Mutagenetix > Incidental Mutation

Incidental Mutation 'R9645:Phf1'

726249

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

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9645 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

27152101-27156882 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

T to C at 27154130 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000073402 (fasta)

Gene Model

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

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

probably null
Transcript: ENSMUST00000073724

SMART Domains

Protein: ENSMUSP00000073402
Gene: ENSMUSG00000024193

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 null
Transcript: ENSMUST00000073724

SMART Domains

Protein: ENSMUSP00000073402
Gene: ENSMUSG00000024193

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A430033K04Rik	T	C	5: 138,644,793 (GRCm39)	V226A	probably benign	Het
Acan	G	T	7: 78,749,653 (GRCm39)	V1475F	probably benign	Het
Acin1	T	A	14: 54,901,913 (GRCm39)	R626S	probably benign	Het
Aff3	T	C	1: 38,249,121 (GRCm39)	K662R	probably damaging	Het
Ankrd11	C	T	8: 123,617,682 (GRCm39)	A2057T	probably benign	Het
Ano9	T	G	7: 140,687,388 (GRCm39)	N309T	probably benign	Het
Ap3d1	G	A	10: 80,545,062 (GRCm39)	S1092L	probably benign	Het
B4galt7	C	T	13: 55,756,556 (GRCm39)	H257Y	probably damaging	Het
BC051665	G	T	13: 60,932,545 (GRCm39)	Q47K	possibly damaging	Het
Brip1	A	G	11: 85,952,512 (GRCm39)	F1090L	probably benign	Het
Cabin1	A	G	10: 75,494,543 (GRCm39)	V1612A	probably benign	Het
Ccar1	A	T	10: 62,602,369 (GRCm39)	D434E	probably benign	Het
Ccdc15	T	C	9: 37,227,083 (GRCm39)	D297G	probably benign	Het
Celsr3	C	A	9: 108,704,691 (GRCm39)	Y391*	probably null	Het
Cfap52	A	G	11: 67,837,179 (GRCm39)	I194T	possibly damaging	Het
Ctif	T	C	18: 75,757,352 (GRCm39)	E67G	probably benign	Het
Cxcr6	T	C	9: 123,639,151 (GRCm39)	F58L	possibly damaging	Het
Cyp2c69	T	C	19: 39,869,593 (GRCm39)	E142G	probably damaging	Het
Dnah6	T	A	6: 73,115,750 (GRCm39)	R1549S	possibly damaging	Het
Duxf3	A	T	10: 58,066,803 (GRCm39)	H75Q	probably benign	Het
Ehbp1	A	T	11: 22,051,052 (GRCm39)	I500N	probably damaging	Het
F13a1	A	T	13: 37,082,154 (GRCm39)	S517T	probably benign	Het
Fbln7	C	T	2: 128,719,316 (GRCm39)	R38C	probably damaging	Het
Fn1	T	C	1: 71,667,629 (GRCm39)	N788S	probably benign	Het
Foxc1	A	T	13: 31,991,882 (GRCm39)	E231V	probably damaging	Het
Gal3st2b	T	C	1: 93,866,328 (GRCm39)	S10P	probably damaging	Het
Gm6899	G	A	11: 26,543,592 (GRCm39)	C53Y	unknown	Het
Hps3	T	C	3: 20,084,831 (GRCm39)	E119G	probably benign	Het
Impg2	A	G	16: 56,038,767 (GRCm39)	E135G	probably damaging	Het
Kalrn	G	A	16: 34,032,583 (GRCm39)	T1155M	probably benign	Het
Kcna6	G	A	6: 126,716,022 (GRCm39)	A289V	probably benign	Het
Kcnh5	T	C	12: 75,134,191 (GRCm39)	M453V	probably benign	Het
Krt222	A	G	11: 99,131,320 (GRCm39)	V75A	possibly damaging	Het
Lmtk3	A	T	7: 45,450,431 (GRCm39)	T1432S	unknown	Het
Ltbp2	G	A	12: 84,837,864 (GRCm39)	P1192L	probably benign	Het
Ltbp3	C	G	19: 5,802,099 (GRCm39)	N758K	probably damaging	Het
Map6d1	T	A	16: 20,055,377 (GRCm39)	H153L	possibly damaging	Het
Mefv	A	G	16: 3,528,782 (GRCm39)	L583P	probably damaging	Het
Mrps28	T	C	3: 8,867,389 (GRCm39)	T160A	probably damaging	Het
Mtcl2	T	C	2: 156,869,390 (GRCm39)	K1082E	probably damaging	Het
Muc6	T	C	7: 141,217,783 (GRCm39)	T2297A	possibly damaging	Het
Mx1	G	T	16: 97,253,409 (GRCm39)	D338E	probably benign	Het
Myom1	G	A	17: 71,399,204 (GRCm39)	R1120H	probably benign	Het
Nif3l1	T	C	1: 58,487,074 (GRCm39)	F87L	probably benign	Het
Or1e35	T	A	11: 73,797,713 (GRCm39)	M202L	probably benign	Het
Or4p22	T	C	2: 88,317,373 (GRCm39)	V99A	possibly damaging	Het
Pex10	T	A	4: 155,153,264 (GRCm39)	L111Q	probably damaging	Het
Pigp	A	T	16: 94,166,278 (GRCm39)	Y143*	probably null	Het
Pou2af2	A	G	9: 51,229,579 (GRCm39)		probably null	Het
Prrc2a	A	G	17: 35,381,176 (GRCm39)		probably null	Het
Psd	GCC	GC	19: 46,301,841 (GRCm39)		probably null	Het
Pum3	A	G	19: 27,403,412 (GRCm39)	S30P	probably benign	Het
Rab12	A	G	17: 66,826,421 (GRCm39)	S97P	probably damaging	Het
Rigi	T	C	4: 40,220,437 (GRCm39)	E482G	possibly damaging	Het
Ros1	A	G	10: 51,948,148 (GRCm39)		probably null	Het
Scp2	A	T	4: 107,948,519 (GRCm39)	Y197N	probably benign	Het
Serpinb10	T	C	1: 107,474,488 (GRCm39)	F217L	possibly damaging	Het
Shank3	T	G	15: 89,409,453 (GRCm39)	M604R	possibly damaging	Het
Slc22a29	A	G	19: 8,184,488 (GRCm39)	S238P	probably benign	Het
Smarcc1	A	G	9: 109,986,410 (GRCm39)	D237G	probably damaging	Het
Stag3	T	C	5: 138,299,701 (GRCm39)	S871P	possibly damaging	Het
Tmem132d	A	G	5: 128,346,075 (GRCm39)	F149S	probably damaging	Het
Tmem25	C	T	9: 44,706,515 (GRCm39)	E333K		Het
Togaram1	T	A	12: 65,066,082 (GRCm39)	Y1695*	probably null	Het
Tox3	G	A	8: 90,984,574 (GRCm39)	P202S	probably damaging	Het
Trim34b	T	A	7: 103,980,474 (GRCm39)	N187K	probably benign	Het
Vcan	A	G	13: 89,841,081 (GRCm39)	S1488P	probably benign	Het
Vps26a	A	C	10: 62,305,791 (GRCm39)	V124G	probably benign	Het
Vps50	T	G	6: 3,516,706 (GRCm39)	S63A	possibly damaging	Het
Wbp4	T	A	14: 79,707,553 (GRCm39)	E186V	possibly damaging	Het
Zfp52	A	G	17: 21,781,937 (GRCm39)	D595G	possibly damaging	Het
Zfr2	C	A	10: 81,084,252 (GRCm39)	S1*	probably null	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
R8165:Phf1	UTSW	17	27,156,044 (GRCm39)	missense	possibly damaging	0.95
X0028:Phf1	UTSW	17	27,155,162 (GRCm39)	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- TGAGAAGCTTGTTGACTCACC -3'
(R):5'- TGCTCAAATGTCCAGCATCC -3'

Sequencing Primer
(F):5'- GAAGCTTGTTGACTCACCTGCAG -3'
(R):5'- TGTCCAGCATCCCAGTCCAG -3'

Posted On

2022-09-12