Mutagenetix > Incidental Mutation

Incidental Mutation 'R1537:Phf1'

169628

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

039576-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1537 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

27152101-27156882 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (1 bp from exon)

DNA Base Change (assembly)

G to A at 27154372 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000073402 (fasta)

Gene Model

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

noncoding transcript
Transcript: ENSMUST00000184739

Coding Region Coverage

1x: 99.1%
3x: 98.2%
10x: 96.0%
20x: 91.7%

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700003H04Rik	T	A	3: 124,372,124 (GRCm39)	H86L	possibly damaging	Het
4930519G04Rik	A	G	5: 115,008,278 (GRCm39)	T31A	probably benign	Het
Ahcyl1	A	G	3: 107,603,505 (GRCm39)	F30S	probably benign	Het
Alox5ap	G	A	5: 149,201,993 (GRCm39)		probably null	Het
Amtn	A	G	5: 88,526,729 (GRCm39)	S53G	probably null	Het
Arap3	A	T	18: 38,122,737 (GRCm39)		probably null	Het
Ash1l	T	A	3: 88,979,783 (GRCm39)	V2769E	probably damaging	Het
Atp8b1	C	T	18: 64,678,335 (GRCm39)	V854M	probably damaging	Het
Bhlha9	C	T	11: 76,563,457 (GRCm39)	S28L	probably benign	Het
Bltp2	T	A	11: 78,180,169 (GRCm39)	Y2150N	probably damaging	Het
Bmpr2	A	G	1: 59,907,285 (GRCm39)	T793A	probably benign	Het
Ccdc80	G	A	16: 44,916,299 (GRCm39)	A352T	probably benign	Het
Chst2	A	T	9: 95,288,194 (GRCm39)	F51I	probably benign	Het
Col14a1	A	G	15: 55,244,163 (GRCm39)	N412S	unknown	Het
Dclk2	T	C	3: 86,713,491 (GRCm39)	I451V	probably damaging	Het
Ddb2	A	G	2: 91,065,234 (GRCm39)	S64P	probably benign	Het
Diaph1	A	G	18: 38,029,146 (GRCm39)		probably null	Het
Dnai3	T	C	3: 145,748,504 (GRCm39)	E870G	probably damaging	Het
Dusp4	G	T	8: 35,285,570 (GRCm39)	R277L	probably benign	Het
Fmnl2	A	G	2: 52,995,549 (GRCm39)	E424G	probably damaging	Het
Garem1	A	T	18: 21,301,931 (GRCm39)		probably null	Het
Gnpat	A	G	8: 125,597,555 (GRCm39)	E39G	probably damaging	Het
Golgb1	A	T	16: 36,719,150 (GRCm39)	Q352L	possibly damaging	Het
Hdlbp	T	C	1: 93,345,096 (GRCm39)	D803G	probably benign	Het
Hps1	A	G	19: 42,748,143 (GRCm39)		probably null	Het
Ilvbl	G	A	10: 78,415,565 (GRCm39)	R327H	probably benign	Het
Itpr3	A	G	17: 27,333,121 (GRCm39)	D1911G	possibly damaging	Het
Lmo7	T	A	14: 102,166,700 (GRCm39)		probably benign	Het
Mcm10	G	A	2: 5,003,591 (GRCm39)	T542I	possibly damaging	Het
Med1	A	G	11: 98,051,772 (GRCm39)	V497A	probably damaging	Het
Mn1	G	A	5: 111,602,646 (GRCm39)	A1295T	probably damaging	Het
Myh7b	A	C	2: 155,473,707 (GRCm39)	D1580A	probably damaging	Het
Naa20	A	G	2: 145,754,438 (GRCm39)	I101V	probably benign	Het
Nav3	T	C	10: 109,702,846 (GRCm39)	Y229C	probably damaging	Het
Obscn	T	C	11: 58,891,575 (GRCm39)	R6986G	unknown	Het
Or51h7	G	A	7: 102,591,547 (GRCm39)	T79I	probably damaging	Het
Or8b4	A	G	9: 37,830,570 (GRCm39)	I211V	probably benign	Het
P2rx3	A	G	2: 84,853,825 (GRCm39)		probably null	Het
Pcdhac2	G	A	18: 37,279,539 (GRCm39)	G840R	possibly damaging	Het
Pclo	A	G	5: 14,762,489 (GRCm39)	N3654S	unknown	Het
Pcnx2	T	A	8: 126,604,188 (GRCm39)	E689D	possibly damaging	Het
Pds5a	A	G	5: 65,804,464 (GRCm39)	S532P	probably benign	Het
Pkp4	G	A	2: 59,045,147 (GRCm39)	V41M	probably damaging	Het
Prlr	T	G	15: 10,328,364 (GRCm39)		probably null	Het
Prr12	G	T	7: 44,678,366 (GRCm39)	A1954D	unknown	Het
Prtg	A	G	9: 72,717,039 (GRCm39)	T127A	probably benign	Het
Ptprh	A	G	7: 4,552,698 (GRCm39)	L884P	probably damaging	Het
Rnf170	T	A	8: 26,629,076 (GRCm39)	D183E	probably benign	Het
Rrp12	A	T	19: 41,875,242 (GRCm39)	H339Q	probably damaging	Het
Rubcnl	T	G	14: 75,278,267 (GRCm39)	S350R	possibly damaging	Het
Sgo2b	T	A	8: 64,379,536 (GRCm39)	T1099S	possibly damaging	Het
Ska2	T	C	11: 87,006,945 (GRCm39)	S17P	probably damaging	Het
Slc38a2	A	G	15: 96,591,034 (GRCm39)	I243T	possibly damaging	Het
Sptan1	T	A	2: 29,916,034 (GRCm39)	D2007E	possibly damaging	Het
Taar5	T	A	10: 23,846,620 (GRCm39)	L6H	probably benign	Het
Tbata	G	T	10: 61,019,270 (GRCm39)		probably null	Het
Tent2	C	T	13: 93,312,076 (GRCm39)	G208D	probably damaging	Het
Tmem107	T	C	11: 68,963,284 (GRCm39)	S98P	probably damaging	Het
Tpst2	A	G	5: 112,456,286 (GRCm39)	D275G	possibly damaging	Het
Ttc28	G	T	5: 111,433,184 (GRCm39)	G2073W	probably damaging	Het
Ttc7	T	C	17: 87,629,891 (GRCm39)	V291A	possibly damaging	Het
Vps13b	T	A	15: 35,792,327 (GRCm39)	N2198K	possibly damaging	Het
Wdr37	A	T	13: 8,887,039 (GRCm39)	D249E	probably benign	Het
Xirp2	G	T	2: 67,340,357 (GRCm39)	C866F	probably damaging	Het
Zfp990	A	G	4: 145,263,566 (GRCm39)	E188G	possibly damaging	Het
Zkscan2	A	G	7: 123,099,064 (GRCm39)	S43P	possibly damaging	Het
Zscan5b	A	G	7: 6,236,850 (GRCm39)	R200G	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
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
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'- CCAGTGTGTCTTTGCAATCGCC -3'
(R):5'- TCTCACCAGCGAAGCTGTAACCTC -3'

Sequencing Primer
(F):5'- TTGCAATCGCCACTAAGGTAAAG -3'
(R):5'- TCATAGAATCTGCACATGGGC -3'

Posted On

2014-04-13