Mutagenetix > Incidental Mutation

Incidental Mutation 'R3802:Phf8'

274387

Institutional Source

Beutler Lab

Gene Symbol

Phf8

Ensembl Gene

ENSMUSG00000041229

Gene Name

PHD finger protein 8

Synonyms

9830141C09Rik

MMRRC Submission

040761-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.480) question?

Stock #

R3802 (G1)

Quality Score

222

Status

Validated

Chromosome

Chromosomal Location

150303668-150416855 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 150355572 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 512 (S512P)

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: S512P

PolyPhen 2 Score 0.891 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000040765
Gene: ENSMUSG00000041229
AA Change: S512P

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: S512P

PolyPhen 2 Score 0.174 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000108287
Gene: ENSMUSG00000041229
AA Change: S512P

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

probably benign
Transcript: ENSMUST00000112670
AA Change: S512P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000108289
Gene: ENSMUSG00000041229
AA Change: S512P

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: S512P

PolyPhen 2 Score 0.891 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000127653
Gene: ENSMUSG00000041229
AA Change: S512P

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

0.0717

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.6%
20x: 96.1%

Validation Efficiency

100% (47/47)

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: 47 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
AAdacl4fm3	A	T	4: 144,430,074 (GRCm39)	L305Q	possibly damaging	Het
Abcc2	C	A	19: 43,810,065 (GRCm39)	N874K	probably benign	Het
Axl	A	T	7: 25,487,902 (GRCm39)	M1K	probably null	Het
Btaf1	A	T	19: 36,963,948 (GRCm39)	T840S	probably benign	Het
Btaf1	A	T	19: 36,966,373 (GRCm39)	H1047L	probably benign	Het
Capn13	G	A	17: 73,646,396 (GRCm39)	P339L	probably benign	Het
Ccdc39	A	T	3: 33,874,044 (GRCm39)	M596K	probably damaging	Het
Cfap20dc	G	T	14: 8,510,931 (GRCm38)	D494E	probably benign	Het
Cfap58	G	T	19: 47,941,498 (GRCm39)	D289Y	possibly damaging	Het
Cnn2	A	G	10: 79,829,329 (GRCm39)	D153G	probably benign	Het
Cstdc2	T	C	2: 148,692,616 (GRCm39)	H62R	probably benign	Het
Cubn	T	C	2: 13,365,164 (GRCm39)	I1625V	probably benign	Het
Gprc5b	C	T	7: 118,582,943 (GRCm39)	D309N	possibly damaging	Het
Grm8	T	G	6: 28,125,635 (GRCm39)	N164H	possibly damaging	Het
Gstm3	G	A	3: 107,871,551 (GRCm39)	T210I	probably benign	Het
Hhipl1	A	G	12: 108,278,566 (GRCm39)	E298G	probably benign	Het
Hivep2	A	G	10: 14,024,705 (GRCm39)	D2173G	possibly damaging	Het
Hsd17b8	A	T	17: 34,245,441 (GRCm39)	V231E	probably damaging	Het
Jarid2	T	A	13: 45,056,307 (GRCm39)	N365K	probably benign	Het
Kank4	A	G	4: 98,668,370 (GRCm39)	S26P	probably damaging	Het
Kpnb1	A	T	11: 97,056,955 (GRCm39)	V638E	possibly damaging	Het
Lipo3	C	T	19: 33,762,257 (GRCm39)	C80Y	probably damaging	Het
Mga	T	A	2: 119,777,820 (GRCm39)	N1788K	probably damaging	Het
Mslnl	G	A	17: 25,961,908 (GRCm39)	V128M	probably damaging	Het
Mtmr10	A	G	7: 63,970,376 (GRCm39)	Y373C	probably benign	Het
Ncoa6	C	T	2: 155,247,484 (GRCm39)	G1940D	probably benign	Het
Nelfe	T	A	17: 35,072,877 (GRCm39)	F166L	possibly damaging	Het
Nfatc3	A	G	8: 106,806,277 (GRCm39)	Y374C	probably damaging	Het
Nhlrc3	A	G	3: 53,366,052 (GRCm39)	V147A	possibly damaging	Het
Or51f1d	A	G	7: 102,701,372 (GRCm39)	Y289C	probably benign	Het
Or8g33	G	A	9: 39,337,582 (GRCm39)	P262S	probably damaging	Het
Pak3	G	A	X: 142,492,727 (GRCm39)	V87I	probably damaging	Het
Papolg	A	T	11: 23,826,449 (GRCm39)	I235N	probably damaging	Het
Pdgfrl	T	C	8: 41,438,594 (GRCm39)	S177P	probably damaging	Het
Plaa	T	C	4: 94,458,125 (GRCm39)	D615G	probably damaging	Het
Prpf4b	T	C	13: 35,067,665 (GRCm39)		probably benign	Het
Sgk1	T	C	10: 21,873,311 (GRCm39)	V259A	probably damaging	Het
Skint4	G	T	4: 111,975,378 (GRCm39)	V113L	probably damaging	Het
Smco1	A	G	16: 32,092,716 (GRCm39)	Y129C	probably benign	Het
Tas2r106	C	A	6: 131,655,329 (GRCm39)	S174I	probably benign	Het
Tektl1	A	C	10: 78,584,314 (GRCm39)	F367C	probably damaging	Het
Tsn	A	T	1: 118,233,026 (GRCm39)	F93I	probably damaging	Het
Vav2	T	C	2: 27,157,235 (GRCm39)		probably benign	Het
Vmn2r63	A	T	7: 42,552,829 (GRCm39)	M809K	probably damaging	Het
Zfp260	G	A	7: 29,804,504 (GRCm39)	E135K	probably benign	Het
Zfp808	T	A	13: 62,319,897 (GRCm39)	H375Q	probably damaging	Het
Zkscan2	A	T	7: 123,094,365 (GRCm39)		probably benign	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
R2265:Phf8	UTSW	X	150,355,597 (GRCm39)	missense	possibly damaging	0.95
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
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'- TTGGGAAGACGAGCAATATCTTTGG -3'
(R):5'- ACTGGTAGCCAAACACCAGG -3'

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

Posted On

2015-04-02