Mutagenetix > Incidental Mutation

Incidental Mutation 'R2265:Phf8'

244120

Institutional Source

Beutler Lab

Gene Symbol

Phf8

Ensembl Gene

ENSMUSG00000041229

Gene Name

PHD finger protein 8

Synonyms

9830141C09Rik

MMRRC Submission

040265-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.457) question?

Stock #

R2265 (G1)

Quality Score

222

Status

Not validated

Chromosome

Chromosomal Location

150303668-150416855 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 150355597 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Serine at position 520 (L520S)

Ref Sequence

ENSEMBL: ENSMUSP00000127653 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000046950] [ENSMUST00000046962] [ENSMUST00000112662] [ENSMUST00000112666] [ENSMUST00000112668] [ENSMUST00000112670] [ENSMUST00000168501]

AlphaFold

Q80TJ7

Predicted Effect

possibly damaging
Transcript: ENSMUST00000046950
AA Change: L520S

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000040765
Gene: ENSMUSG00000041229
AA Change: L520S

Domain	Start	End	E-Value	Type
PHD	7	54	1.16e-9	SMART
JmjC	195	351	2.69e-49	SMART
low complexity region	480	498	N/A	INTRINSIC
low complexity region	549	565	N/A	INTRINSIC
low complexity region	733	742	N/A	INTRINSIC
low complexity region	749	771	N/A	INTRINSIC
low complexity region	789	794	N/A	INTRINSIC
low complexity region	872	900	N/A	INTRINSIC
low complexity region	912	941	N/A	INTRINSIC
low complexity region	986	995	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000046962

SMART Domains

Protein: ENSMUSP00000041312
Gene: ENSMUSG00000041229

Domain	Start	End	E-Value	Type
PHD	7	54	1.16e-9	SMART
JmjC	195	351	2.69e-49	SMART
low complexity region	448	464	N/A	INTRINSIC
low complexity region	632	641	N/A	INTRINSIC
low complexity region	648	670	N/A	INTRINSIC
low complexity region	688	693	N/A	INTRINSIC
low complexity region	771	779	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000112662

SMART Domains

Protein: ENSMUSP00000108281
Gene: ENSMUSG00000041229

Domain	Start	End	E-Value	Type
PHD	7	54	1.16e-9	SMART
JmjC	195	351	2.69e-49	SMART
low complexity region	448	464	N/A	INTRINSIC
low complexity region	632	641	N/A	INTRINSIC
low complexity region	648	670	N/A	INTRINSIC
low complexity region	688	693	N/A	INTRINSIC
low complexity region	771	779	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000112666

SMART Domains

Protein: ENSMUSP00000108285
Gene: ENSMUSG00000041229

Domain	Start	End	E-Value	Type
PHD	7	54	1.16e-9	SMART
JmjC	195	351	2.69e-49	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000112668
AA Change: L520S

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000108287
Gene: ENSMUSG00000041229
AA Change: L520S

Domain	Start	End	E-Value	Type
PHD	7	54	1.16e-9	SMART
JmjC	195	351	2.69e-49	SMART
low complexity region	480	498	N/A	INTRINSIC
low complexity region	549	565	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000112670
AA Change: L520S

PolyPhen 2 Score 0.612 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000108289
Gene: ENSMUSG00000041229
AA Change: L520S

Domain	Start	End	E-Value	Type
PHD	7	54	1.16e-9	SMART
JmjC	195	351	2.69e-49	SMART
low complexity region	480	498	N/A	INTRINSIC
low complexity region	549	565	N/A	INTRINSIC
low complexity region	733	742	N/A	INTRINSIC
low complexity region	749	771	N/A	INTRINSIC
low complexity region	789	794	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000151941

SMART Domains

Protein: ENSMUSP00000116792
Gene: ENSMUSG00000041229

Domain	Start	End	E-Value	Type
PDB:4DO0\|A	2	71	2e-44	PDB
low complexity region	78	94	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000168501
AA Change: L520S

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000127653
Gene: ENSMUSG00000041229
AA Change: L520S

Domain	Start	End	E-Value	Type
PHD	7	54	1.16e-9	SMART
JmjC	195	351	2.69e-49	SMART
low complexity region	480	498	N/A	INTRINSIC
low complexity region	549	565	N/A	INTRINSIC
low complexity region	733	742	N/A	INTRINSIC
low complexity region	749	771	N/A	INTRINSIC
low complexity region	789	794	N/A	INTRINSIC
low complexity region	872	900	N/A	INTRINSIC
low complexity region	912	941	N/A	INTRINSIC
low complexity region	986	995	N/A	INTRINSIC

Meta Mutation Damage Score

0.2015

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 94.9%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a histone lysine demethylase that preferentially acts on histones in the monomethyl or dimethyl states. The encoded protein requires Fe(2+) ion, 2-oxoglutarate, and oxygen for its catalytic activity. Defects in this gene are a cause of mental retardation syndromic X-linked Siderius type (MRXSSD). Four transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A830018L16Rik	T	C	1: 12,042,328 (GRCm39)		probably null	Het
Aadac	T	A	3: 59,944,737 (GRCm39)	D136E	probably damaging	Het
Abca16	A	G	7: 120,030,383 (GRCm39)	D165G	probably benign	Het
Adam24	T	A	8: 41,133,110 (GRCm39)	S193T	possibly damaging	Het
Adra2b	T	C	2: 127,205,791 (GRCm39)	S103P	probably damaging	Het
Agrn	C	T	4: 156,263,675 (GRCm39)	G173R	probably damaging	Het
Alg11	T	A	8: 22,555,630 (GRCm39)	V255E	probably benign	Het
Aox1	C	A	1: 58,120,679 (GRCm39)	D857E	probably damaging	Het
Apob	T	C	12: 8,065,475 (GRCm39)	F4115S	possibly damaging	Het
Bdkrb2	A	G	12: 105,558,484 (GRCm39)	T242A	probably benign	Het
Cdca7	T	C	2: 72,312,834 (GRCm39)	L190P	probably benign	Het
Cenpe	A	G	3: 134,967,397 (GRCm39)	T2180A	probably benign	Het
Cep41	T	A	6: 30,660,915 (GRCm39)	I126F	possibly damaging	Het
Col16a1	C	A	4: 129,946,711 (GRCm39)	H111Q	probably benign	Het
Cops3	T	C	11: 59,718,716 (GRCm39)	T193A	probably benign	Het
Dbr1	G	A	9: 99,461,463 (GRCm39)	V153M	probably damaging	Het
Ddx4	A	G	13: 112,757,810 (GRCm39)	Y290H	probably benign	Het
Dgkb	T	A	12: 38,240,107 (GRCm39)	S461R	possibly damaging	Het
Dipk2b	A	G	X: 18,289,926 (GRCm39)	S179P	possibly damaging	Het
Dnajc28	T	C	16: 91,413,200 (GRCm39)	N372S	probably benign	Het
Dner	CGCTGCTGCTGCTGCTGCTGCTGCTGC	CGCTGCTGCTGCTGCTGCTGCTGC	1: 84,563,270 (GRCm39)		probably benign	Het
Dock3	C	A	9: 106,818,525 (GRCm39)	V1190F	probably damaging	Het
Exosc1	A	G	19: 41,919,857 (GRCm39)	S54P	probably damaging	Het
Fbxw22	C	T	9: 109,213,062 (GRCm39)	R295K	probably benign	Het
Foxo1	T	C	3: 52,253,333 (GRCm39)	S499P	probably benign	Het
Heatr5a	T	C	12: 51,940,528 (GRCm39)	D1444G	possibly damaging	Het
Hspa2	T	G	12: 76,452,962 (GRCm39)	I552S	probably benign	Het
Imp4	T	A	1: 34,482,928 (GRCm39)	I173N	probably damaging	Het
Itgal	A	G	7: 126,905,873 (GRCm39)	I352V	possibly damaging	Het
Kcnh6	G	A	11: 105,924,643 (GRCm39)	R816Q	probably benign	Het
Kcnh8	GAGACCAACGAGCAGCTGATGCTTCAGA	GAGA	17: 53,032,934 (GRCm39)	74	probably benign	Het
Kcnip3	G	T	2: 127,306,981 (GRCm39)	A173D	probably benign	Het
Kir3dl1	A	G	X: 135,425,784 (GRCm39)	R53G	probably benign	Het
Klhl31	A	G	9: 77,557,440 (GRCm39)	D52G	possibly damaging	Het
Klk1b21	T	C	7: 43,753,863 (GRCm39)	I49T	possibly damaging	Het
Lama2	T	A	10: 26,868,932 (GRCm39)	I2838F	probably damaging	Het
Lilrb4a	T	A	10: 51,367,633 (GRCm39)	Y58*	probably null	Het
Lsmem1	GTACATACATACATACATACATACATACA	GTACATACATACATACATACATACATACATACA	12: 40,235,260 (GRCm39)		probably null	Het
Mpdz	A	G	4: 81,301,628 (GRCm39)	S266P	probably damaging	Het
Mrc2	G	A	11: 105,239,257 (GRCm39)		probably null	Het
Mroh7	T	C	4: 106,578,124 (GRCm39)	N185D	probably benign	Het
Mybphl	A	G	3: 108,272,317 (GRCm39)	E2G	probably damaging	Het
Mycbp2	T	C	14: 103,500,185 (GRCm39)	D937G	probably benign	Het
Myo18b	A	G	5: 112,930,539 (GRCm39)	M1799T	probably damaging	Het
Nr4a2	T	A	2: 57,002,018 (GRCm39)	D145V	possibly damaging	Het
Ntmt1	C	A	2: 30,710,472 (GRCm39)	N58K	probably benign	Het
Or10ak16	A	T	4: 118,751,071 (GRCm39)	R264W	probably damaging	Het
Or2m12	A	G	16: 19,105,305 (GRCm39)	Y63H	probably damaging	Het
Or4f54	A	G	2: 111,123,524 (GRCm39)	T304A	probably benign	Het
Or51f1d	G	A	7: 102,701,344 (GRCm39)	V280I	probably benign	Het
Or52n20	T	C	7: 104,320,067 (GRCm39)	F53L	probably benign	Het
Or8k28	T	C	2: 86,286,558 (GRCm39)	Y19C	possibly damaging	Het
Ovch2	A	T	7: 107,383,782 (GRCm39)	M521K	probably damaging	Het
P2ry13	T	C	3: 59,117,449 (GRCm39)	M110V	probably damaging	Het
P2ry14	T	C	3: 59,022,992 (GRCm39)	N165S	probably damaging	Het
Pcdhb19	A	T	18: 37,630,736 (GRCm39)	H177L	probably damaging	Het
Pjvk	T	G	2: 76,487,797 (GRCm39)	S230A	possibly damaging	Het
Plch2	T	C	4: 155,077,461 (GRCm39)	E423G	probably benign	Het
Rad9b	T	C	5: 122,489,405 (GRCm39)	Y41C	probably damaging	Het
Ranbp3l	A	T	15: 9,057,194 (GRCm39)	I286F	probably damaging	Het
Rtel1	T	A	2: 180,996,161 (GRCm39)	V739D	probably damaging	Het
Slc35a3	T	C	3: 116,467,285 (GRCm39)	K325E	possibly damaging	Het
Spag17	C	A	3: 99,969,182 (GRCm39)		probably null	Het
Spg11	A	T	2: 121,938,788 (GRCm39)	C389S	possibly damaging	Het
Srsf4	T	C	4: 131,624,993 (GRCm39)	V130A	probably damaging	Het
Taar8b	T	C	10: 23,967,270 (GRCm39)	N308S	probably damaging	Het
Tas2r117	T	A	6: 132,780,188 (GRCm39)	C109S	probably benign	Het
Tlr5	T	A	1: 182,802,600 (GRCm39)	S635T	possibly damaging	Het
Ttc21a	G	T	9: 119,788,074 (GRCm39)	C833F	possibly damaging	Het
Vash2	T	C	1: 190,682,410 (GRCm39)	N347D	probably damaging	Het
Vcp	G	A	4: 42,980,833 (GRCm39)	A759V	possibly damaging	Het
Vmn2r18	T	C	5: 151,510,127 (GRCm39)	E82G	probably damaging	Het
Vps13c	T	C	9: 67,828,229 (GRCm39)	V1461A	possibly damaging	Het
Zfp616	T	C	11: 73,976,289 (GRCm39)	Y853H	possibly damaging	Het

Other mutations in Phf8

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01288:Phf8	APN	X	150,330,921 (GRCm39)	critical splice donor site	probably null
IGL01693:Phf8	APN	X	150,333,871 (GRCm39)	missense	probably damaging	1.00
IGL02437:Phf8	APN	X	150,414,356 (GRCm39)	missense	possibly damaging	0.96
IGL02494:Phf8	APN	X	150,408,227 (GRCm39)	missense	probably benign	0.08
R0389:Phf8	UTSW	X	150,335,618 (GRCm39)	missense	probably benign	0.05
R2268:Phf8	UTSW	X	150,355,597 (GRCm39)	missense	possibly damaging	0.95
R3801:Phf8	UTSW	X	150,355,572 (GRCm39)	missense	possibly damaging	0.89
R3802:Phf8	UTSW	X	150,355,572 (GRCm39)	missense	possibly damaging	0.89
R3803:Phf8	UTSW	X	150,355,572 (GRCm39)	missense	possibly damaging	0.89
R3804:Phf8	UTSW	X	150,355,572 (GRCm39)	missense	possibly damaging	0.89

Predicted Primers

PCR Primer
(F):5'- CCCTCGTGTACTAATACTCTTGTAGG -3'
(R):5'- ACTGGTAGCCAAACACCAGG -3'

Sequencing Primer
(F):5'- ACGAGCAATATCTTTGGGCTGC -3'
(R):5'- CACCAGGGGCCCTAAGAGATG -3'

Posted On

2014-10-16