp	G	T	10: 79,661,777 (GRCm39)	V65L	possibly damaging	Het
Mov10	A	G	3: 104,706,912 (GRCm39)	V666A	probably benign	Het
Mycbp2	A	T	14: 103,485,194 (GRCm39)	D1102E	probably damaging	Het
Myef2	G	T	2: 124,939,860 (GRCm39)		probably null	Het
Myo1e	T	A	9: 70,303,216 (GRCm39)	I1079N	probably damaging	Het
Nisch	G	T	14: 30,899,228 (GRCm39)		probably benign	Het
Obox7	T	C	7: 14,399,346 (GRCm39)	S191P	probably benign	Het
Or11h7	T	C	14: 50,891,465 (GRCm39)	V257A	probably benign	Het
Or13p10	A	G	4: 118,523,385 (GRCm39)	I224V	probably damaging	Het
Or14c40	C	T	7: 86,313,331 (GRCm39)	L154F	probably benign	Het
Or1j11	G	A	2: 36,311,658 (GRCm39)	V83M	probably benign	Het
Or5w14	A	T	2: 87,541,422 (GRCm39)	V276D	possibly damaging	Het
Or7d9	A	G	9: 20,197,873 (GRCm39)	R301G	probably damaging	Het
Phyh	A	T	2: 4,943,164 (GRCm39)	N337I	probably damaging	Het
Poteg	A	T	8: 27,985,060 (GRCm39)		probably benign	Het
Prag1	G	T	8: 36,571,500 (GRCm39)	K694N	probably damaging	Het
Proser2	C	T	2: 6,107,870 (GRCm39)	E49K	probably damaging	Het
Pskh1	T	C	8: 106,656,389 (GRCm39)	V355A	possibly damaging	Het
Psmc2	T	C	5: 22,004,549 (GRCm39)	V182A	possibly damaging	Het
Rbfox1	A	G	16: 7,124,333 (GRCm39)		probably benign	Het
Slc26a7	A	T	4: 14,621,221 (GRCm39)	I55K	possibly damaging	Het
Slc5a8	G	A	10: 88,761,648 (GRCm39)		probably null	Het
Slitrk3	T	C	3: 72,957,672 (GRCm39)	R367G	probably damaging	Het
Snrnp40	C	G	4: 130,271,836 (GRCm39)		probably null	Het
Spata31	A	G	13: 65,068,953 (GRCm39)	E367G	probably benign	Het
Srrm3	A	T	5: 135,863,892 (GRCm39)		probably null	Het
Ssmem1	T	C	6: 30,517,507 (GRCm39)	S6P	probably damaging	Het
Swap70	A	G	7: 109,821,034 (GRCm39)	D6G	probably benign	Het
Syt1	T	C	10: 108,419,776 (GRCm39)	E295G	probably damaging	Het
Tap2	A	T	17: 34,424,927 (GRCm39)	I192F	possibly damaging	Het
Tgoln1	C	T	6: 72,591,068 (GRCm39)	R348H	probably damaging	Het
Tln2	C	T	9: 67,134,389 (GRCm39)	V1373I	possibly damaging	Het
Tmc2	A	G	2: 130,089,854 (GRCm39)	D613G	possibly damaging	Het
Tmem62	T	A	2: 120,837,483 (GRCm39)	Y597N	probably benign	Het
Trhr2	T	A	8: 123,084,185 (GRCm39)	T272S	probably damaging	Het
Vmn2r92	T	C	17: 18,372,198 (GRCm39)	S3P	probably benign	Het
Wdfy3	A	T	5: 102,089,313 (GRCm39)	I627N	probably damaging	Het
Zfhx4	T	C	3: 5,478,076 (GRCm39)	S3564P	probably damaging	Het
Zfp467	T	G	6: 48,416,013 (GRCm39)	E213A	possibly damaging	Het
Zfp746	T	G	6: 48,041,411 (GRCm39)	K437N	probably damaging	Het
Zfp853	A	G	5: 143,274,840 (GRCm39)		probably benign	Het
Zranb1	T	A	7: 132,551,496 (GRCm39)	V49D	probably benign	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
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
R8165:Phf1	UTSW	17	27,156,044 (GRCm39)	missense	possibly damaging	0.95
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'- TGAAGCCCAGACTAGCATCAGTCC -3'
(R):5'- GCATGAAAGTGCCAGTGTGTGAATG -3'

Sequencing Primer
(F):5'- GACTAGCATCAGTCCTGCCC -3'
(R):5'- AGGCTGTCAGAAGATGCCC -3'

Posted On

2014-05-09